diff --git a/docs/404.html b/docs/404.html index 52ea5fbc7..489b45aba 100644 --- a/docs/404.html +++ b/docs/404.html @@ -18,7 +18,7 @@ - +
- +
@@ -161,16 +161,16 @@

Page not found (404)

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.0.9.

+ - - + diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 7891d2884..4b3eec8b4 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -3,7 +3,7 @@ - +
- +
@@ -327,15 +327,15 @@

How to Apply These Terms

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.0.9.

+ - - + diff --git a/docs/articles/Cell_Bender_Functions.html b/docs/articles/Cell_Bender_Functions.html index c6fb03cec..a3c8cf79c 100644 --- a/docs/articles/Cell_Bender_Functions.html +++ b/docs/articles/Cell_Bender_Functions.html @@ -12,13 +12,14 @@ + - +
- +
@@ -141,7 +142,7 @@

Cell Bender Functionality & Plotting

-

Compiled: December 05, +

Compiled: December 06, 2024

Source: vignettes/articles/Cell_Bender_Functions.Rmd @@ -803,7 +804,9 @@

Optional Parameters -

+ +
@@ -816,16 +819,16 @@

Optional Parameters

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.0.9.

+ - - + diff --git a/docs/articles/Color_Palettes.html b/docs/articles/Color_Palettes.html index 6f379313d..59a65759a 100644 --- a/docs/articles/Color_Palettes.html +++ b/docs/articles/Color_Palettes.html @@ -12,13 +12,14 @@ + - +
- +

Customized Color Palettes & Themes

-

Compiled: December 05, +

Compiled: December 06, 2024

Source: vignettes/articles/Color_Palettes.Rmd @@ -388,7 +389,9 @@

Suggestions/Enhancements? -

+ +
@@ -401,16 +404,16 @@

Suggestions/Enhancements?

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.0.9.

+ - - + diff --git a/docs/articles/FAQ.html b/docs/articles/FAQ.html index fda63a926..40341030c 100644 --- a/docs/articles/FAQ.html +++ b/docs/articles/FAQ.html @@ -12,13 +12,14 @@ + - +
- +

Frequently Asked Questions

-

Compiled: December 05, +

Compiled: December 06, 2024

Source: vignettes/articles/FAQ.Rmd @@ -250,16 +251,16 @@

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.0.9.

+ - - + diff --git a/docs/articles/Gene_Expression_Plotting.html b/docs/articles/Gene_Expression_Plotting.html index 3f773da34..05195e170 100644 --- a/docs/articles/Gene_Expression_Plotting.html +++ b/docs/articles/Gene_Expression_Plotting.html @@ -12,13 +12,14 @@ + - +
- +
@@ -141,7 +142,7 @@

Plotting #1: Analysis Plots

-

Compiled: December 05, +

Compiled: December 06, 2024

Source: vignettes/articles/Gene_Expression_Plotting.Rmd @@ -1875,7 +1876,9 @@

DimPlot Layout Plots -

+ +
@@ -1888,16 +1891,16 @@

DimPlot Layout Plots

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.0.9.

+ - - + diff --git a/docs/articles/Helpers_and_Utilities.html b/docs/articles/Helpers_and_Utilities.html index 51e26ac22..53ddecf44 100644 --- a/docs/articles/Helpers_and_Utilities.html +++ b/docs/articles/Helpers_and_Utilities.html @@ -12,13 +12,14 @@ + - +
- +
@@ -141,7 +142,7 @@

General Helpers & Utilities

-

Compiled: December 05, +

Compiled: December 06, 2024

Source: vignettes/articles/Helpers_and_Utilities.Rmd @@ -1280,7 +1281,9 @@

Seq_zeros -

+ +
@@ -1293,16 +1296,16 @@

Seq_zeros

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.0.9.

+ - - + diff --git a/docs/articles/Installation.html b/docs/articles/Installation.html index c60fed825..206e75977 100644 --- a/docs/articles/Installation.html +++ b/docs/articles/Installation.html @@ -12,13 +12,14 @@ + - +
- +

Installation Instructions for scCustomize

-

Compiled: December 05, +

Compiled: December 06, 2024

Source: vignettes/articles/Installation.Rmd @@ -211,7 +212,9 @@

Develop branch -

+ +
@@ -224,16 +227,16 @@

Develop branch

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.0.9.

+ - - + diff --git a/docs/articles/Iterative_Plotting.html b/docs/articles/Iterative_Plotting.html index 4e909127b..28c21f4cd 100644 --- a/docs/articles/Iterative_Plotting.html +++ b/docs/articles/Iterative_Plotting.html @@ -12,13 +12,14 @@ + - +
- +

Plotting #4: Iterative Plotting Functions

-

Compiled: December 05, +

Compiled: December 06, 2024

Source: vignettes/articles/Iterative_Plotting.Rmd @@ -261,7 +262,9 @@

More Information -

+ +
@@ -274,16 +277,16 @@

More Information

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.0.9.

+ - - + diff --git a/docs/articles/LIGER_Functions.html b/docs/articles/LIGER_Functions.html index d1f8543e7..65e49a008 100644 --- a/docs/articles/LIGER_Functions.html +++ b/docs/articles/LIGER_Functions.html @@ -12,13 +12,14 @@ + - +
- +

LIGER Plotting & Functionality

-

Compiled: December 05, +

Compiled: December 06, 2024

Source: vignettes/articles/LIGER_Functions.Rmd @@ -451,7 +452,9 @@

Gene Utilities -

+ +
@@ -464,16 +467,16 @@

Gene Utilities

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.0.9.

+ - - + diff --git a/docs/articles/Markers_and_Cluster_Annotation.html b/docs/articles/Markers_and_Cluster_Annotation.html index 81ba2f75e..d7fc57917 100644 --- a/docs/articles/Markers_and_Cluster_Annotation.html +++ b/docs/articles/Markers_and_Cluster_Annotation.html @@ -12,13 +12,14 @@ + - +
- +
@@ -142,7 +143,7 @@

Marker Identification & Cluster Annotation Helpers

-

Compiled: December 05, +

Compiled: December 06, 2024

Source: vignettes/articles/Markers_and_Cluster_Annotation.Rmd @@ -1136,7 +1137,9 @@

Renaming Clusters -

+ +
@@ -1149,16 +1152,16 @@

Renaming Clusters

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.0.9.

+ - - + diff --git a/docs/articles/Misc_Functions.html b/docs/articles/Misc_Functions.html index 39891c0bb..eab917375 100644 --- a/docs/articles/Misc_Functions.html +++ b/docs/articles/Misc_Functions.html @@ -12,13 +12,14 @@ + - +
- +

Misc Functions

-

Compiled: December 05, +

Compiled: December 06, 2024

Source: vignettes/articles/Misc_Functions.Rmd @@ -237,7 +238,9 @@

Adapting Function Yourself -

+ +
@@ -250,16 +253,16 @@

Adapting Function Yourself

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.0.9.

+ - - + diff --git a/docs/articles/Object_Conversion.html b/docs/articles/Object_Conversion.html index 4a5428a7d..63148119d 100644 --- a/docs/articles/Object_Conversion.html +++ b/docs/articles/Object_Conversion.html @@ -12,13 +12,14 @@ + - +
- +
@@ -141,7 +142,7 @@

Object Format Conversion

-

Compiled: December 05, +

Compiled: December 06, 2024

Source: vignettes/articles/Object_Conversion.Rmd @@ -320,7 +321,9 @@

Accepted values for convert_to -

+ +
@@ -333,16 +336,16 @@

Accepted values for convert_to

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.0.9.

+ - - + diff --git a/docs/articles/Object_QC_Functions.html b/docs/articles/Object_QC_Functions.html index d9ac14efd..bc92ba2b0 100644 --- a/docs/articles/Object_QC_Functions.html +++ b/docs/articles/Object_QC_Functions.html @@ -12,13 +12,14 @@ + - +
- +
@@ -141,7 +142,7 @@

Object QC Functions

-

Compiled: December 05, +

Compiled: December 06, 2024

Source: vignettes/articles/Object_QC_Functions.Rmd @@ -643,7 +644,9 @@

Add QC Metrics from Pathway Gene + +

@@ -656,16 +659,16 @@

Add QC Metrics from Pathway Gene

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.0.9.

+ - - + diff --git a/docs/articles/QC_Plots.html b/docs/articles/QC_Plots.html index c99afae32..7b52e82f2 100644 --- a/docs/articles/QC_Plots.html +++ b/docs/articles/QC_Plots.html @@ -12,13 +12,14 @@ + - +
- +
@@ -141,7 +142,7 @@

Plotting #2: QC Plots & Analysis

-

Compiled: December 05, +

Compiled: December 06, 2024

Source: vignettes/articles/QC_Plots.Rmd @@ -724,7 +725,9 @@

Plot Number of Cells/Nuclei per S + +

@@ -737,16 +740,16 @@

Plot Number of Cells/Nuclei per S

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.0.9.

+ - - + diff --git a/docs/articles/Read_and_Write_Functions.html b/docs/articles/Read_and_Write_Functions.html index 5372ab6de..f244bc716 100644 --- a/docs/articles/Read_and_Write_Functions.html +++ b/docs/articles/Read_and_Write_Functions.html @@ -12,13 +12,14 @@ + - +
- +

Read & Write Data Functions

-

Compiled: December 05, +

Compiled: December 06, 2024

Source: vignettes/articles/Read_and_Write_Functions.Rmd @@ -490,7 +491,9 @@

Write 10X Genomi + +

@@ -503,16 +506,16 @@

Write 10X Genomi

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.0.9.

+ - - + diff --git a/docs/articles/Sequencing_QC_Plots.html b/docs/articles/Sequencing_QC_Plots.html index 93032d147..2d18aa5a7 100644 --- a/docs/articles/Sequencing_QC_Plots.html +++ b/docs/articles/Sequencing_QC_Plots.html @@ -12,13 +12,14 @@ + - +
- +
@@ -141,7 +142,7 @@

Plotting #3: Sequencing QC Plots/Analysis

-

Compiled: December 05, +

Compiled: December 06, 2024

Source: vignettes/articles/Sequencing_QC_Plots.Rmd @@ -884,7 +885,9 @@

Barcode Rank Plots -

+ +
@@ -897,16 +900,16 @@

Barcode Rank Plots

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.0.9.

+ - - + diff --git a/docs/articles/Spatial_Plotting.html b/docs/articles/Spatial_Plotting.html index b477721a9..c778e470b 100644 --- a/docs/articles/Spatial_Plotting.html +++ b/docs/articles/Spatial_Plotting.html @@ -12,13 +12,14 @@ + - +
- +

Plotting #5: Spatial Plotting Functions

-

Compiled: December 05, +

Compiled: December 06, 2024

Source: vignettes/articles/Spatial_Plotting.Rmd @@ -231,7 +232,9 @@

Spatial DimPlots -

+ +
@@ -244,16 +247,16 @@

Spatial DimPlots

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.0.9.

+ - - + diff --git a/docs/articles/Statistics.html b/docs/articles/Statistics.html index 0a4a9bf8d..9a0e21232 100644 --- a/docs/articles/Statistics.html +++ b/docs/articles/Statistics.html @@ -12,13 +12,14 @@ + - +
- +
@@ -141,7 +142,7 @@

Statistics Functions

-

Compiled: December 05, +

Compiled: December 06, 2024

Source: vignettes/articles/Statistics.Rmd @@ -1828,7 +1829,9 @@

Plotting Median Data -

+ +
@@ -1841,16 +1844,16 @@

Plotting Median Data

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.0.9.

+ - - + diff --git a/docs/articles/Update_Gene_Symbols.html b/docs/articles/Update_Gene_Symbols.html index d7208ac7c..abd1da447 100644 --- a/docs/articles/Update_Gene_Symbols.html +++ b/docs/articles/Update_Gene_Symbols.html @@ -12,13 +12,14 @@ + - +
- +
@@ -141,7 +142,7 @@

Updating Gene Symbols

-

Compiled: December 05, +

Compiled: December 06, 2024

Source: vignettes/articles/Update_Gene_Symbols.Rmd @@ -257,9 +258,7 @@

Inappropriate renamingLet’s run our test symbol set:

 results <- Updated_HGNC_Symbols(input_data = test_symbols)
-
## Downloading HGNC data from:
-## https://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt
-## Input features contained 3 gene symbols
+
## Input features contained 3 gene symbols
 ## ✔ 3 were already approved symbols.
 ## → 0 were updated to approved symbol.
 ## ✖ 0 were not found in HGNC dataset and remain unchanged.

@@ -355,7 +354,7 @@ 
Inappropriate renaming## ✖ 12,591 were not found in HGNC dataset and remain unchanged.
-
## 0.824 sec elapsed
+
## 0.806 sec elapsed

Examining the Results @@ -611,9 +610,7 @@

Updating Mouse Gene Symbols# Get updated symbols updated_symbols <- Updated_MGI_Symbols(input_data = Features(marsh_mouse_micro))

-
## Downloading MGI data from:
-## https://www.informatics.jax.org/downloads/reports/MGI_EntrezGene.rpt
-## Input features contained 12,674 gene symbols
+
## Input features contained 12,674 gene symbols
 ## ✔ 12,055 were already approved symbols.
 ## → 531 were updated to approved symbol.
 ## ✖ 90 were not found in MGI dataset and remain unchanged.

@@ -622,7 +619,9 @@ 
Updating Mouse Gene Symbols
 
-
+ +
@@ -635,16 +634,16 @@

Updating Mouse Gene Symbols

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.0.9.

+ - - + diff --git a/docs/articles/index.html b/docs/articles/index.html index 936641050..3de9d8bee 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -3,7 +3,7 @@ - +
- +
@@ -165,15 +165,15 @@

All vignettes

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.0.9.

+ - - + diff --git a/docs/authors.html b/docs/authors.html index 12eff8b63..ea8ac1a57 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -3,7 +3,7 @@ - +
- +
@@ -116,21 +116,21 @@

Authors and Citation

- +

  • Samuel Marsh. Author, maintainer.

  • -

    Ming Tang. Contributor. +

    Ming Tang. Contributor.

  • -

    Velina Kozareva. Contributor. +

    Velina Kozareva. Contributor.

  • -

    Lucas Graybuck. Contributor. +

    Lucas Graybuck. Contributor.

@@ -144,7 +144,7 @@

Citation

Marsh S (2024). scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing. -R package version 3.0.0, https://samuel-marsh.github.io/scCustomize/, https://doi.org/10.5281/zenodo.5706431, https://github.com/samuel-marsh/scCustomize. +R package version 3.0.0, https://samuel-marsh.github.io/scCustomize/, https://doi.org/10.5281/zenodo.5706431, https://github.com/samuel-marsh/scCustomize. 

@Manual{,
   title = {scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing},
@@ -165,15 +165,15 @@ 
Citation

 
 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       
 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/index.html b/docs/index.html
index dc4ba2c13..8794eeec2 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -19,7 +19,7 @@
 
 
 
-
+    
 
     

       

 
 
-
+      
 
       

   

@@ -324,16 +324,16 @@ 
Developers

 
 

   

-
Site built with pkgdown 2.1.0.

+
Site built with pkgdown 2.0.9.

 

 
       
 

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/news/index.html b/docs/news/index.html
index c9094f886..be55d63c4 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -117,7 +117,7 @@ 
Changelog 

     

 
     

-
scCustomize 3.0.0 (2024-12-05)

+
scCustomize 3.0.0 (2024-12-05)2024-12-05

 

 
Added

 
Major Updates to Functionality with rliger Package:
Added new utility functions to interact with liger v2.0.0+ object format change:

@@ -143,7 +143,8 @@ 
AddedChanges
-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 52153f2c1..0ffa5e706 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,26 +1,27 @@
 pandoc: '3.2'
-pkgdown: 2.1.0
+pkgdown: 2.0.9
 pkgdown_sha: ~
 articles:
-  articles/Cell_Bender_Functions: Cell_Bender_Functions.html
-  articles/Color_Palettes: Color_Palettes.html
-  articles/FAQ: FAQ.html
-  articles/Gene_Expression_Plotting: Gene_Expression_Plotting.html
-  articles/Helpers_and_Utilities: Helpers_and_Utilities.html
-  articles/Installation: Installation.html
-  articles/Iterative_Plotting: Iterative_Plotting.html
-  articles/LIGER_Functions: LIGER_Functions.html
-  articles/Markers_and_Cluster_Annotation: Markers_and_Cluster_Annotation.html
-  articles/Misc_Functions: Misc_Functions.html
-  articles/Object_Conversion: Object_Conversion.html
-  articles/Object_QC_Functions: Object_QC_Functions.html
-  articles/QC_Plots: QC_Plots.html
-  articles/Read_and_Write_Functions: Read_and_Write_Functions.html
-  articles/Sequencing_QC_Plots: Sequencing_QC_Plots.html
-  articles/Spatial_Plotting: Spatial_Plotting.html
-  articles/Statistics: Statistics.html
-  articles/Update_Gene_Symbols: Update_Gene_Symbols.html
-last_built: 2024-12-05T19:28Z
+  Cell_Bender_Functions: Cell_Bender_Functions.html
+  Color_Palettes: Color_Palettes.html
+  FAQ: FAQ.html
+  Gene_Expression_Plotting: Gene_Expression_Plotting.html
+  Helpers_and_Utilities: Helpers_and_Utilities.html
+  Installation: Installation.html
+  Iterative_Plotting: Iterative_Plotting.html
+  LIGER_Functions: LIGER_Functions.html
+  Markers_and_Cluster_Annotation: Markers_and_Cluster_Annotation.html
+  Misc_Functions: Misc_Functions.html
+  Object_Conversion: Object_Conversion.html
+  Object_QC_Functions: Object_QC_Functions.html
+  QC_Plots: QC_Plots.html
+  Read_and_Write_Functions: Read_and_Write_Functions.html
+  Sequencing_QC_Plots: Sequencing_QC_Plots.html
+  Spatial_Plotting: Spatial_Plotting.html
+  Statistics: Statistics.html
+  Update_Gene_Symbols: Update_Gene_Symbols.html
+last_built: 2024-12-06T15:33Z
 urls:
   reference: https://samuel-marsh.github.io/scCustomize/reference
   article: https://samuel-marsh.github.io/scCustomize/articles
+
diff --git a/docs/reference/Add_Alt_Feature_ID.html b/docs/reference/Add_Alt_Feature_ID.html
index 468835c80..7c0377f6d 100644
--- a/docs/reference/Add_Alt_Feature_ID.html
+++ b/docs/reference/Add_Alt_Feature_ID.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -134,44 +134,44 @@ 
Add Alternative Feature IDs

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
object name.

 
 
-
features_tsv_file

+
features_tsv_file

 
output file from Cell Ranger used for creation of Seurat object.
 (Either provide this of hdf5_file)

 
 
-
hdf5_file

+
hdf5_file

 
output file from Cell Ranger used for creation of Seurat object.
 (Either provide this of features_tsv_file)

 
 
-
assay

+
assay

 
name of assay(s) to add the alternative features to.  Can specify "all"
 to add to all assays.

 
 
-
data_name

+
data_name

 
name to use for data.frame when stored in @misc slot.

 
 
-
overwrite

+
overwrite

 
logical, whether to overwrite item with the same data_name in the
 @misc slot of object (default is FALSE).

 
 

     

     
Value

-    
Seurat Object with new entries in the obj@misc slot.

+    
+
+
Seurat Object with new entries in the obj@misc slot.

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 # Using features.tsv.gz file
    # Either file from filtered or raw outputs can be used as they are identical.
 obj <- Add_Alt_Feature_ID(seurat_object = obj,
@@ -182,7 +182,7 @@ 
Examples

    # Though it is faster to load filtered_feature_bc file due to droplet filtering
 obj <- Add_Alt_Feature_ID(seurat_object = obj,
 hdf5_file = "sample01/outs/outs/filtered_feature_bc_matrix.h5", assay = "RNA")
-} # }
+}
 
 

     

@@ -198,15 +198,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Add_CellBender_Diff.html b/docs/reference/Add_CellBender_Diff.html
index 89a1838e7..e8ad98b17 100644
--- a/docs/reference/Add_CellBender_Diff.html
+++ b/docs/reference/Add_CellBender_Diff.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -127,31 +127,31 @@ 
Calculate and add differences post-cell bender analysis

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
object name.

 
 
-
raw_assay_name

+
raw_assay_name

 
name of the assay containing the raw data.

 
 
-
cell_bender_assay_name

+
cell_bender_assay_name

 
name of the assay containing the Cell Bender'ed data.

 
 

     

     
Value

-    
Seurat object with 2 new columns in the meta.data slot.

+    
+
+
Seurat object with 2 new columns in the meta.data slot.

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 object <- Add_CellBender_Diff(seurat_object = obj, raw_assay_name = "RAW",
 cell_bender_assay_name = "RNA")
-} # }
+}
 
 

     

@@ -167,15 +167,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Add_Cell_Complexity.html b/docs/reference/Add_Cell_Complexity.html
index 7b729e9a4..48346f93c 100644
--- a/docs/reference/Add_Cell_Complexity.html
+++ b/docs/reference/Add_Cell_Complexity.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -124,7 +124,7 @@ 
Add Cell Complexity

     

     
Add_Cell_Complexity(object, ...)
 
-# S3 method for class 'liger'
+# S3 method for liger
 Add_Cell_Complexity(
   object,
   meta_col_name = "log10GenesPerUMI",
@@ -132,7 +132,7 @@ 
Add Cell Complexity

   ...
 )
 
-# S3 method for class 'Seurat'
+# S3 method for Seurat
 Add_Cell_Complexity(
   object,
   meta_col_name = "log10GenesPerUMI",
@@ -144,41 +144,41 @@ 
Add Cell Complexity

 
     

     
Arguments

-
-
-
object

+    
object

 
Seurat or LIGER object

 
 
-
...

+
...

 
Arguments passed to other methods

 
 
-
meta_col_name

+
meta_col_name

 
name to use for new meta data column.  Default is "log10GenesPerUMI".

 
 
-
overwrite

+
overwrite

 
Logical.  Whether to overwrite existing an meta.data column.  Default is FALSE meaning that
 function will abort if column with name provided to meta_col_name is present in meta.data slot.

 
 
-
assay

+
assay

 
assay to use in calculation.  Default is "RNA".  Note This should only be changed if
 storing corrected and uncorrected assays in same object (e.g. outputs of both Cell Ranger and Cell Bender).

 
 

     

     
Value

-    
An object of the same class as object with columns added to object meta data.

+    
+
+
An object of the same class as object with columns added to object meta data.

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 # Liger
 liger_object <- Add_Cell_Complexity(object = liger_object)
-} # }
+}
 
 # Seurat
 library(Seurat)
@@ -198,15 +198,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Add_Cell_QC_Metrics.html b/docs/reference/Add_Cell_QC_Metrics.html
index d0df741f4..0ba6fc58c 100644
--- a/docs/reference/Add_Cell_QC_Metrics.html
+++ b/docs/reference/Add_Cell_QC_Metrics.html
@@ -4,7 +4,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -126,7 +126,7 @@ 
Add Multiple Cell Quality Control Values with Single Function

     

     
Add_Cell_QC_Metrics(object, ...)
 
-# S3 method for class 'liger'
+# S3 method for liger
 Add_Cell_QC_Metrics(
   object,
   add_mito_ribo = TRUE,
@@ -161,7 +161,7 @@ 
Add Multiple Cell Quality Control Values with Single Function

   ...
 )
 
-# S3 method for class 'Seurat'
+# S3 method for Seurat
 Add_Cell_QC_Metrics(
   object,
   species,
@@ -199,174 +199,176 @@ 
Add Multiple Cell Quality Control Values with Single Function

 
     

     
Arguments

-
-
-
object

+    
object

 
Seurat or LIGER object

 
 
-
...

+
...

 
Arguments passed to other methods

 
 
-
add_mito_ribo

+
add_mito_ribo

 
logical, whether to add percentage of counts belonging to mitochondrial/ribosomal
 genes to object (Default is TRUE).

 
 
-
add_complexity

+
add_complexity

 
logical, whether to add Cell Complexity to object (Default is TRUE).

 
 
-
add_top_pct

+
add_top_pct

 
logical, whether to add Top Gene Percentages to object (Default is TRUE).

 
 
-
add_MSigDB

+
add_MSigDB

 
logical, whether to add percentages of counts belonging to genes from of mSigDB hallmark
 gene lists: "HALLMARK_OXIDATIVE_PHOSPHORYLATION", "HALLMARK_APOPTOSIS", and "HALLMARK_DNA_REPAIR" to
 object (Default is TRUE).

 
 
-
add_IEG

+
add_IEG

 
logical, whether to add percentage of counts belonging to IEG genes to object (Default is TRUE).

 
 
-
add_hemo

+
add_hemo

 
logical, whether to add percentage of counts belonging to homoglobin genes to object (Default is TRUE).

 
 
-
add_cell_cycle

+
add_cell_cycle

 
logical, whether to addcell cycle scores and phase based on
 CellCycleScoring.  Only applicable if species = "human".  (Default is TRUE).

 
 
-
species

+
species

 
Species of origin for given Seurat Object.  If mouse, human, marmoset, zebrafish, rat,
 drosophila, rhesus macaque, or chicken (name or abbreviation) are provided the function will automatically
 generate patterns and features.

 
 
-
mito_name

+
mito_name

 
name to use for the new meta.data column containing percent mitochondrial counts.
 Default is "percent_mito".

 
 
-
ribo_name

+
ribo_name

 
name to use for the new meta.data column containing percent ribosomal counts.
 Default is "percent_ribo".

 
 
-
mito_ribo_name

+
mito_ribo_name

 
name to use for the new meta.data column containing percent
 mitochondrial+ribosomal counts.  Default is "percent_mito_ribo".

 
 
-
complexity_name

+
complexity_name

 
name to use for new meta data column for Add_Cell_Complexity.
 Default is "log10GenesPerUMI".

 
 
-
top_pct_name

+
top_pct_name

 
name to use for new meta data column for Add_Top_Gene_Pct.
 Default is "percent_topXX", where XX is equal to the value provided to num_top_genes.

 
 
-
oxphos_name

+
oxphos_name

 
name to use for new meta data column for percentage of MSigDB oxidative phosphorylation
 counts.  Default is "percent_oxphos".

 
 
-
apop_name

+
apop_name

 
name to use for new meta data column for percentage of MSigDB apoptosis counts.
 Default is "percent_apop".

 
 
-
dna_repair_name

+
dna_repair_name

 
name to use for new meta data column for percentage of MSigDB DNA repair
 counts.  Default is "percent_dna_repair"..

 
 
-
ieg_name

+
ieg_name

 
name to use for new meta data column for percentage of IEG counts.  Default is "percent_ieg".

 
 
-
hemo_name

+
hemo_name

 
name to use for the new meta.data column containing percent hemoglobin counts.
 Default is "percent_mito".

 
 
-
mito_pattern

+
mito_pattern

 
A regex pattern to match features against for mitochondrial genes (will set automatically if
 species is mouse or human; marmoset features list saved separately).

 
 
-
ribo_pattern

+
ribo_pattern

 
A regex pattern to match features against for ribosomal genes
 (will set automatically if species is in default list).

 
 
-
hemo_pattern

+
hemo_pattern

 
A regex pattern to match features against for hemoglobin genes
 (will set automatically if species is in default list).

 
 
-
mito_features

+
mito_features

 
A list of mitochondrial gene names to be used instead of using regex pattern.
 Will override regex pattern if both are present (including default saved regex patterns).

 
 
-
ribo_features

+
ribo_features

 
A list of ribosomal gene names to be used instead of using regex pattern.
 Will override regex pattern if both are present (including default saved regex patterns).

 
 
-
hemo_features

+
hemo_features

 
A list of hemoglobin gene names to be used instead of using regex pattern.
 Will override regex pattern if both are present (including default saved regex patterns).

 
 
-
ensembl_ids

+
ensembl_ids

 
logical, whether feature names in the object are gene names or
 ensembl IDs (default is FALSE; set TRUE if feature names are ensembl IDs).

 
 
-
num_top_genes

+
num_top_genes

 
An integer vector specifying the size(s) of the top set of high-abundance genes.
 Used to compute the percentage of library size occupied by the most highly expressed genes in each cell.

 
 
-
assay

+
assay

 
assay to use in calculation.  Default is "RNA".  Note This should only be changed if
 storing corrected and uncorrected assays in same object (e.g. outputs of both Cell Ranger and Cell Bender).

 
 
-
list_species_names

+
list_species_names

 
returns list of all accepted values to use for default species names which
 contain internal regex/feature lists (human, mouse, marmoset, zebrafish, rat, drosophila, rhesus macaque, and
 chicken).  Default is FALSE.

 
 
-
overwrite

+
overwrite

 
Logical.  Whether to overwrite existing an meta.data column.  Default is FALSE meaning that
 function will abort if column with name provided to meta_col_name is present in meta.data slot.

 
 

     

     
Value

-    
A liger Object

+    
+
+
A liger Object

+
+
 
A Seurat Object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 obj <- Add_Cell_QC_Metrics(object = obj, species = "Human")
-} # }
+}
 
-if (FALSE) { # \dontrun{
+if (FALSE) {
 obj <- Add_Cell_QC_Metrics(object = obj, species = "Human")
-} # }
+}
 
 

     

@@ -382,15 +384,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Add_Hemo.html b/docs/reference/Add_Hemo.html
index c9d727909..98550ba5e 100644
--- a/docs/reference/Add_Hemo.html
+++ b/docs/reference/Add_Hemo.html
@@ -4,7 +4,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -126,7 +126,7 @@ 
Add Hemoglobin percentages

     

     
Add_Hemo(object, ...)
 
-# S3 method for class 'liger'
+# S3 method for liger
 Add_Hemo(
   object,
   species,
@@ -139,7 +139,7 @@ 
Add Hemoglobin percentages

   ...
 )
 
-# S3 method for class 'Seurat'
+# S3 method for Seurat
 Add_Hemo(
   object,
   species,
@@ -156,73 +156,73 @@ 
Add Hemoglobin percentages

 
     

     
Arguments

-
-
-
object

+    
object

 
Seurat or LIGER object

 
 
-
...

+
...

 
Arguments passed to other methods

 
 
-
species

+
species

 
Species of origin for given Seurat Object.  If mouse, human, marmoset, zebrafish, rat,
 drosophila, rhesus macaque, or chicken (name or abbreviation) are provided the function will automatically
 generate hemo_pattern values.

 
 
-
hemo_name

+
hemo_name

 
name to use for the new meta.data column containing percent hemoglobin counts.
 Default is "percent_hemo".

 
 
-
hemo_pattern

+
hemo_pattern

 
A regex pattern to match features against for hemoglobin genes (will set automatically if
 species is mouse or human; marmoset features list saved separately).

 
 
-
hemo_features

+
hemo_features

 
A list of hemoglobin gene names to be used instead of using regex pattern.

 
 
-
ensembl_ids

+
ensembl_ids

 
logical, whether feature names in the object are gene names or
 ensembl IDs (default is FALSE; set TRUE if feature names are ensembl IDs).

 
 
-
overwrite

+
overwrite

 
Logical.  Whether to overwrite existing meta.data columns.  Default is FALSE meaning that
 function will abort if columns with any one of the names provided to hemo_name is
 present in meta.data slot.

 
 
-
list_species_names

+
list_species_names

 
returns list of all accepted values to use for default species names which
 contain internal regex/feature lists (human, mouse, marmoset, zebrafish, rat, drosophila, and
 rhesus macaque).  Default is FALSE.

 
 
-
assay

+
assay

 
Assay to use (default is the current object default assay).

 
 

     

     
Value

-    
An object of the same class as object with columns added to object meta data.

+    
+
+
An object of the same class as object with columns added to object meta data.

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 # Liger
 liger_object <- Add_Hemo(object = liger_object, species = "human")
-} # }
+}
 
-if (FALSE) { # \dontrun{
+if (FALSE) {
 # Seurat
 seurat_object <- Add_Hemo(object = seurat_object, species = "human")
-} # }
+}
 
 

     

@@ -238,15 +238,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Add_Mito_Ribo.html b/docs/reference/Add_Mito_Ribo.html
index 0652f9f2c..399e3a890 100644
--- a/docs/reference/Add_Mito_Ribo.html
+++ b/docs/reference/Add_Mito_Ribo.html
@@ -4,7 +4,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -126,7 +126,7 @@ 
Add Mito and Ribo percentages

     

     
Add_Mito_Ribo(object, ...)
 
-# S3 method for class 'liger'
+# S3 method for liger
 Add_Mito_Ribo(
   object,
   species,
@@ -143,7 +143,7 @@ 
Add Mito and Ribo percentages

   ...
 )
 
-# S3 method for class 'Seurat'
+# S3 method for Seurat
 Add_Mito_Ribo(
   object,
   species,
@@ -165,101 +165,101 @@ 
Add Mito and Ribo percentages

 
     

     
Arguments

-
-
-
object

+    
object

 
Seurat or LIGER object

 
 
-
...

+
...

 
Arguments passed to other methods

 
 
-
species

+
species

 
Species of origin for given Seurat Object.  If mouse, human, marmoset, zebrafish, rat,
 drosophila, rhesus macaque, or chicken (name or abbreviation) are provided the function will automatically
 generate mito_pattern and ribo_pattern values.

 
 
-
mito_name

+
mito_name

 
name to use for the new meta.data column containing percent mitochondrial counts.
 Default is "percent_mito".

 
 
-
ribo_name

+
ribo_name

 
name to use for the new meta.data column containing percent ribosomal counts.
 Default is "percent_ribo".

 
 
-
mito_ribo_name

+
mito_ribo_name

 
name to use for the new meta.data column containing percent
 mitochondrial+ribosomal counts.  Default is "percent_mito_ribo".

 
 
-
mito_pattern

+
mito_pattern

 
A regex pattern to match features against for mitochondrial genes (will set automatically if
 species is mouse, human, zebrafish, rat, drosophila, rhesus macaque, or chicken;
 marmoset features list saved separately).

 
 
-
ribo_pattern

+
ribo_pattern

 
A regex pattern to match features against for ribosomal genes
 (will set automatically if species is mouse, human, marmoset, zebrafish, rat,
 drosophila, rhesus macaque, or chicken).

 
 
-
mito_features

+
mito_features

 
A list of mitochondrial gene names to be used instead of using regex pattern.
 Will override regex pattern if both are present (including default saved regex patterns).

 
 
-
ribo_features

+
ribo_features

 
A list of ribosomal gene names to be used instead of using regex pattern.
 Will override regex pattern if both are present (including default saved regex patterns).

 
 
-
ensembl_ids

+
ensembl_ids

 
logical, whether feature names in the object are gene names or
 ensembl IDs (default is FALSE; set TRUE if feature names are ensembl IDs).

 
 
-
overwrite

+
overwrite

 
Logical.  Whether to overwrite existing meta.data columns.  Default is FALSE meaning that
 function will abort if columns with any one of the names provided to mito_name ribo_name or
 mito_ribo_name is present in meta.data slot.

 
 
-
list_species_names

+
list_species_names

 
returns list of all accepted values to use for default species names which
 contain internal regex/feature lists (human, mouse, marmoset, zebrafish, rat, drosophila, rhesus macaque, and
 chicken).  Default is FALSE.

 
 
-
assay

+
assay

 
Assay to use (default is the current object default assay).

 
 
-
species_prefix

+
species_prefix

 
the species prefix in front of gene symbols in object if providing two species for
 multi-species aligned dataset.

 
 

     

     
Value

-    
An object of the same class as object with columns added to object meta data.

+    
+
+
An object of the same class as object with columns added to object meta data.

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 # Liger
 liger_object <- Add_Mito_Ribo(object = liger_object, species = "human")
-} # }
+}
 
-if (FALSE) { # \dontrun{
+if (FALSE) {
 # Seurat
 seurat_object <- Add_Mito_Ribo(object = seurat_object, species = "human")
-} # }
+}
 
 

     

@@ -275,15 +275,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Add_Pct_Diff.html b/docs/reference/Add_Pct_Diff.html
index 9c1ae5b4f..1dc5e84f9 100644
--- a/docs/reference/Add_Pct_Diff.html
+++ b/docs/reference/Add_Pct_Diff.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -132,41 +132,41 @@ 
Add percentage difference to DE results

 
     

     
Arguments

-
-
-
marker_dataframe

+    
marker_dataframe

 
data.frame containing the results of FindMarkers,  FindAllMarkers, or other DE test data.frame.

 
 
-
pct.1_name

+
pct.1_name

 
the name of data.frame column corresponding to percent expressed in group 1.
 Default is Seurat default "pct.1".

 
 
-
pct.2_name

+
pct.2_name

 
the name of data.frame column corresponding to percent expressed in group 2.
 Default is Seurat default "pct.2".

 
 
-
overwrite

+
overwrite

 
logical.  If the marker_dataframe already contains column named "pct_diff" whether to
 overwrite or return error message.  Default is FALSE.

 
 

     

     
Value

-    
Returns input marker_dataframe with additional "pct_diff" column.

+    
+
+
Returns input marker_dataframe with additional "pct_diff" column.

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 marker_df <- FindAllMarkers(object = obj_name)
 marker_df <- Add_Pct_Diff(marker_dataframe = marker_df)
 # or piped with function
 marker_df <- FindAllMarkers(object = obj_name) %>%
   Add_Pct_Diff()
-} # }
+}
 
 

     

@@ -182,15 +182,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Add_Sample_Meta.html b/docs/reference/Add_Sample_Meta.html
index f506e83d5..1bfd11da2 100644
--- a/docs/reference/Add_Sample_Meta.html
+++ b/docs/reference/Add_Sample_Meta.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -134,34 +134,32 @@ 
Add Sample Level Meta Data

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
object name.

 
 
-
meta_data

+
meta_data

 
data.frame/tibble containing meta data or path to file to read.  Must be formatted as
 either data.frame or tibble.

 
 
-
join_by_seurat

+
join_by_seurat

 
name of the column in seurat_object@meta.data that contains matching
 variables to join_by_meta in meta_data.

 
 
-
join_by_meta

+
join_by_meta

 
name of the column in meta_data that contains matching
 variables to join_by_seurat in seurat_object@meta.data.

 
 
-
na_ok

+
na_ok

 
logical, is it ok to add NA values to seurat_object@meta.data.  Default is FALSE.
 Be very careful if setting TRUE because if there is error in join operation it may result in all
 @meta.data values being replaced with NA.

 
 
-
overwrite

+
overwrite

 
logical, if there are shared columns between seurat_object@meta.data and meta_data
 should the current seurat_object@meta.data columns be overwritten.  Default is FALSE.  This parameter
 excludes values provided to join_by_seurat and join_by_meta.

@@ -169,12 +167,14 @@ 
Arguments

 

     

     
Value

-    
Seurat object with new @meta.data columns

+    
+
+
Seurat object with new @meta.data columns

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 # meta_data present in environment
 sample_level_meta <- data.frame(...)
 obj <- Add_Sample_Meta(seurat_object = obj, meta_data = sample_level_meta,
@@ -183,7 +183,7 @@ 
Examples

 # from meta data file
 obj <- Add_Sample_Meta(seurat_object = obj, meta_data = "meta_data/sample_level_meta.csv",
 join_by_seurat = "orig.ident", join_by_meta = "sample_ID")
-} # }
+}
 
 

     

@@ -199,15 +199,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Add_Top_Gene_Pct.html b/docs/reference/Add_Top_Gene_Pct.html
index 7e7bb84cc..fa112c4d2 100644
--- a/docs/reference/Add_Top_Gene_Pct.html
+++ b/docs/reference/Add_Top_Gene_Pct.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -124,7 +124,7 @@ 
Add Percent of High Abundance Genes

     

     
Add_Top_Gene_Pct(object, ...)
 
-# S3 method for class 'liger'
+# S3 method for liger
 Add_Top_Gene_Pct(
   object,
   num_top_genes = 50,
@@ -134,7 +134,7 @@ 
Add Percent of High Abundance Genes

   ...
 )
 
-# S3 method for class 'Seurat'
+# S3 method for Seurat
 Add_Top_Gene_Pct(
   object,
   num_top_genes = 50,
@@ -148,43 +148,45 @@ 
Add Percent of High Abundance Genes

 
     

     
Arguments

-
-
-
object

+    
object

 
Seurat or LIGER object.

 
 
-
...

+
...

 
Arguments passed to other methods

 
 
-
num_top_genes

+
num_top_genes

 
An integer vector specifying the size(s) of the top set of high-abundance genes.
 Used to compute the percentage of library size occupied by the most highly expressed genes in each cell.

 
 
-
meta_col_name

+
meta_col_name

 
name to use for new meta data column.  Default is "percent_topXX", where XX is
 equal to the value provided to num_top_genes.

 
 
-
overwrite

+
overwrite

 
Logical.  Whether to overwrite existing an meta.data column.  Default is FALSE meaning that
 function will abort if column with name provided to meta_col_name is present in meta.data slot.

 
 
-
verbose

+
verbose

 
logical, whether to print messages with status updates, default is TRUE.

 
 
-
assay

+
assay

 
assay to use in calculation.  Default is "RNA".  Note This should only be changed if
 storing corrected and uncorrected assays in same object (e.g. outputs of both Cell Ranger and Cell Bender).

 
 

     

     
Value

-    
A liger Object

+    
+
+
A liger Object

+
+
 
A Seurat Object

     

     

@@ -203,14 +205,14 @@ 
See also

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 liger_object <- Add_Top_Gene_Pct(object = liger_object, num_top_genes = 50)
-} # }
+}
 
-if (FALSE) { # \dontrun{
+if (FALSE) {
 library(Seurat)
 pbmc_small <- Add_Top_Gene_Pct(seurat_object = pbmc_small, num_top_genes = 50)
-} # }
+}
 
 

     

@@ -226,15 +228,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Barcode_Plot.html b/docs/reference/Barcode_Plot.html
index 9f4fb3ccf..25c19fc3b 100644
--- a/docs/reference/Barcode_Plot.html
+++ b/docs/reference/Barcode_Plot.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -133,44 +133,44 @@ 
Create Barcode Rank Plot

 
     

     
Arguments

-
-
-
br_out

+    
br_out

 
DFrame output from barcodeRanks.

 
 
-
pt.size

+
pt.size

 
point size for plotting, default is 6.

 
 
-
plot_title

+
plot_title

 
Title for plot, default is "Barcode Ranks".

 
 
-
raster_dpi

+
raster_dpi

 
Pixel resolution for rasterized plots, passed to geom_scattermore().
 Default is c(1024, 1024).

 
 
-
plateau

+
plateau

 
numerical value at which to add vertical line designating estimated
 empty droplet plateau (default is NULL).

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 mat <- Read10X_h5(filename = "raw_feature_bc_matrix.h5")
 
 br_results <- DropletUtils::barcodeRanks(mat)
 
 Barcode_Plot(br_out = br_results)
-} # }
+}
 
 

     

@@ -186,15 +186,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Blank_Theme.html b/docs/reference/Blank_Theme.html
index 4cc070e60..77895c4ff 100644
--- a/docs/reference/Blank_Theme.html
+++ b/docs/reference/Blank_Theme.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -127,15 +127,15 @@ 
Blank Theme

 
     

     
Arguments

-
-
-
...

+    
...

 
extra arguments passed to ggplot2::theme().

 
 

     

     
Value

-    
Returns a list-like object of class theme.

+    
+
+
Returns a list-like object of class theme.

     

 
     

@@ -161,15 +161,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Case_Check.html b/docs/reference/Case_Check.html
index 3d17166ad..80d6dc5d4 100644
--- a/docs/reference/Case_Check.html
+++ b/docs/reference/Case_Check.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -133,40 +133,40 @@ 
Check for alternate case features

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
gene_list

+
gene_list

 
vector of genes to check.

 
 
-
case_check_msg

+
case_check_msg

 
logical. Whether to print message to console if alternate case features are
 found in addition to inclusion in returned list.  Default is TRUE.

 
 
-
return_features

+
return_features

 
logical. Whether to return vector of alternate case features.  Default is TRUE.

 
 
-
assay

+
assay

 
Name of assay to pull feature names from. If NULL will use the result of DefaultAssay(seurat_object).

 
 

     

     
Value

-    
If features found returns vector of found alternate case features and prints message depending on
+    
+
+
If features found returns vector of found alternate case features and prints message depending on
 parameters specified.

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 alt_features <- Case_Check(seurat_object = obj_name, gene_list = DEG_list)
-} # }
+}
 
 

     

@@ -182,15 +182,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/CellBender_Diff_Plot.html b/docs/reference/CellBender_Diff_Plot.html
index 76af78c05..77c86cb49 100644
--- a/docs/reference/CellBender_Diff_Plot.html
+++ b/docs/reference/CellBender_Diff_Plot.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -149,115 +149,115 @@ 
Plot Number of Cells/Nuclei per Sample

 
     

     
Arguments

-
-
-
feature_diff_df

+    
feature_diff_df

 
name of data.frame created using CellBender_Feature_Diff.

 
 
-
pct_diff_threshold

+
pct_diff_threshold

 
threshold to use for feature plotting.  Resulting plot will only contain
 features which exhibit percent change >= value.  Default is 25.

 
 
-
num_features

+
num_features

 
Number of features to plot.  Will ignore pct_diff_threshold and return
 plot with specified number of features.  Default is NULL.

 
 
-
label

+
label

 
logical, whether or not to label the features that have largest percent difference
 between raw and CellBender counts (Default is TRUE).

 
 
-
num_labels

+
num_labels

 
Number of features to label if label = TRUE, (default is 20).

 
 
-
min_count_label

+
min_count_label

 
Minimum number of raw counts per feature necessary to be included in
 plot labels (default is 1)

 
 
-
repel

+
repel

 
logical, whether to use geom_text_repel to create a nicely-repelled labels; this is
 slow when a lot of points are being plotted. If using repel, set xnudge and ynudge to 0, (Default is TRUE).

 
 
-
custom_labels

+
custom_labels

 
A custom set of features to label instead of the features most different between
 raw and CellBender counts.

 
 
-
plot_line

+
plot_line

 
logical, whether to plot diagonal line with slope = 1 (Default is TRUE).

 
 
-
plot_title

+
plot_title

 
Plot title.

 
 
-
x_axis_label

+
x_axis_label

 
Label for x axis.

 
 
-
y_axis_label

+
y_axis_label

 
Label for y axis.

 
 
-
xnudge

+
xnudge

 
Amount to nudge X and Y coordinates of labels by.

 
 
-
ynudge

+
ynudge

 
Amount to nudge X and Y coordinates of labels by.

 
 
-
max.overlaps

+
max.overlaps

 
passed to geom_text_repel, exclude text labels that
 overlap too many things. Defaults to 100.

 
 
-
label_color

+
label_color

 
Color to use for text labels.

 
 
-
fontface

+
fontface

 
font face to use for text labels (“plain”, “bold”, “italic”, “bold.italic”) (Default is "bold").

 
 
-
label_size

+
label_size

 
text size for feature labels (passed to geom_text_repel).

 
 
-
bg.color

+
bg.color

 
color to use for shadow/outline of text labels (passed to geom_text_repel) (Default is white).

 
 
-
bg.r

+
bg.r

 
radius to use for shadow/outline of text labels (passed to geom_text_repel) (Default is 0.15).

 
 
-
...

+
...

 
Extra parameters passed to geom_text_repel through
 LabelPoints.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 # get cell bender differences data.frame
 cb_stats <- CellBender_Feature_Diff(seurat_object - obj, raw_assay = "RAW",
 cell_bender_assay = "RNA")
 
 # plot
 CellBender_Diff_Plot(feature_diff_df = cb_stats, pct_diff_threshold = 25)
-} # }
+}
 
 

     

@@ -273,15 +273,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/CellBender_Feature_Diff.html b/docs/reference/CellBender_Feature_Diff.html
index 8c05b47ba..0af528e66 100644
--- a/docs/reference/CellBender_Feature_Diff.html
+++ b/docs/reference/CellBender_Feature_Diff.html
@@ -4,7 +4,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -135,40 +135,40 @@ 
CellBender Feature Differences

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
raw_assay

+
raw_assay

 
Name of the assay containing the raw count data.

 
 
-
cell_bender_assay

+
cell_bender_assay

 
Name of the assay containing the CellBender count data.

 
 
-
raw_mat

+
raw_mat

 
Name of raw count matrix in environment if not using Seurat object.

 
 
-
cell_bender_mat

+
cell_bender_mat

 
Name of CellBender count matrix in environment if not using Seurat object.

 
 

     

     
Value

-    
A data.frame containing summed raw counts, CellBender counts, count difference, and
+    
+
+
A data.frame containing summed raw counts, CellBender counts, count difference, and
 percent difference in counts.

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 cb_stats <- CellBender_Feature_Diff(seurat_object - obj, raw_assay = "RAW",
 cell_bender_assay = "RNA")
-} # }
+}
 
 

     

@@ -184,15 +184,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Cell_Highlight_Plot.html b/docs/reference/Cell_Highlight_Plot.html
index 037da5918..15f9129dd 100644
--- a/docs/reference/Cell_Highlight_Plot.html
+++ b/docs/reference/Cell_Highlight_Plot.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -143,77 +143,77 @@ 
Meta Highlight Plot

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
cells_highlight

+
cells_highlight

 
Cell names to highlight in named list.

 
 
-
highlight_color

+
highlight_color

 
Color to highlight cells.

 
 
-
background_color

+
background_color

 
non-highlighted cell colors (default is "lightgray")..

 
 
-
pt.size

+
pt.size

 
point size for both highlighted cluster and background.

 
 
-
aspect_ratio

+
aspect_ratio

 
Control the aspect ratio (y:x axes ratio length).  Must be numeric value;
 Default is NULL.

 
 
-
figure_plot

+
figure_plot

 
logical.  Whether to remove the axes and plot with legend on left of plot denoting
 axes labels.  (Default is FALSE).  Requires split_seurat = TRUE.

 
 
-
raster

+
raster

 
Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 200,000 cells.

 
 
-
raster.dpi

+
raster.dpi

 
Pixel resolution for rasterized plots, passed to geom_scattermore().
 Default is c(512, 512).

 
 
-
label

+
label

 
Whether to label the highlighted meta data variable(s).  Default is FALSE.

 
 
-
split.by

+
split.by

 
Variable in @meta.data to split the plot by.

 
 
-
split_seurat

+
split_seurat

 
logical.  Whether or not to display split plots like Seurat (shared y axis) or as
 individual plots in layout.  Default is FALSE.

 
 
-
reduction

+
reduction

 
Dimensionality Reduction to use (if NULL then defaults to Object default).

 
 
-
ggplot_default_colors

+
ggplot_default_colors

 
logical.  If highlight_color = NULL, Whether or not to return plot
 using default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

 
 
-
...

+
...

 
Extra parameters passed toDimPlot.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

@@ -245,15 +245,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Cells.html b/docs/reference/Cells.html
index 8f4a53f19..47bfc7b8d 100644
--- a/docs/reference/Cells.html
+++ b/docs/reference/Cells.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -122,42 +122,42 @@ 
Extract Cells from LIGER Object

     

 
     

-    
# S3 method for class 'liger'
+    
# S3 method for liger
 Cells(x, by_dataset = FALSE, ...)

     

 
     

     
Arguments

-
-
-
x

+    
x

 
LIGER object name.

 
 
-
by_dataset

+
by_dataset

 
logical, whether to return list with vector of cell barcodes for each
 dataset in LIGER object or to return single vector of cell barcodes across all
 datasets in object (default is FALSE; return vector of cells).

 
 
-
...

+
...

 
Arguments passed to other methods

 
 

     

     
Value

-    
vector or list depending on by_dataset parameter

+    
+
+
vector or list depending on by_dataset parameter

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 # return single vector of all cells
 all_features <- Cells(x = object, by_dataset = FALSE)
 
 # return list of vectors containing cells from each individual dataset in object
 dataset_features <- Cells(x = object, by_dataset = TRUE)
-} # }
+}
 
 

     

@@ -173,15 +173,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Cells_by_Identities_LIGER.html b/docs/reference/Cells_by_Identities_LIGER.html
index 4c05190f4..9b6fa6890 100644
--- a/docs/reference/Cells_by_Identities_LIGER.html
+++ b/docs/reference/Cells_by_Identities_LIGER.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -127,17 +127,15 @@ 
Extract Cells by identity

 
     

     
Arguments

-
-
-
liger_object

+    
liger_object

 
LIGER object name.

 
 
-
group.by

+
group.by

 
name of meta data column to use, default is current default clustering.

 
 
-
by_dataset

+
by_dataset

 
logical, whether to return list with entries for cell barcodes for each
 identity in group.by
 or to return list of lists (1 entry per dataset and each ident within the dataset)
@@ -146,18 +144,20 @@ 
Arguments

 

     

     
Value

-    
list or list of lists depending on by_dataset parameter

+    
+
+
list or list of lists depending on by_dataset parameter

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 # return single vector of all cells
 cells_by_idents <- Cells_by_Identities_LIGER(liger_object = object, by_dataset = FALSE)
 
 # return list of vectors containing cells from each individual dataset in object
 cells_by_idents_by_dataset <- Cells_by_Identities_LIGER(liger_object = object, by_dataset = TRUE)
-} # }
+}
 
 

     

@@ -173,15 +173,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Cells_per_Sample.html b/docs/reference/Cells_per_Sample.html
index efb81978e..ba14c4828 100644
--- a/docs/reference/Cells_per_Sample.html
+++ b/docs/reference/Cells_per_Sample.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -127,20 +127,20 @@ 
Cells per Sample

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object

 
 
-
sample_col

+
sample_col

 
column name in meta.data that contains sample ID information.  Default is NULL and
 will use "orig.ident column

 
 

     

     
Value

-    
A data.frame

+    
+
+
A data.frame

     

 
     

@@ -162,15 +162,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Change_Delim_All.html b/docs/reference/Change_Delim_All.html
index 93d4b5eac..b100bf069 100644
--- a/docs/reference/Change_Delim_All.html
+++ b/docs/reference/Change_Delim_All.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -127,30 +127,30 @@ 
Change all delimiters in cell name

 
     

     
Arguments

-
-
-
data

+    
data

 
Either matrix/data.frame or list of matrices/data.frames with the cell barcodes in the column names.

 
 
-
current_delim

+
current_delim

 
a single value of current delimiter.

 
 
-
new_delim

+
new_delim

 
a single value of new delimiter desired.

 
 

     

     
Value

-    
matrix or data.frame with new column names.

+    
+
+
matrix or data.frame with new column names.

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 dge_matrix <- Change_Delim_All(data = dge_matrix, current_delim = ".", new_delim = "-")
-} # }
+}
 
 

     

@@ -166,15 +166,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Change_Delim_Prefix.html b/docs/reference/Change_Delim_Prefix.html
index 42a6c8f74..28a8bd63f 100644
--- a/docs/reference/Change_Delim_Prefix.html
+++ b/docs/reference/Change_Delim_Prefix.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -127,30 +127,30 @@ 
Change barcode prefix delimiter

 
     

     
Arguments

-
-
-
data

+    
data

 
Either matrix/data.frame or list of matrices/data.frames with the cell barcodes in the column names.

 
 
-
current_delim

+
current_delim

 
a single value of current delimiter.

 
 
-
new_delim

+
new_delim

 
a single value of new delimiter desired.

 
 

     

     
Value

-    
matrix or data.frame with new column names.

+    
+
+
matrix or data.frame with new column names.

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 dge_matrix <- Change_Delim_Prefix(data = dge_matrix, current_delim = ".", new_delim = "-")
-} # }
+}
 
 

     

@@ -166,15 +166,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Change_Delim_Suffix.html b/docs/reference/Change_Delim_Suffix.html
index ebf34028e..b2cd64483 100644
--- a/docs/reference/Change_Delim_Suffix.html
+++ b/docs/reference/Change_Delim_Suffix.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -127,30 +127,30 @@ 
Change barcode suffix delimiter

 
     

     
Arguments

-
-
-
data

+    
data

 
Either matrix/data.frame or list of matrices/data.frames with the cell barcodes in the column names.

 
 
-
current_delim

+
current_delim

 
a single value of current delimiter.

 
 
-
new_delim

+
new_delim

 
a single value of new delimiter desired.

 
 

     

     
Value

-    
matrix or data.frame with new column names.

+    
+
+
matrix or data.frame with new column names.

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 dge_matrix <- Change_Delim_Suffix(data = dge_matrix, current_delim = ".", new_delim = "-")
-} # }
+}
 
 

     

@@ -166,15 +166,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/CheckMatrix_scCustom.html b/docs/reference/CheckMatrix_scCustom.html
index f56d56284..2b9862c59 100644
--- a/docs/reference/CheckMatrix_scCustom.html
+++ b/docs/reference/CheckMatrix_scCustom.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -130,13 +130,11 @@ 
Check Matrix Validity

 
     

     
Arguments

-
-
-
object

+    
object

 
A matrix

 
 
-
checks

+
checks

 
Type of checks to perform, choose one or more from:
  • “infinite”: Emit a warning if any value is infinite
    • 
 
  • “logical”: Emit a warning if any value is a logical
    • 
 
  • “integer”: Emit a warning if any value is not
@@ -148,7 +146,11 @@ 
    Arguments
    
 

     

     
Value

-    
Emits warnings for each test and invisibly returns NULL

+    
+
+
Emits warnings for each test and invisibly returns NULL

+
+
     

     

     
References

@@ -157,10 +159,10 @@ 
References

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 mat <- Read10X(...)
 CheckMatrix_scCustom(object = mat)
-} # }
+}
 
 

     

@@ -176,15 +178,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Cluster_Highlight_Plot.html b/docs/reference/Cluster_Highlight_Plot.html
index c2a332f1a..e64f7dc6e 100644
--- a/docs/reference/Cluster_Highlight_Plot.html
+++ b/docs/reference/Cluster_Highlight_Plot.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -145,86 +145,86 @@ 
Cluster Highlight Plot

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
cluster_name

+
cluster_name

 
Name(s) (or number(s)) identity of cluster to be highlighted.

 
 
-
highlight_color

+
highlight_color

 
Color(s) to highlight cells.  The default is NULL and plot will use
 scCustomize_Palette().

 
 
-
background_color

+
background_color

 
non-highlighted cell colors.

 
 
-
pt.size

+
pt.size

 
point size for both highlighted cluster and background.

 
 
-
aspect_ratio

+
aspect_ratio

 
Control the aspect ratio (y:x axes ratio length).  Must be numeric value;
 Default is NULL.

 
 
-
figure_plot

+
figure_plot

 
logical.  Whether to remove the axes and plot with legend on left of plot denoting
 axes labels.  (Default is FALSE).  Requires split_seurat = TRUE.

 
 
-
raster

+
raster

 
Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 200,000 cells.

 
 
-
raster.dpi

+
raster.dpi

 
Pixel resolution for rasterized plots, passed to geom_scattermore().
 Default is c(512, 512).

 
 
-
label

+
label

 
Whether to label the highlighted cluster(s).  Default is FALSE.

 
 
-
split.by

+
split.by

 
Feature to split plots by (i.e. "orig.ident").

 
 
-
split_seurat

+
split_seurat

 
logical.  Whether or not to display split plots like Seurat (shared y axis) or as
 individual plots in layout.  Default is FALSE.

 
 
-
split_title_size

+
split_title_size

 
size for plot title labels when using split.by.

 
 
-
num_columns

+
num_columns

 
Number of columns in plot layout.  Only valid if split.by != NULL.

 
 
-
reduction

+
reduction

 
Dimensionality Reduction to use (if NULL then defaults to Object default).

 
 
-
ggplot_default_colors

+
ggplot_default_colors

 
logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

 
 
-
...

+
...

 
Extra parameters passed to DimPlot.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

@@ -247,15 +247,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Cluster_Stats_All_Samples.html b/docs/reference/Cluster_Stats_All_Samples.html
index e4b861a1f..021c3269f 100644
--- a/docs/reference/Cluster_Stats_All_Samples.html
+++ b/docs/reference/Cluster_Stats_All_Samples.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -127,26 +127,26 @@ 
Calculate Cluster Stats

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
group_by_var

+
group_by_var

 
meta data column to classify samples (default = "orig.ident").

 
 

     

     
Value

-    
A data.frame with rows in order of frequency

+    
+
+
A data.frame with rows in order of frequency

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 stats <- Cluster_Stats_All_Samples(seurat_object = object, group_by_var = "orig.ident")
-} # }
+}
 
 

     

@@ -162,15 +162,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Clustered_DotPlot.html b/docs/reference/Clustered_DotPlot.html
index e30a53b0e..af36a9556 100644
--- a/docs/reference/Clustered_DotPlot.html
+++ b/docs/reference/Clustered_DotPlot.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -170,67 +170,65 @@ 
Clustered DotPlot

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
features

+
features

 
Features to plot.

 
 
-
split.by

+
split.by

 
Variable in @meta.data to split the identities plotted by.

 
 
-
colors_use_exp

+
colors_use_exp

 
Color palette to use for plotting expression scale.  Default is viridis::plasma(n = 20, direction = -1).

 
 
-
exp_color_min

+
exp_color_min

 
Minimum scaled average expression threshold (everything smaller will be set to this).
 Default is -2.

 
 
-
exp_color_middle

+
exp_color_middle

 
What scaled expression value to use for the middle of the provided colors_use_exp.
 By default will be set to value in middle of exp_color_min and exp_color_max.

 
 
-
exp_color_max

+
exp_color_max

 
Minimum scaled average expression threshold (everything smaller will be set to this).
 Default is 2.

 
 
-
exp_value_type

+
exp_value_type

 
Whether to plot average normalized expression or
 scaled average normalized expression.  Only valid when split.by is provided.

 
 
-
print_exp_quantiles

+
print_exp_quantiles

 
Whether to print the quantiles of expression data in addition to plots.
 Default is FALSE.  NOTE: These values will be altered by choices of exp_color_min and exp_color_min
 if there are values below or above those cutoffs, respectively.

 
 
-
colors_use_idents

+
colors_use_idents

 
specify color palette to used for identity labels.  By default if
 number of levels plotted is less than or equal to 36 it will use "polychrome" and if greater than 36
 will use "varibow" with shuffle = TRUE both from DiscretePalette_scCustomize.

 
 
-
show_ident_colors

+
show_ident_colors

 
logical, whether to show colors for idents on the column/rows of the plot
 (default is TRUE).

 
 
-
x_lab_rotate

+
x_lab_rotate

 
How to rotate column labels.  By default set to TRUE which rotates labels 45 degrees.
 If set FALSE rotation is set to 0 degrees.  Users can also supply custom angle for text rotation.

 
 
-
plot_padding

+
plot_padding

 
if plot needs extra white space padding so no plot or labels are cutoff.
 The parameter accepts TRUE or numeric vector of length 4.  If TRUE padding will be set to
 c(2, 10, 0 0) (bottom, left, top, right).  Can also be customized further with numeric
@@ -238,140 +236,142 @@ 
Arguments

 Default is NULL, no padding.

 
 
-
flip

+
flip

 
logical, whether to flip the axes of final plot.  Default is FALSE; rows = features and
 columns = idents.

 
 
-
k

+
k

 
Value to use for k-means clustering on features  Sets (km) parameter in ComplexHeatmap::Heatmap().
 From ComplexHeatmap::Heatmap(): Apply k-means clustering on rows. If the value is larger than 1, the
 heatmap will be split by rows according to the k-means clustering. For each row slice, hierarchical
 clustering is still applied with parameters above.

 
 
-
feature_km_repeats

+
feature_km_repeats

 
Number of k-means runs to get a consensus k-means clustering for features.
 Note if feature_km_repeats is set to value greater than one, the final number of groups might be
 smaller than row_km, but this might mean the original row_km is not a good choice.  Default is 1000.

 
 
-
ident_km_repeats

+
ident_km_repeats

 
Number of k-means runs to get a consensus k-means clustering. Similar to
 feature_km_repeats.  Default is 1000.

 
 
-
row_label_size

+
row_label_size

 
Size of the feature labels.  Provided to row_names_gp in Heatmap call.

 
 
-
row_label_fontface

+
row_label_fontface

 
Fontface to use for row labels.  Provided to row_names_gp in Heatmap call.

 
 
-
grid_color

+
grid_color

 
color to use for heatmap grid.  Default is NULL which "removes" grid by using NA color.

 
 
-
cluster_feature

+
cluster_feature

 
logical, whether to cluster and reorder feature axis.  Default is TRUE.

 
 
-
cluster_ident

+
cluster_ident

 
logical, whether to cluster and reorder identity axis.  Default is TRUE.

 
 
-
column_label_size

+
column_label_size

 
Size of the feature labels.  Provided to column_names_gp in Heatmap call.

 
 
-
legend_label_size

+
legend_label_size

 
Size of the legend text labels.  Provided to labels_gp in Heatmap legend call.

 
 
-
legend_title_size

+
legend_title_size

 
Size of the legend title text labels.  Provided to title_gp in Heatmap legend call.

 
 
-
legend_position

+
legend_position

 
Location of the plot legend (default is "right").

 
 
-
legend_orientation

+
legend_orientation

 
Orientation of the legend (default is NULL).

 
 
-
show_ident_legend

+
show_ident_legend

 
logical, whether to show the color legend for idents in plot (default is TRUE).

 
 
-
show_row_names

+
show_row_names

 
logical, whether to show row names on plot (default is TRUE).

 
 
-
show_column_names

+
show_column_names

 
logical, whether to show column names on plot (default is TRUE).

 
 
-
column_names_side

+
column_names_side

 
Should the row names be on the "bottom" or "top" of plot.  Default is "bottom".

 
 
-
row_names_side

+
row_names_side

 
Should the row names be on the "left" or "right" of plot.  Default is "right".

 
 
-
raster

+
raster

 
Logical, whether to render in raster format (faster plotting, smaller files).  Default is FALSE.

 
 
-
plot_km_elbow

+
plot_km_elbow

 
Logical, whether or not to return the Sum Squared Error Elbow Plot for k-means clustering.
 Estimating elbow of this plot is one way to determine "optimal" value for k.
 Based on: https://stackoverflow.com/a/15376462/15568251.

 
 
-
elbow_kmax

+
elbow_kmax

 
The maximum value of k to use for plot_km_elbow.  Suggest setting larger value so the
 true shape of plot can be observed.  Value must be 1 less than number of features provided.  If NULL parameter
 will be set dependent on length of feature list up to elbow_kmax = 20.

 
 
-
assay

+
assay

 
Name of assay to use, defaults to the active assay.

 
 
-
group.by

+
group.by

 
Group (color) cells in different ways (for example, orig.ident).

 
 
-
idents

+
idents

 
Which classes to include in the plot (default is all).

 
 
-
show_parent_dend_line

+
show_parent_dend_line

 
Logical, Sets parameter of same name in ComplexHeatmap::Heatmap().
 From ComplexHeatmap::Heatmap(): When heatmap is split, whether to add a dashed line to mark parent
 dendrogram and children dendrograms.  Default is TRUE.

 
 
-
ggplot_default_colors

+
ggplot_default_colors

 
logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

 
 
-
color_seed

+
color_seed

 
random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.

 
 
-
seed

+
seed

 
Sets seed for reproducible plotting (ComplexHeatmap plot).

 
 

     

     
Value

-    
A ComplexHeatmap or if plot_km_elbow = TRUE a list containing ggplot2 object and ComplexHeatmap.

+    
+
+
A ComplexHeatmap or if plot_km_elbow = TRUE a list containing ggplot2 object and ComplexHeatmap.

     

     

     
References

@@ -417,15 +417,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/ColorBlind_Pal.html b/docs/reference/ColorBlind_Pal.html
index fc8dd5050..118073fe4 100644
--- a/docs/reference/ColorBlind_Pal.html
+++ b/docs/reference/ColorBlind_Pal.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -127,7 +127,9 @@ 
Color Universal Design Short Palette

 
     

     
Value

-    
modified/reordered color palette (8 colors) based on ditto-seq

+    
+
+
modified/reordered color palette (8 colors) based on ditto-seq

     

     

     
References

@@ -155,15 +157,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Convert_Assay.html b/docs/reference/Convert_Assay.html
index 83bd3dc3c..77b84b4a9 100644
--- a/docs/reference/Convert_Assay.html
+++ b/docs/reference/Convert_Assay.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -127,18 +127,16 @@ 
Convert between Seurat Assay types

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
assay

+
assay

 
name(s) of assays to convert.  Default is NULL and will check with users
 which assays they want to convert.

 
 
-
convert_to

+
convert_to

 
value of what assay type to convert current assays to.
 #'
  • Accepted values for V3/4 are: "Assay", "assay", "V3", or "v3".
    • 
 
  • Accepted values for V5 are: "Assay5", "assay5", "V5", or "v5".
    • 
@@ -148,13 +146,13 @@ 
    Arguments
    
 
     
    
     
    Examples
    
-    
    if (FALSE) { # \dontrun{
+    
    if (FALSE) {
 # Convert to V3/4 assay
 obj <- Convert_Assay(seurat_object = obj, convert_to = "V3")
 
 # Convert to 5 assay
 obj <- Convert_Assay(seurat_object = obj, convert_to = "V5")
-} # }
+}
 
 
    
     
    
@@ -170,15 +168,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.1.0.
    
+  
    Site built with pkgdown 2.0.9.
    
 
    
 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Copy_From_GCP.html b/docs/reference/Copy_From_GCP.html
index 7394786ff..b86e54d54 100644
--- a/docs/reference/Copy_From_GCP.html
+++ b/docs/reference/Copy_From_GCP.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -127,26 +127,26 @@ 
Copy folder from GCP bucket from R Console

 
     

     
Arguments

-
-
-
folder_file_path

+    
folder_file_path

 
folder to be copied to GCP bucket.

 
 
-
gcp_bucket_path

+
gcp_bucket_path

 
GCP bucket path to copy to files.

 
 

     

     
Value

-    
No return value.  Performs system copy from GCP bucket.

+    
+
+
No return value.  Performs system copy from GCP bucket.

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 Copy_From_GCP(folder_file_path = "plots/", gcp_bucket_path = "gs://bucket_name_and_folder_path")
-} # }
+}
 
 

     

@@ -162,15 +162,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Copy_To_GCP.html b/docs/reference/Copy_To_GCP.html
index c6ceda4d5..c2ac1cbf1 100644
--- a/docs/reference/Copy_To_GCP.html
+++ b/docs/reference/Copy_To_GCP.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -127,26 +127,26 @@ 
Copy folder to GCP bucket from R Console

 
     

     
Arguments

-
-
-
folder_file_path

+    
folder_file_path

 
folder to be copied to GCP bucket.

 
 
-
gcp_bucket_path

+
gcp_bucket_path

 
GCP bucket path to copy to files.

 
 

     

     
Value

-    
No return value.  Performs system copy to GCP bucket.

+    
+
+
No return value.  Performs system copy to GCP bucket.

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 Copy_To_GCP(folder_file_path = "plots/", gcp_bucket_path = "gs://bucket_name_and_folder_path")
-} # }
+}
 
 

     

@@ -162,15 +162,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Create_10X_H5.html b/docs/reference/Create_10X_H5.html
index 5a1e4954a..b038b0373 100644
--- a/docs/reference/Create_10X_H5.html
+++ b/docs/reference/Create_10X_H5.html
@@ -4,7 +4,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -134,34 +134,34 @@ 
Create H5 from 10X Outputs

 
     

     
Arguments

-
-
-
raw_data_file_path

+    
raw_data_file_path

 
file path to raw data file(s).

 
 
-
source_type

+
source_type

 
type of source data (Default is "10X").  Alternatively can provide "Matrix" or "data.frame".

 
 
-
save_file_path

+
save_file_path

 
file path to directory to save file.

 
 
-
save_name

+
save_name

 
name prefix for output H5 file.

 
 

     

     
Value

-    
A HDF5 format file that will be recognized as 10X Cell Ranger formatted file by Seurat or LIGER.

+    
+
+
A HDF5 format file that will be recognized as 10X Cell Ranger formatted file by Seurat or LIGER.

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 Create_10X_H5(raw_data_file_path = "file_path", save_file_path = "file_path2", save_name = "NAME")
-} # }
+}
 
 

     

@@ -177,15 +177,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Create_CellBender_Merged_Seurat.html b/docs/reference/Create_CellBender_Merged_Seurat.html
index 7e5e77a6a..e94fa8981 100644
--- a/docs/reference/Create_CellBender_Merged_Seurat.html
+++ b/docs/reference/Create_CellBender_Merged_Seurat.html
@@ -4,7 +4,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -136,46 +136,46 @@ 
Create Seurat Object with Cell Bender and Raw data

 
     

     
Arguments

-
-
-
raw_cell_bender_matrix

+    
raw_cell_bender_matrix

 
matrix file containing the cell bender correct counts.

 
 
-
raw_counts_matrix

+
raw_counts_matrix

 
matrix file contain the uncorrected Cell Ranger (or other) counts.

 
 
-
raw_assay_name

+
raw_assay_name

 
a key value to use specifying the name of assay.  Default is "RAW".

 
 
-
min_cells

+
min_cells

 
value to supply to min.cells parameter of CreateSeuratObject.
 Default is 5.

 
 
-
min_features

+
min_features

 
value to supply to min.features parameter of CreateSeuratObject.
 Default is 200.

 
 
-
...

+
...

 
Extra parameters passed to CreateSeuratObject.

 
 

     

     
Value

-    
A Seurat Object contain both the Cell Bender corrected counts ("RNA" assay) and uncorrected
+    
+
+
A Seurat Object contain both the Cell Bender corrected counts ("RNA" assay) and uncorrected
 counts ("RAW" assay; or other name specified to raw_assay_name).

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 seurat_obj <- Create_CellBender_Merged_Seurat(raw_cell_bender_matrix = cb_matrix,
 raw_counts_matrix = cr_matrix)
-} # }
+}
 
 

     

@@ -191,15 +191,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Create_Cluster_Annotation_File.html b/docs/reference/Create_Cluster_Annotation_File.html
index 26fe8fc2c..b81f0775c 100644
--- a/docs/reference/Create_Cluster_Annotation_File.html
+++ b/docs/reference/Create_Cluster_Annotation_File.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -130,27 +130,27 @@ 
Create cluster annotation csv file

 
     

     
Arguments

-
-
-
file_path

+    
file_path

 
path to directory to save file.  Default is current working directory.

 
 
-
file_name

+
file_name

 
name to use for annotation file.  Function automatically adds file type ".csv" suffix.
 Default is "cluster_annotation".

 
 

     

     
Value

-    
No value returned.  Creates .csv file.

+    
+
+
No value returned.  Creates .csv file.

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 Create_Cluster_Annotation_File(file_path = "cluster_annotation_folder_name")
-} # }
+}
 
 

     

@@ -166,15 +166,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Dark2_Pal.html b/docs/reference/Dark2_Pal.html
index 610df5bfc..75eb1583e 100644
--- a/docs/reference/Dark2_Pal.html
+++ b/docs/reference/Dark2_Pal.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -127,7 +127,9 @@ 
Dark2 Palette

 
     

     
Value

-    
"Dark2" color palette (8 colors)

+    
+
+
"Dark2" color palette (8 colors)

     

     

     
References

@@ -156,15 +158,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/DimPlot_All_Samples.html b/docs/reference/DimPlot_All_Samples.html
index 9f84b1996..aad8f3989 100644
--- a/docs/reference/DimPlot_All_Samples.html
+++ b/docs/reference/DimPlot_All_Samples.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -140,62 +140,62 @@ 
DimPlot by Meta Data Column

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
meta_data_column

+
meta_data_column

 
Meta data column to split plots by.

 
 
-
colors_use

+
colors_use

 
single color to use for all plots or a vector of colors equal to the number of plots.

 
 
-
pt.size

+
pt.size

 
Adjust point size for plotting.

 
 
-
aspect_ratio

+
aspect_ratio

 
Control the aspect ratio (y:x axes ratio length).  Must be numeric value;
 Default is NULL.

 
 
-
title_size

+
title_size

 
size for plot title labels.

 
 
-
num_columns

+
num_columns

 
number of columns in final layout plot.

 
 
-
reduction

+
reduction

 
Dimensionality Reduction to use (if NULL then defaults to Object default).

 
 
-
dims

+
dims

 
Which dimensions to plot.  Defaults to c(1,2) if not specified.

 
 
-
raster

+
raster

 
Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 200,000 cells.

 
 
-
raster.dpi

+
raster.dpi

 
Pixel resolution for rasterized plots, passed to geom_scattermore().
 Default is c(512, 512).

 
 
-
...

+
...

 
Extra parameters passed to DimPlot.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

@@ -222,15 +222,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/DimPlot_LIGER.html b/docs/reference/DimPlot_LIGER.html
index a9fd6feaf..6e57fd1bd 100644
--- a/docs/reference/DimPlot_LIGER.html
+++ b/docs/reference/DimPlot_LIGER.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -150,122 +150,122 @@ 
DimPlot LIGER Version

 
     

     
Arguments

-
-
-
liger_object

+    
liger_object

 
liger liger_object.  Need to perform clustering before calling this function

 
 
-
group_by

+
group_by

 
Variable to be plotted.  If NULL will plot clusters from liger@clusters slot.
 If combination = TRUE will plot both clusters and meta data variable.

 
 
-
split_by

+
split_by

 
Variable to split plots by.

 
 
-
colors_use_cluster

+
colors_use_cluster

 
colors to use for plotting by clusters.  By default if number of levels plotted is
 less than or equal to 36 will use "polychrome" and if greater than 36 will use "varibow" with shuffle = TRUE
 both from DiscretePalette_scCustomize.

 
 
-
colors_use_meta

+
colors_use_meta

 
colors to use for plotting by meta data (cell.data) variable.  By default if number
 of levels plotted is less than or equal to 36 it will use "polychrome" and if greater than 36 will use
 "varibow" with shuffle = TRUE both from DiscretePalette_scCustomize.

 
 
-
pt_size

+
pt_size

 
Adjust point size for plotting.

 
 
-
shuffle

+
shuffle

 
logical. Whether to randomly shuffle the order of points. This can be useful for crowded plots
 if points of interest are being buried. (Default is TRUE).

 
 
-
shuffle_seed

+
shuffle_seed

 
Sets the seed if randomly shuffling the order of points.

 
 
-
reduction_label

+
reduction_label

 
What to label the x and y axes of resulting plots.  LIGER does not store name of
 technique and therefore needs to be set manually.  Default is "UMAP". (only valid for
 rliger < 2.0.0).

 
 
-
reduction

+
reduction

 
specify reduction to use when plotting.  Default is current object
 default reduction (only valid for rliger v2.0.0 or greater).

 
 
-
aspect_ratio

+
aspect_ratio

 
Control the aspect ratio (y:x axes ratio length).  Must be numeric value;
 Default is NULL.

 
 
-
label

+
label

 
logical.  Whether or not to label the clusters.  ONLY applies to plotting by cluster.  Default is TRUE.

 
 
-
label_size

+
label_size

 
size of cluster labels.

 
 
-
label_repel

+
label_repel

 
logical.  Whether to repel cluster labels from each other if plotting by
 cluster (if group_by = NULL or group_by = "cluster).  Default is FALSE.

 
 
-
label_box

+
label_box

 
logical.  Whether to put a box around the label text (uses geom_text vs geom_label).
 Default is FALSE.

 
 
-
label_color

+
label_color

 
Color to use for cluster labels.  Default is "black".

 
 
-
combination

+
combination

 
logical, whether to return patchwork displaying both plots side by side.  (Default is FALSE).

 
 
-
raster

+
raster

 
Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 200,000 cells.

 
 
-
raster.dpi

+
raster.dpi

 
Pixel resolution for rasterized plots, passed to geom_scattermore().
 Default is c(512, 512).

 
 
-
num_columns

+
num_columns

 
Number of columns in plot layout.  Only valid if split.by != NULL.

 
 
-
ggplot_default_colors

+
ggplot_default_colors

 
logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

 
 
-
color_seed

+
color_seed

 
random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.

 
 

     

     
Value

-    
A ggplot/patchwork object

+    
+
+
A ggplot/patchwork object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 DimPlot_LIGER(liger_object = obj_name, reduction_label = "UMAP")
-} # }
+}
 
 

     

@@ -281,15 +281,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/DimPlot_scCustom.html b/docs/reference/DimPlot_scCustom.html
index 457663069..7e6af24bf 100644
--- a/docs/reference/DimPlot_scCustom.html
+++ b/docs/reference/DimPlot_scCustom.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -155,134 +155,134 @@ 
DimPlot with modified default settings

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
colors_use

+
colors_use

 
color palette to use for plotting.  By default if number of levels plotted is less than
 or equal to 36 it will use "polychrome" and if greater than 36 will use "varibow" with shuffle = TRUE
 both from DiscretePalette_scCustomize.

 
 
-
pt.size

+
pt.size

 
Adjust point size for plotting.

 
 
-
reduction

+
reduction

 
Dimensionality Reduction to use (if NULL then defaults to Object default).

 
 
-
group.by

+
group.by

 
Name of one or more metadata columns to group (color) cells by (for example, orig.ident);
 default is the current active.ident of the object.

 
 
-
split.by

+
split.by

 
Feature to split plots by (i.e. "orig.ident").

 
 
-
split_seurat

+
split_seurat

 
logical.  Whether or not to display split plots like Seurat (shared y axis) or as
 individual plots in layout.  Default is FALSE.

 
 
-
figure_plot

+
figure_plot

 
logical.  Whether to remove the axes and plot with legend on left of plot denoting
 axes labels.  (Default is FALSE).  Requires split_seurat = TRUE.

 
 
-
aspect_ratio

+
aspect_ratio

 
Control the aspect ratio (y:x axes ratio length).  Must be numeric value;
 Default is NULL.

 
 
-
add_prop_plot

+
add_prop_plot

 
logical, whether to add plot to returned layout with the number of cells per identity
 (or percent of cells per identity).  Default is FALSE.

 
 
-
prop_plot_percent

+
prop_plot_percent

 
logical, if add_prop_plot = TRUE this parameter controls whether
 proportion plot shows raw cell number or percent of cells per identity.  Default is FALSE; plots raw cell number.

 
 
-
prop_plot_x_log

+
prop_plot_x_log

 
logical, if add_prop_plot = TRUE this parameter controls whether to change x axis
 to log10 scale (Default is FALSE).

 
 
-
prop_plot_label

+
prop_plot_label

 
logical, if add_prop_plot = TRUE this parameter controls whether to label the bars with total number of cells or percentages; Default is FALSE.

 
 
-
shuffle

+
shuffle

 
logical. Whether to randomly shuffle the order of points. This can be useful for crowded
 plots if points of interest are being buried. (Default is TRUE).

 
 
-
seed

+
seed

 
Sets the seed if randomly shuffling the order of points.

 
 
-
label

+
label

 
Whether to label the clusters.  By default if group.by = NULL label = TRUE, and
 otherwise it is FALSE.

 
 
-
label.size

+
label.size

 
Sets size of labels.

 
 
-
label.color

+
label.color

 
Sets the color of the label text.

 
 
-
label.box

+
label.box

 
Whether to put a box around the label text (geom_text vs geom_label).

 
 
-
dims

+
dims

 
Which dimensions to plot.  Defaults to c(1,2) if not specified.

 
 
-
repel

+
repel

 
Repel labels.

 
 
-
raster

+
raster

 
Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 200,000 cells.

 
 
-
raster.dpi

+
raster.dpi

 
Pixel resolution for rasterized plots, passed to geom_scattermore().
 Default is c(512, 512).

 
 
-
num_columns

+
num_columns

 
Number of columns in plot layout.  Only valid if split.by != NULL.

 
 
-
ggplot_default_colors

+
ggplot_default_colors

 
logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

 
 
-
color_seed

+
color_seed

 
random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.

 
 
-
...

+
...

 
Extra parameters passed to DimPlot.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

     

     
References

@@ -311,15 +311,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/DiscretePalette_scCustomize.html b/docs/reference/DiscretePalette_scCustomize.html
index 92109e194..ecc4614fc 100644
--- a/docs/reference/DiscretePalette_scCustomize.html
+++ b/docs/reference/DiscretePalette_scCustomize.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -132,29 +132,29 @@ 
Discrete color palettes

 
     

     
Arguments

-
-
-
num_colors

+    
num_colors

 
Number of colors to be generated.

 
 
-
palette

+
palette

 
Options are
 "alphabet", "alphabet2", "glasbey", "polychrome", "stepped", "ditto_seq", "varibow".

 
 
-
shuffle_pal

+
shuffle_pal

 
randomly shuffle the outputted palette.  Most useful for varibow palette as
 that is normally an ordered palette.

 
 
-
seed

+
seed

 
random seed for the palette shuffle.  Default = 123.

 
 

     

     
Value

-    
A vector of colors

+    
+
+
A vector of colors

     

     

     
References

@@ -192,15 +192,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/DotPlot_scCustom.html b/docs/reference/DotPlot_scCustom.html
index 9d0a6c177..c7c6a9e5c 100644
--- a/docs/reference/DotPlot_scCustom.html
+++ b/docs/reference/DotPlot_scCustom.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -138,52 +138,52 @@ 
Customized DotPlot

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
features

+
features

 
Features to plot.

 
 
-
group.by

+
group.by

 
Name of metadata variable (column) to group cells by (for example, orig.ident);
 default is the current active.ident of the object.

 
 
-
colors_use

+
colors_use

 
specify color palette to used.  Default is viridis_plasma_dark_high.

 
 
-
remove_axis_titles

+
remove_axis_titles

 
logical. Whether to remove the x and y axis titles.  Default = TRUE.

 
 
-
x_lab_rotate

+
x_lab_rotate

 
Rotate x-axis labels 45 degrees (Default is FALSE).

 
 
-
y_lab_rotate

+
y_lab_rotate

 
Rotate x-axis labels 45 degrees (Default is FALSE).

 
 
-
facet_label_rotate

+
facet_label_rotate

 
Rotate facet labels on grouped DotPlots by 45 degrees (Default is FALSE).

 
 
-
flip_axes

+
flip_axes

 
whether or not to flip and X and Y axes (Default is FALSE).

 
 
-
...

+
...

 
Extra parameters passed to DotPlot.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

@@ -211,15 +211,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Embeddings.html b/docs/reference/Embeddings.html
index dc7e4a090..d2d76d9c5 100644
--- a/docs/reference/Embeddings.html
+++ b/docs/reference/Embeddings.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -122,48 +122,48 @@ 
Extract matrix of embeddings

     

 
     

-    
# S3 method for class 'liger'
+    
# S3 method for liger
 Embeddings(object, reduction = NULL, iNMF = FALSE, check_only = FALSE, ...)

     

 
     

     
Arguments

-
-
-
object

+    
object

 
LIGER object name.

 
 
-
reduction

+
reduction

 
name of dimensionality reduction to pull

 
 
-
iNMF

+
iNMF

 
logical, whether to extract iNMF h.norm matrix instead of dimensionality reduction embeddings.

 
 
-
check_only

+
check_only

 
logical, return TRUE if valid reduction is present.

 
 
-
...

+
...

 
Arguments passed to other methods

 
 

     

     
Value

-    
matrix

+    
+
+
matrix

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 # Extract embedding matrix for current dimensionality reduction
 UMAP_coord <- Embeddings(object = liger_object)
 
 # Extract iNMF h.norm matrix
 iNMF_mat <- Embeddings(object = liger_object, reduction = "iNMF")
-} # }
+}
 
 

     

@@ -179,15 +179,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Extract_Modality.html b/docs/reference/Extract_Modality.html
index 336276bd7..c32c83800 100644
--- a/docs/reference/Extract_Modality.html
+++ b/docs/reference/Extract_Modality.html
@@ -4,7 +4,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -129,23 +129,23 @@ 
Extract multi-modal data into list by modality

 
     

     
Arguments

-
-
-
matrix_list

+    
matrix_list

 
list of matrices to split by modality

 
 

     

     
Value

-    
list of lists, with one sublist per data modality.  Sub-list contain 1 matrix entry per sample

+    
+
+
list of lists, with one sublist per data modality.  Sub-list contain 1 matrix entry per sample

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 multi_mat <- Read10X(...)
 new_multi_mat <- Extract_Modality(matrix_list = multi_mat)
-} # }
+}
 
 

     

@@ -161,15 +161,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Extract_Sample_Meta.html b/docs/reference/Extract_Sample_Meta.html
index e0819deb2..e252b9a5f 100644
--- a/docs/reference/Extract_Sample_Meta.html
+++ b/docs/reference/Extract_Sample_Meta.html
@@ -4,7 +4,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -135,23 +135,21 @@ 
Extract sample level meta.data

 
     

     
Arguments

-
-
-
object

+    
object

 
Seurat object

 
 
-
sample_name

+
sample_name

 
meta.data column to use as sample.  Output data.frame will contain one row per
 level or unique value in this variable.

 
 
-
variables_include

+
variables_include

 
@meta.data columns to keep in final data.frame.  All other columns will
 be discarded.  Default is NULL.

 
 
-
variables_exclude

+
variables_exclude

 
columns to discard in final data.frame.  Many cell level columns are
 irrelevant at the sample level (e.g., nFeature_RNA, percent_mito).
  • Default parameter value is NULL but internally will set to discard nFeature_ASSAY(s),
 nCount_ASSAY(s), percent_mito, percent_ribo, percent_mito_ribo, and log10GenesPerUMI.
    • 
@@ -161,14 +159,16 @@ 
    Arguments
    
 

 
 
-
include_all

+
include_all

 
logical, whether or not to include all object meta data columns in output data.frame.
 Default is FALSE.

 
 

     

     
Value

-    
Returns a data.frame with one row per sample_name.

+    
+
+
Returns a data.frame with one row per sample_name.

     

 
     

@@ -200,15 +200,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Extract_Top_Markers.html b/docs/reference/Extract_Top_Markers.html
index 9c90bf7a4..85d1f68e5 100644
--- a/docs/reference/Extract_Top_Markers.html
+++ b/docs/reference/Extract_Top_Markers.html
@@ -4,7 +4,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -139,62 +139,62 @@ 
Extract Top N Marker Genes

 
     

     
Arguments

-
-
-
marker_dataframe

+    
marker_dataframe

 
data.frame output from FindAllMarkers or similar analysis.

 
 
-
num_genes

+
num_genes

 
number of genes per group (e.g., cluster) to include in output list.

 
 
-
group_by

+
group_by

 
column name of marker_dataframe to group data by.  Default is "cluster" based on
 FindAllMarkers.

 
 
-
rank_by

+
rank_by

 
column name of marker_dataframe to rank data by when selecting num_genes per group_by.
 Default is "avg_log2FC" based on FindAllMarkers.

 
 
-
gene_column

+
gene_column

 
column name of marker_dataframe that contains the gene IDs.  Default is "gene"
 based on FindAllMarkers.

 
 
-
gene_rownames_to_column

+
gene_rownames_to_column

 
logical. Whether gene IDs are stored in rownames and should be moved to
 column.  Default is FALSE.

 
 
-
data_frame

+
data_frame

 
Logical, whether or not to return filtered data.frame of the original markers_dataframe or
 to return a vector of gene IDs.  Default is FALSE.

 
 
-
named_vector

+
named_vector

 
Logical, whether or not to name the vector of gene names that is returned by the function.
 If TRUE will name the vector using the column provided to group_by.  Default is TRUE.

 
 
-
make_unique

+
make_unique

 
Logical, whether an unnamed vector should return only unique values.  Default is FALSE.
 Not applicable when data_frame = TRUE or named_vector = TRUE.

 
 

     

     
Value

-    
filtered data.frame, vector, or named vector containing gene IDs.

+    
+
+
filtered data.frame, vector, or named vector containing gene IDs.

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 top10_genes <- Extract_Top_Markers(marker_dataframe = markers_results, num_genes = 10,
 group_by = "cluster", rank_by = "avg_log2FC")
-} # }
+}
 
 

     

@@ -210,15 +210,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Factor_Cor_Plot.html b/docs/reference/Factor_Cor_Plot.html
index 045513a16..ac6893f7d 100644
--- a/docs/reference/Factor_Cor_Plot.html
+++ b/docs/reference/Factor_Cor_Plot.html
@@ -5,7 +5,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -145,78 +145,78 @@ 
Factor Correlation Plot

 
     

     
Arguments

-
-
-
object

+    
object

 
liger or Seurat object.

 
 
-
colors_use

+
colors_use

 
Color palette to use for correlation values.
 Default is RColorBrewer::RdBu if positive_only = FALSE.
 If positive_only = TRUE the default is viridis.
 Users can also supply vector of 3 colors (low, mid, high).

 
 
-
label

+
label

 
logical, whether to add correlation values to plot result.

 
 
-
label_threshold

+
label_threshold

 
threshold for adding correlation values if label = TRUE.  Default
 is 0.5.

 
 
-
label_size

+
label_size

 
size of correlation labels

 
 
-
plot_title

+
plot_title

 
Plot title.

 
 
-
plot_type

+
plot_type

 
Controls plotting full matrix, or just the upper or lower triangles.
 Accepted values are: "full" (default), "upper", or "lower".

 
 
-
positive_only

+
positive_only

 
logical, whether to limit the plotted values to only positive
 correlations (negative values set to 0); default is FALSE.

 
 
-
x_lab_rotate

+
x_lab_rotate

 
logical, whether to rotate the axes labels on the x-axis.  Default is TRUE.

 
 
-
cluster

+
cluster

 
logical, whether to cluster the plot using hclust (default TRUE).  If FALSE
 factors are listed in numerical order.

 
 
-
cluster_rect

+
cluster_rect

 
logical, whether to add rectangles around the clustered areas on plot,
 default is FALSE.

 
 
-
cluster_rect_num

+
cluster_rect_num

 
number of rectangles to add to the plot, default NULL.

 
 
-
cluster_rect_col

+
cluster_rect_col

 
color to use for rectangles, default MULL (will set color automatically).

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 Factor_Cor_Plot(object = obj)
-} # }
+}
 
 

     

@@ -232,15 +232,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/FeaturePlot_DualAssay.html b/docs/reference/FeaturePlot_DualAssay.html
index 3826b63f8..a09de0f0e 100644
--- a/docs/reference/FeaturePlot_DualAssay.html
+++ b/docs/reference/FeaturePlot_DualAssay.html
@@ -4,7 +4,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -149,102 +149,102 @@ 
Customize FeaturePlot of two assays

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
features

+
features

 
Feature(s) to plot.

 
 
-
assay1

+
assay1

 
name of assay one.  Default is "RAW" as featured in Create_CellBender_Merged_Seurat

 
 
-
assay2

+
assay2

 
name of assay two  Default is "RNA" as featured in Create_CellBender_Merged_Seurat

 
 
-
colors_use

+
colors_use

 
list of colors or color palette to use.

 
 
-
colors_use_assay2

+
colors_use_assay2

 
optional, a second color palette to use for the second assay.

 
 
-
na_color

+
na_color

 
color to use for points below lower limit.

 
 
-
order

+
order

 
whether to move positive cells to the top (default = TRUE).

 
 
-
pt.size

+
pt.size

 
Adjust point size for plotting.

 
 
-
aspect_ratio

+
aspect_ratio

 
Control the aspect ratio (y:x axes ratio length).  Must be numeric value;
 Default is NULL.

 
 
-
reduction

+
reduction

 
Dimensionality Reduction to use (if NULL then defaults to Object default).

 
 
-
na_cutoff

+
na_cutoff

 
Value to use as minimum expression cutoff.  To set no cutoff set to NA.

 
 
-
raster

+
raster

 
Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 200,000 cells.

 
 
-
raster.dpi

+
raster.dpi

 
Pixel resolution for rasterized plots, passed to geom_scattermore().
 Default is c(512, 512).

 
 
-
layer

+
layer

 
Which layer to pull expression data from?  Default is "data".

 
 
-
num_columns

+
num_columns

 
Number of columns in plot layout.  If number of features > 1 then num_columns
 dictates the number of columns in overall layout (num_columns = 1 means stacked layout & num_columns = 2
 means adjacent layout).

 
 
-
alpha_exp

+
alpha_exp

 
new alpha level to apply to expressing cell color palette (colors_use).  Must be
 value between 0-1.

 
 
-
alpha_na_exp

+
alpha_na_exp

 
new alpha level to apply to non-expressing cell color palette (na_color).  Must be
 value between 0-1.

 
 
-
...

+
...

 
Extra parameters passed to FeaturePlot.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 FeaturePlot_DualAssay(seurat_object = object, features = "Cx3cr1", assay1 = "RAW", assay2 = "RNA",
 colors_use = viridis_plasma_dark_high, na_color = "lightgray")
-} # }
+}
 
 

     

@@ -260,15 +260,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/FeaturePlot_scCustom.html b/docs/reference/FeaturePlot_scCustom.html
index 6f5109239..347547a77 100644
--- a/docs/reference/FeaturePlot_scCustom.html
+++ b/docs/reference/FeaturePlot_scCustom.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -150,111 +150,111 @@ 
Customize FeaturePlot

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
features

+
features

 
Feature(s) to plot.

 
 
-
colors_use

+
colors_use

 
list of colors or color palette to use.

 
 
-
na_color

+
na_color

 
color to use for points below lower limit.

 
 
-
order

+
order

 
whether to move positive cells to the top (default = TRUE).

 
 
-
pt.size

+
pt.size

 
Adjust point size for plotting.

 
 
-
reduction

+
reduction

 
Dimensionality Reduction to use (if NULL then defaults to Object default).

 
 
-
na_cutoff

+
na_cutoff

 
Value to use as minimum expression cutoff.  This will be lowest value plotted use
 palette provided to colors_use.  Leave as default value to plot only positive non-zero values using
 color scale and zero/negative values as NA.  To plot all values using color palette set to NA.

 
 
-
raster

+
raster

 
Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 200,000 cells.

 
 
-
raster.dpi

+
raster.dpi

 
Pixel resolution for rasterized plots, passed to geom_scattermore().
 Default is c(512, 512).

 
 
-
split.by

+
split.by

 
Variable in @meta.data to split the plot by.

 
 
-
split_collect

+
split_collect

 
logical, whether to collect the legends/guides when plotting with split.by.
 Default is TRUE if one value is provided to features otherwise is set to FALSE.

 
 
-
aspect_ratio

+
aspect_ratio

 
Control the aspect ratio (y:x axes ratio length).  Must be numeric value;
 Default is NULL.

 
 
-
figure_plot

+
figure_plot

 
logical.  Whether to remove the axes and plot with legend on left of plot denoting
 axes labels.  (Default is FALSE).  Requires split_seurat = TRUE.

 
 
-
num_columns

+
num_columns

 
Number of columns in plot layout.

 
 
-
layer

+
layer

 
Which layer to pull expression data from?  Default is "data".

 
 
-
alpha_exp

+
alpha_exp

 
new alpha level to apply to expressing cell color palette (colors_use).  Must be
 value between 0-1.

 
 
-
alpha_na_exp

+
alpha_na_exp

 
new alpha level to apply to non-expressing cell color palette (na_color).  Must be
 value between 0-1.

 
 
-
label

+
label

 
logical, whether to label the clusters.  Default is FALSE.

 
 
-
label_feature_yaxis

+
label_feature_yaxis

 
logical, whether to place feature labels on secondary y-axis as opposed to
 above legend key.  Default is FALSE.  When setting label_feature_yaxis = TRUE the number of columns
 in plot output will automatically be set to the number of levels in split.by'

 
 
-
combine

+
combine

 
Combine plots into a single patchworked ggplot object.
 If FALSE, return a list of ggplot objects.

 
 
-
...

+
...

 
Extra parameters passed to FeaturePlot.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

@@ -287,15 +287,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/FeatureScatter_scCustom.html b/docs/reference/FeatureScatter_scCustom.html
index 943f11684..e33ad473b 100644
--- a/docs/reference/FeatureScatter_scCustom.html
+++ b/docs/reference/FeatureScatter_scCustom.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -147,94 +147,94 @@ 
Modified version of FeatureScatter

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
feature1

+
feature1

 
First feature to plot.

 
 
-
feature2

+
feature2

 
Second feature to plot.

 
 
-
cells

+
cells

 
Cells to include on the scatter plot.

 
 
-
colors_use

+
colors_use

 
color for the points on plot.

 
 
-
pt.size

+
pt.size

 
Adjust point size for plotting.

 
 
-
group.by

+
group.by

 
Name of one or more metadata columns to group (color) cells by (for example, orig.ident).
 Default is active ident.

 
 
-
split.by

+
split.by

 
Feature to split plots by (i.e. "orig.ident").

 
 
-
split_seurat

+
split_seurat

 
logical.  Whether or not to display split plots like Seurat (shared y axis) or as
 individual plots in layout.  Default is FALSE.

 
 
-
shuffle

+
shuffle

 
logical, whether to randomly shuffle the order of points. This can be useful for crowded plots if points of interest are being buried. Default is TRUE.

 
 
-
aspect_ratio

+
aspect_ratio

 
Control the aspect ratio (y:x axes ratio length).  Must be numeric value;
 Default is NULL.

 
 
-
title_size

+
title_size

 
size for plot title labels. Does NOT apply if split_seurat = TRUE.

 
 
-
plot.cor

+
plot.cor

 
Display correlation in plot subtitle (or title if split_seurat = TRUE).

 
 
-
num_columns

+
num_columns

 
number of columns in final layout plot.

 
 
-
raster

+
raster

 
Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 200,000 cells.

 
 
-
raster.dpi

+
raster.dpi

 
Pixel resolution for rasterized plots, passed to geom_scattermore().
 Default is c(512, 512).

 
 
-
ggplot_default_colors

+
ggplot_default_colors

 
logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

 
 
-
color_seed

+
color_seed

 
random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.

 
 
-
...

+
...

 
Extra parameters passed to FeatureScatter.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

@@ -269,15 +269,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Feature_Present.html b/docs/reference/Feature_Present.html
index a6bde2a3e..b6b35235c 100644
--- a/docs/reference/Feature_Present.html
+++ b/docs/reference/Feature_Present.html
@@ -4,7 +4,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -138,59 +138,59 @@ 
Check if genes/features are present

 
     

     
Arguments

-
-
-
data

+    
data

 
Name of input data.  Currently only data of classes: Seurat, liger, data.frame,
 dgCMatrix, dgTMatrix, tibble are accepted.  Gene_IDs must be present in rownames of the data.

 
 
-
features

+
features

 
vector of features to check.

 
 
-
case_check

+
case_check

 
logical. Whether or not to check if features are found if the case is changed from the
 input list (Sentence case to Upper and vice versa).  Default is TRUE.

 
 
-
case_check_msg

+
case_check_msg

 
logical. Whether to print message to console if alternate case features are found
 in addition to inclusion in returned list.  Default is TRUE.

 
 
-
print_msg

+
print_msg

 
logical. Whether message should be printed if all features are found.  Default is TRUE.

 
 
-
omit_warn

+
omit_warn

 
logical. Whether to print message about features that are not found in current object.
 Default is TRUE.

 
 
-
return_none

+
return_none

 
logical. Whether list of found vs. bad features should still be returned if no
 features are found.  Default is FALSE.

 
 
-
seurat_assay

+
seurat_assay

 
Name of assay to pull feature names from if data is Seurat Object.
 Default is NULL which will check against features from all assays present.

 
 

     

     
Value

-    
A list of length 3 containing 1) found features, 2) not found features, 3) features found if
+    
+
+
A list of length 3 containing 1) found features, 2) not found features, 3) features found if
 case was modified.

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 features <- Feature_Present(data = obj_name, features = DEG_list, print_msg = TRUE,
 case_check = TRUE)
 found_features <- features[[1]]
-} # }
+}
 
 

     

@@ -206,15 +206,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Features.html b/docs/reference/Features.html
index 1fdb9d830..a7c989cf1 100644
--- a/docs/reference/Features.html
+++ b/docs/reference/Features.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -122,42 +122,42 @@ 
Extract Features from LIGER Object

     

 
     

-    
# S3 method for class 'liger'
+    
# S3 method for liger
 Features(x, by_dataset = FALSE, ...)

     

 
     

     
Arguments

-
-
-
x

+    
x

 
LIGER object name.

 
 
-
by_dataset

+
by_dataset

 
logical, whether to return list with vector of features for each dataset in
 LIGER object or to return single vector of unique features across all datasets in object
 (default is FALSE; return vector of unique features)

 
 
-
...

+
...

 
Arguments passed to other methods

 
 

     

     
Value

-    
vector or list depending on by_dataset parameter

+    
+
+
vector or list depending on by_dataset parameter

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 # return single vector of all unique features
 all_features <- Features(x = object, by_dataset = FALSE)
 
 # return list of vectors containing features from each individual dataset in object
 dataset_features <- Features(x = object, by_dataset = TRUE)
-} # }
+}
 
 

     

@@ -173,15 +173,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Fetch_Meta.html b/docs/reference/Fetch_Meta.html
index 8249f3634..15f2ed117 100644
--- a/docs/reference/Fetch_Meta.html
+++ b/docs/reference/Fetch_Meta.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -124,28 +124,28 @@ 
Get meta data from object

     

     
Fetch_Meta(object, ...)
 
-# S3 method for class 'liger'
+# S3 method for liger
 Fetch_Meta(object, ...)
 
-# S3 method for class 'Seurat'
+# S3 method for Seurat
 Fetch_Meta(object, ...)

     

 
     

     
Arguments

-
-
-
object

+    
object

 
Object of class Seurat or liger.

 
 
-
...

+
...

 
Arguments passed to other methods

 
 

     

     
Value

-    
A data.frame containing cell-level meta data

+    
+
+
A data.frame containing cell-level meta data

     

 
     

@@ -180,15 +180,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Find_Factor_Cor.html b/docs/reference/Find_Factor_Cor.html
index 3bd32b1aa..39605e55c 100644
--- a/docs/reference/Find_Factor_Cor.html
+++ b/docs/reference/Find_Factor_Cor.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -127,26 +127,26 @@ 
Find Factor Correlations

 
     

     
Arguments

-
-
-
object

+    
object

 
LIGER/Seurat object name.

 
 
-
reduction

+
reduction

 
reduction name to pull loadings for.  Only valid if supplying a Seurat object.

 
 

     

     
Value

-    
correlation matrix

+    
+
+
correlation matrix

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 factor_correlations <- Find_Factor_Cor(object = object)
-} # }
+}
 
 

     

@@ -162,15 +162,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Hue_Pal.html b/docs/reference/Hue_Pal.html
index 7b7790e39..3dd1905a2 100644
--- a/docs/reference/Hue_Pal.html
+++ b/docs/reference/Hue_Pal.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -127,15 +127,15 @@ 
Hue_Pal

 
     

     
Arguments

-
-
-
num_colors

+    
num_colors

 
number of colors to return in palette.

 
 

     

     
Value

-    
hue color palette (as many colors as desired)

+    
+
+
hue color palette (as many colors as desired)

     

 
     

@@ -158,15 +158,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Idents.html b/docs/reference/Idents.html
index f17a93811..608328302 100644
--- a/docs/reference/Idents.html
+++ b/docs/reference/Idents.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -122,32 +122,34 @@ 
Extract or set default identities from object

     

 
     

-    
# S3 method for class 'liger'
+    
# S3 method for liger
 Idents(object, ...)
 
-# S3 method for class 'liger'
+# S3 method for liger
 Idents(object, ...) <- value

     

 
     

     
Arguments

-
-
-
object

+    
object

 
LIGER object name.

 
 
-
...

+
...

 
Arguments passed to other methods

 
 
-
value

+
value

 
name of column in cellMeta slot to set as new default cluster/ident

 
 

     

     
Value

-    
factor

+    
+
+
factor

+
+
 
object

     

     

@@ -158,15 +160,15 @@ 
Note

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 # Extract idents
 object_idents <- Idents(object = liger_object)
-} # }
+}
 
-if (FALSE) { # \dontrun{
+if (FALSE) {
 # Set idents
 Idents(object = liger_object) <- "new_annotation"
-} # }
+}
 
 

     

@@ -182,15 +184,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Iterate_Barcode_Rank_Plot.html b/docs/reference/Iterate_Barcode_Rank_Plot.html
index 4c56fad54..172ebb23d 100644
--- a/docs/reference/Iterate_Barcode_Rank_Plot.html
+++ b/docs/reference/Iterate_Barcode_Rank_Plot.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -140,74 +140,74 @@ 
Iterative Barcode Rank Plots

 
     

     
Arguments

-
-
-
dir_path_h5

+    
dir_path_h5

 
path to parent directory (if multi_directory = TRUE) or directory containing
 all h5 files (if multi_directory = FALSE).

 
 
-
multi_directory

+
multi_directory

 
logical, whether or not all h5 files are in their own subdirectories or in a
 single directory (default is TRUE; each in own subdirectory (e.g. output from Cell Ranger)).

 
 
-
h5_filename

+
h5_filename

 
Either the file name of h5 file (if multi_directory = TRUE) or the shared
 suffix (if multi_directory = FALSE)

 
 
-
cellranger_multi

+
cellranger_multi

 
logical, whether the outputs to be read are from Cell Ranger multi as opposed
 to Cell Ranger count (default is FALSE).  Only valid if multi_directory = FALSE.

 
 
-
parallel

+
parallel

 
logical, should files be read in parallel (default is FALSE).

 
 
-
num_cores

+
num_cores

 
Number of cores to use in parallel if parallel = TRUE.

 
 
-
file_path

+
file_path

 
file path to use for saving PDF output.

 
 
-
file_name

+
file_name

 
Name of PDF output file.

 
 
-
pt.size

+
pt.size

 
point size for plotting, default is 6.

 
 
-
raster_dpi

+
raster_dpi

 
Pixel resolution for rasterized plots, passed to geom_scattermore().
 Default is c(1024, 1024).

 
 
-
plateau

+
plateau

 
numerical values at which to add vertical line designating estimated
 empty droplet plateau (default is NULL).  Must be vector equal in length to number of samples.

 
 
-
...

+
...

 
Additional parameters passed to Read10X_h5_Multi_Directory or Read10X_h5_GEO.

 
 

     

     
Value

-    
pdf document

+    
+
+
pdf document

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 Iterate_Barcode_Rank_Plot(dir_path_h5 = "H5_PATH/", multi_directory = TRUE,
 h5_filename = "raw_feature_bc_matrix", parallel = TRUE, num_cores = 12, file_path = "OUTPUT_PATH",
 file_name = "Barcode_Rank_Plots")
-} # }
+}
 
 

     

@@ -223,15 +223,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Iterate_Cluster_Highlight_Plot.html b/docs/reference/Iterate_Cluster_Highlight_Plot.html
index 9e957620a..2162a1e1d 100644
--- a/docs/reference/Iterate_Cluster_Highlight_Plot.html
+++ b/docs/reference/Iterate_Cluster_Highlight_Plot.html
@@ -4,7 +4,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -142,70 +142,70 @@ 
Iterate Cluster Highlight Plot

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
highlight_color

+
highlight_color

 
Color to highlight cells (default "navy").  Can provide either single color to use for
 all clusters/plots or a vector of colors equal to the number of clusters to use (in order) for the clusters/plots.

 
 
-
background_color

+
background_color

 
non-highlighted cell colors.

 
 
-
pt.size

+
pt.size

 
point size for both highlighted cluster and background.

 
 
-
reduction

+
reduction

 
Dimensionality Reduction to use (if NULL then defaults to Object default).

 
 
-
file_path

+
file_path

 
directory file path and/or file name prefix.  Defaults to current wd.

 
 
-
file_name

+
file_name

 
name suffix to append after sample name.

 
 
-
file_type

+
file_type

 
File type to save output as.  Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".

 
 
-
single_pdf

-
saves all plots to single PDF file (default = FALSE).  `file_type“ must be .pdf

+
single_pdf

+
saves all plots to single PDF file (default = FALSE).  `file_type`` must be .pdf

 
 
-
dpi

+
dpi

 
dpi for image saving.

 
 
-
raster

+
raster

 
Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 200,000 cells.

 
 
-
...

+
...

 
Extra parameters passed toDimPlot.

 
 

     

     
Value

-    
Saved plots

+    
+
+
Saved plots

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 Iterate_Cluster_Highlight_Plot(seurat_object = object, highlight_color = "navy",
 background_color = "lightgray", file_path = "path/", file_name = "name", file_type = "pdf",
 single_pdf = TRUE)
-} # }
+}
 
 

     

@@ -221,15 +221,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Iterate_DimPlot_bySample.html b/docs/reference/Iterate_DimPlot_bySample.html
index b6ddef7cd..75897a704 100644
--- a/docs/reference/Iterate_DimPlot_bySample.html
+++ b/docs/reference/Iterate_DimPlot_bySample.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -143,81 +143,81 @@ 
Iterate DimPlot By Sample

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
sample_column

+
sample_column

 
name of meta.data column containing sample names/ids (default is "orig.ident").

 
 
-
file_path

+
file_path

 
directory file path and/or file name prefix.  Defaults to current wd.

 
 
-
file_name

+
file_name

 
name suffix to append after sample name.

 
 
-
file_type

+
file_type

 
File type to save output as.  Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".

 
 
-
single_pdf

-
saves all plots to single PDF file (default = FALSE).  `file_type“ must be .pdf

+
single_pdf

+
saves all plots to single PDF file (default = FALSE).  `file_type`` must be .pdf

 
 
-
dpi

+
dpi

 
dpi for image saving.

 
 
-
color

+
color

 
color scheme to use.

 
 
-
no_legend

+
no_legend

 
logical, whether or not to include plot legend, default is TRUE.

 
 
-
title_prefix

+
title_prefix

 
Value that should be used for plot title prefix if no_legend = TRUE.
 If NULL the value of meta_data_column will be used.  Default is NULL.

 
 
-
reduction

+
reduction

 
Dimensionality Reduction to use (default is object default).

 
 
-
dims

+
dims

 
Dimensions to plot.

 
 
-
pt.size

+
pt.size

 
Adjust point size for plotting.

 
 
-
raster

+
raster

 
Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 200,000 cells.

 
 
-
...

+
...

 
Extra parameters passed to DimPlot.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 Iterate_DimPlot_bySample(seurat_object = object, file_path = "plots/", file_name = "tsne",
 file_type = ".jpg", dpi = 600, color = "black")
-} # }
+}
 
 

     

@@ -233,15 +233,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Iterate_FeaturePlot_scCustom.html b/docs/reference/Iterate_FeaturePlot_scCustom.html
index 23b3d307c..4e2a707f1 100644
--- a/docs/reference/Iterate_FeaturePlot_scCustom.html
+++ b/docs/reference/Iterate_FeaturePlot_scCustom.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -150,114 +150,114 @@ 
Iterative Plotting of Gene Lists using Custom FeaturePlots

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
features

+
features

 
vector of features to plot.  If a named vector is provided then the names for each gene
 will be incorporated into plot title if single_pdf = TRUE or into file name if FALSE.

 
 
-
colors_use

+
colors_use

 
color scheme to use.

 
 
-
na_color

+
na_color

 
color for non-expressed cells.

 
 
-
na_cutoff

+
na_cutoff

 
Value to use as minimum expression cutoff.  To set no cutoff set to NA.

 
 
-
split.by

+
split.by

 
Variable in @meta.data to split the plot by.

 
 
-
order

+
order

 
whether to move positive cells to the top (default = TRUE).

 
 
-
return_plots

+
return_plots

 
logical. Whether to return plots to list instead of saving them to file(s).  Default is FALSE.

 
 
-
file_path

+
file_path

 
directory file path and/or file name prefix.  Defaults to current wd.

 
 
-
file_name

+
file_name

 
name suffix and file extension.

 
 
-
file_type

+
file_type

 
File type to save output as.  Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".

 
 
-
single_pdf

+
single_pdf

 
saves all plots to single PDF file (default = FALSE).

 
 
-
features_per_page

+
features_per_page

 
numeric, number of features to plot on single page if single_pdf = TRUE.  Default is 1.

 
 
-
num_columns

+
num_columns

 
Number of columns in plot layout (only applicable if single_pdf = TRUE AND
 features_per_page > 1).

 
 
-
landscape

+
landscape

 
logical, when plotting multiple features per page in single PDF whether to use landscape or portrait
 page dimensions (default is TRUE).

 
 
-
dpi

+
dpi

 
dpi for image saving.

 
 
-
pt.size

+
pt.size

 
Adjust point size for plotting.

 
 
-
reduction

+
reduction

 
Dimensionality Reduction to use (if NULL then defaults to Object default).

 
 
-
raster

+
raster

 
Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 200,000 cells.

 
 
-
alpha_exp

+
alpha_exp

 
new alpha level to apply to expressing cell color palette (colors_use).  Must be
 value between 0-1.

 
 
-
alpha_na_exp

+
alpha_na_exp

 
new alpha level to apply to non-expressing cell color palette (na_color).  Must be
 value between 0-1.

 
 
-
...

+
...

 
Extra parameters passed to FeaturePlot.

 
 

     

     
Value

-    
Saved plots

+    
+
+
Saved plots

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 Iterate_FeaturePlot_scCustom(seurat_object = object, features = DEG_list,
 colors_use = viridis_plasma_dark_high, na_color = "lightgray", file_path = "plots/",
 file_name = "tsne", file_type = ".jpg", dpi = 600)
-} # }
+}
 
 

     

@@ -273,15 +273,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Iterate_Meta_Highlight_Plot.html b/docs/reference/Iterate_Meta_Highlight_Plot.html
index 224eeeb60..46fac8a04 100644
--- a/docs/reference/Iterate_Meta_Highlight_Plot.html
+++ b/docs/reference/Iterate_Meta_Highlight_Plot.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -145,92 +145,92 @@ 
Iterate Meta Highlight Plot

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
meta_data_column

+
meta_data_column

 
Name of the column in seurat_object@meta.data slot to pull value from for highlighting.

 
 
-
new_meta_order

+
new_meta_order

 
The order in which to plot each level within meta_data_column if single_PDF is TRUE.

 
 
-
meta_data_sort

+
meta_data_sort

 
logical.  Whether or not to sort and relevel the levels in meta_data_column if
 single_PDF is TRUE.  Default is TRUE.

 
 
-
highlight_color

+
highlight_color

 
Color to highlight cells (default "navy").  Can provide either single color to use for
 all clusters/plots or a vector of colors equal to the number of clusters to use (in order) for the clusters/plots.

 
 
-
background_color

+
background_color

 
non-highlighted cell colors.

 
 
-
pt.size

+
pt.size

 
point size for both highlighted cluster and background.

 
 
-
no_legend

+
no_legend

 
logical, whether or not to remove plot legend and move to plot title.  Default is FALSE.

 
 
-
title_prefix

+
title_prefix

 
Value that should be used for plot title prefix if no_legend = TRUE.
 If NULL the value of meta_data_column will be used.  Default is NULL.

 
 
-
reduction

+
reduction

 
Dimensionality Reduction to use (if NULL then defaults to Object default).

 
 
-
file_path

+
file_path

 
directory file path and/or file name prefix.  Defaults to current wd.

 
 
-
file_name

+
file_name

 
name suffix to append after sample name.

 
 
-
file_type

+
file_type

 
File type to save output as.  Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".

 
 
-
single_pdf

-
saves all plots to single PDF file (default = FALSE).  `file_type“ must be .pdf

+
single_pdf

+
saves all plots to single PDF file (default = FALSE).  `file_type`` must be .pdf

 
 
-
dpi

+
dpi

 
dpi for image saving.

 
 
-
raster

+
raster

 
Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 200,000 cells.

 
 
-
...

+
...

 
Extra parameters passed toDimPlot.

 
 

     

     
Value

-    
Saved plots

+    
+
+
Saved plots

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 Iterate_Meta_Highlight_Plot(seurat_object = object, meta_data_column = "sample_id",
 highlight_color = "navy", background_color = "lightgray", file_path = "path/",
 file_name = "name", file_type = "pdf", single_pdf = TRUE)
-} # }
+}
 
 

     

@@ -246,15 +246,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Iterate_PC_Loading_Plots.html b/docs/reference/Iterate_PC_Loading_Plots.html
index b219b6f51..1de0fd0a0 100644
--- a/docs/reference/Iterate_PC_Loading_Plots.html
+++ b/docs/reference/Iterate_PC_Loading_Plots.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -134,36 +134,36 @@ 
Iterate PC Loading Plots

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
dims_plot

+
dims_plot

 
number of PCs to plot (integer).  Default is all dims present in PCA.

 
 
-
file_path

+
file_path

 
directory file path to save file.

 
 
-
name_prefix

+
name_prefix

 
prefix for file name (optional).

 
 
-
file_name

+
file_name

 
suffix for file name.  Default is "PC_Loading_Plots".

 
 
-
return_plots

+
return_plots

 
Whether to return the plot list (Default is FALSE).  Must assign to environment
 to save plot list.

 
 

     

     
Value

-    
A list of plots outputted as pdf

+    
+
+
A list of plots outputted as pdf

     

     

     
See also

@@ -172,9 +172,9 @@ 
See also

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 Iterate_PC_Loading_Plots(seurat_object = seurat, dims_plot = 25, file_path = "plots/")
-} # }
+}
 
 

     

@@ -190,15 +190,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Iterate_Plot_Density_Custom.html b/docs/reference/Iterate_Plot_Density_Custom.html
index 8c8f1f476..abd11f77e 100644
--- a/docs/reference/Iterate_Plot_Density_Custom.html
+++ b/docs/reference/Iterate_Plot_Density_Custom.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -142,76 +142,76 @@ 
Iterative Plotting of Gene Lists using Custom Density Plots

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
gene_list

+
gene_list

 
vector of genes to plot.  If a named vector is provided then the names for each gene
 will be incorporated into plot title if single_pdf = TRUE or into file name if FALSE.

 
 
-
viridis_palette

+
viridis_palette

 
color scheme to use.

 
 
-
custom_palette

+
custom_palette

 
color for non-expressed cells.

 
 
-
pt.size

+
pt.size

 
Adjust point size for plotting.

 
 
-
file_path

+
file_path

 
directory file path and/or file name prefix.  Defaults to current wd.

 
 
-
file_name

+
file_name

 
name suffix and file extension.

 
 
-
file_type

+
file_type

 
File type to save output as.  Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".

 
 
-
single_pdf

-
saves all plots to single PDF file (default = FALSE).  `file_type“ must be .pdf.

+
single_pdf

+
saves all plots to single PDF file (default = FALSE).  `file_type`` must be .pdf.

 
 
-
dpi

+
dpi

 
dpi for image saving.

 
 
-
reduction

+
reduction

 
Dimensionality Reduction to use (if NULL then defaults to Object default)

 
 
-
combine

+
combine

 
Create a single plot? If FALSE, a list with ggplot objects is returned.

 
 
-
joint

+
joint

 
NULL.  This function only supports joint = FALSE.  Leave as NULL to generate plots.  To iterate joint plots see function: Iterate_Plot_Density_Joint.

 
 
-
...

+
...

 
Extra parameters passed to plot_density.

 
 

     

     
Value

-    
Saved plots

+    
+
+
Saved plots

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 Iterate_Plot_Density_Custom(seurat_object = object, gene_list = DEG_list, viridis_palette = "magma",
 file_path = "plots/", file_name = "_density_plots", file_type = ".jpg", dpi = 600)
-} # }
+}
 
 

     

@@ -227,15 +227,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Iterate_Plot_Density_Joint.html b/docs/reference/Iterate_Plot_Density_Joint.html
index 7cbb20dc8..793925134 100644
--- a/docs/reference/Iterate_Plot_Density_Joint.html
+++ b/docs/reference/Iterate_Plot_Density_Joint.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -142,78 +142,78 @@ 
Iterative Plotting of Gene Lists using Custom Joint Density Plots

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
gene_list

+
gene_list

 
a list of vectors of genes to plot jointly.  Each entry in the list will be plotted
 for the joint density.  All entries in list must be greater than 2 features.  If a named list is provided
 then the names for each list entry will be incorporated into plot title if single_pdf = TRUE or
 into file name if FALSE.

 
 
-
viridis_palette

+
viridis_palette

 
color scheme to use.

 
 
-
custom_palette

+
custom_palette

 
color for non-expressed cells.

 
 
-
pt.size

+
pt.size

 
Adjust point size for plotting.

 
 
-
file_path

+
file_path

 
directory file path and/or file name prefix.  Defaults to current wd.

 
 
-
file_name

+
file_name

 
name suffix and file extension.

 
 
-
file_type

+
file_type

 
File type to save output as.  Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".

 
 
-
single_pdf

-
saves all plots to single PDF file (default = FALSE).  `file_type“ must be .pdf.

+
single_pdf

+
saves all plots to single PDF file (default = FALSE).  `file_type`` must be .pdf.

 
 
-
dpi

+
dpi

 
dpi for image saving.

 
 
-
reduction

+
reduction

 
Dimensionality Reduction to use (if NULL then defaults to Object default)

 
 
-
combine

+
combine

 
Create a single plot? If FALSE, a list with ggplot objects is returned.

 
 
-
joint

+
joint

 
NULL.  This function only supports joint = FALSE.  Leave as NULL to generate plots.  To iterate joint plots see function: Iterate_Plot_Density_Joint.

 
 
-
...

+
...

 
Extra parameters passed to plot_density.

 
 

     

     
Value

-    
Saved plots

+    
+
+
Saved plots

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 Iterate_Plot_Density_Joint(seurat_object = object, gene_list = DEG_list, viridis_palette = "magma",
 file_path = "plots/", file_name = "joint_plots", file_type = ".jpg", dpi = 600)
-} # }
+}
 
 

     

@@ -229,15 +229,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Iterate_VlnPlot_scCustom.html b/docs/reference/Iterate_VlnPlot_scCustom.html
index d10b8f3e1..c005c2b34 100644
--- a/docs/reference/Iterate_VlnPlot_scCustom.html
+++ b/docs/reference/Iterate_VlnPlot_scCustom.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -143,85 +143,85 @@ 
Iterative Plotting of Gene Lists using VlnPlot_scCustom

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
features

+
features

 
vector of features to plot.

 
 
-
colors_use

+
colors_use

 
color palette to use for plotting.  By default if number of levels plotted is less than
 or equal to 36 it will use "polychrome" and if greater than 36 will use "varibow" with shuffle = TRUE
 both from DiscretePalette_scCustomize.

 
 
-
pt.size

+
pt.size

 
point size for plotting.

 
 
-
group.by

+
group.by

 
Name of one or more metadata columns to group (color) plot by (for example, orig.ident);
 default is the current active.ident of the object.

 
 
-
split.by

+
split.by

 
Feature to split plots by (i.e. "orig.ident").

 
 
-
file_path

+
file_path

 
directory file path and/or file name prefix.  Defaults to current wd.

 
 
-
file_name

+
file_name

 
name suffix and file extension.

 
 
-
file_type

+
file_type

 
File type to save output as.  Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".

 
 
-
single_pdf

-
saves all plots to single PDF file (default = FALSE).  `file_type“ must be .pdf.

+
single_pdf

+
saves all plots to single PDF file (default = FALSE).  `file_type`` must be .pdf.

 
 
-
raster

+
raster

 
Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 100,000 total points plotted (# Cells x # of features).

 
 
-
dpi

+
dpi

 
dpi for image saving.

 
 
-
ggplot_default_colors

+
ggplot_default_colors

 
logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

 
 
-
color_seed

+
color_seed

 
random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.

 
 
-
...

+
...

 
Extra parameters passed to VlnPlot.

 
 

     

     
Value

-    
Saved plots

+    
+
+
Saved plots

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 Iterate_VlnPlot_scCustom(seurat_object = object, features = DEG_list, colors = color_list,
 file_path = "plots/", file_name = "_vln", file_type = ".jpg", dpi = 600)
-} # }
+}
 
 

     

@@ -237,15 +237,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/JCO_Four.html b/docs/reference/JCO_Four.html
index 69e87ff85..1567f949e 100644
--- a/docs/reference/JCO_Four.html
+++ b/docs/reference/JCO_Four.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -127,7 +127,9 @@ 
Four Color Palette (JCO)

 
     

     
Value

-    
4 color palette from the JCO ggsci palette

+    
+
+
4 color palette from the JCO ggsci palette

     

     

     
References

@@ -156,15 +158,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Liger_to_Seurat.html b/docs/reference/Liger_to_Seurat.html
index 82a69cee1..ed132556a 100644
--- a/docs/reference/Liger_to_Seurat.html
+++ b/docs/reference/Liger_to_Seurat.html
@@ -4,7 +4,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -142,68 +142,68 @@ 
Create a Seurat object containing the data from a liger object 
     
Arguments

-
-
-
liger_object

+    
liger_object

 
liger object.

 
 
-
nms

+
nms

 
By default, labels cell names with dataset of origin (this is to account for cells in
 different datasets which may have same name). Other names can be passed here as vector, must have
 same length as the number of datasets. (default names(H)).

 
 
-
renormalize

+
renormalize

 
Whether to log-normalize raw data using Seurat defaults (default TRUE).

 
 
-
use.liger.genes

+
use.liger.genes

 
Whether to carry over variable genes (default TRUE).

 
 
-
by.dataset

+
by.dataset

 
Include dataset of origin in cluster identity in Seurat object (default FALSE).

 
 
-
keep_meta

+
keep_meta

 
logical. Whether to transfer additional metadata (nGene/nUMI/dataset already transferred)
 to new Seurat Object.  Default is TRUE.

 
 
-
reduction_label

+
reduction_label

 
Name of dimensionality reduction technique used.  Enables accurate transfer
 or name to Seurat object instead of defaulting to "tSNE".

 
 
-
seurat_assay

+
seurat_assay

 
Name to set for assay in Seurat Object.  Default is "RNA".

 
 
-
assay_type

+
assay_type

 
what type of Seurat assay to create in new object (Assay vs Assay5).
 Default is NULL which will default to the current user settings.
 See Convert_Assay parameter convert_to for acceptable values.

 
 
-
add_barcode_names

+
add_barcode_names

 
logical, whether to add dataset names to the cell barcodes when
 creating Seurat object, default is FALSE.

 
 
-
barcode_prefix

+
barcode_prefix

 
logical, if add_barcode_names = TRUE should the names be added as
 prefix to current cell barcodes/names or a suffix (default is TRUE; prefix).

 
 
-
barcode_cell_id_delimiter

+
barcode_cell_id_delimiter

 
The delimiter to use when adding dataset id to barcode
 prefix/suffix.  Default is "_".

 
 

     

     
Value

-    
Seurat object with raw.data, scale.data, reduction_label, iNMF, and ident slots set.

+    
+
+
Seurat object with raw.data, scale.data, reduction_label, iNMF, and ident slots set.

     

     

     
Details

@@ -219,9 +219,9 @@ 
References

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 seurat_object <- Liger_to_Seurat(liger_object = LIGER_OBJ, reduction_label = "UMAP")
-} # }
+}
 

     

   

@@ -236,15 +236,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/MAD_Stats.html b/docs/reference/MAD_Stats.html
index 41d0177ec..708fb9411 100644
--- a/docs/reference/MAD_Stats.html
+++ b/docs/reference/MAD_Stats.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -133,42 +133,42 @@ 
Median Absolute Deviation Statistics

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
group_by_var

+
group_by_var

 
Column in meta.data slot to group results by (default = "orig.ident").

 
 
-
default_var

+
default_var

 
logical.  Whether to include the default meta.data variables of: "nCount_RNA",
 "nFeature_RNA", "percent_mito", "percent_ribo", "percent_mito_ribo", and "log10GenesPerUMI"
 in addition to variables supplied to mad_var.

 
 
-
mad_var

+
mad_var

 
Column(s) in @meta.data to calculate medians for in addition to defaults.
 Must be of class() integer or numeric.

 
 
-
mad_num

+
mad_num

 
integer value to multiply the MAD in returned data.frame (default is 2).
 Often helpful when calculating a outlier range to base of of median + (X*MAD).

 
 

     

     
Value

-    
A data.frame.

+    
+
+
A data.frame.

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 mad_stats <- MAD_Stats(seurat_object = obj, group_by_var = "orig.ident")
-} # }
+}
 
 

     

@@ -184,15 +184,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Median_Stats.html b/docs/reference/Median_Stats.html
index 5cb68dba2..722d8e9ec 100644
--- a/docs/reference/Median_Stats.html
+++ b/docs/reference/Median_Stats.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -132,37 +132,37 @@ 
Median Statistics

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
group_by_var

+
group_by_var

 
Column in meta.data slot to group results by (default = "orig.ident").

 
 
-
default_var

+
default_var

 
logical.  Whether to include the default meta.data variables of: "nCount_RNA",
 "nFeature_RNA", "percent_mito", "percent_ribo", "percent_mito_ribo", and "log10GenesPerUMI"
 in addition to variables supplied to median_var.

 
 
-
median_var

+
median_var

 
Column(s) in @meta.data to calculate medians for in addition to defaults.
 Must be of class() integer or numeric.

 
 

     

     
Value

-    
A data.frame.

+    
+
+
A data.frame.

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 med_stats <- Median_Stats(seurat_object - obj, group_by_var = "orig.ident")
-} # }
+}
 
 

     

@@ -178,15 +178,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Merge_Seurat_List.html b/docs/reference/Merge_Seurat_List.html
index e2d944c25..cd32748fa 100644
--- a/docs/reference/Merge_Seurat_List.html
+++ b/docs/reference/Merge_Seurat_List.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -132,38 +132,38 @@ 
Merge a list of Seurat Objects

 
     

     
Arguments

-
-
-
list_seurat

+    
list_seurat

 
list composed of multiple Seurat Objects.

 
 
-
add.cell.ids

+
add.cell.ids

 
A character vector of equal length to the number of objects in list_seurat.
 Appends the corresponding values to the start of each objects' cell names.  See merge.

 
 
-
merge.data

+
merge.data

 
Merge the data slots instead of just merging the counts (which requires renormalization).
 This is recommended if the same normalization approach was applied to all objects.
 See merge.

 
 
-
project

+
project

 
Project name for the Seurat object. See merge.

 
 

     

     
Value

-    
A Seurat Object

+    
+
+
A Seurat Object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 object_list <- list(obj1, obj2, obj3, ...)
 merged_object <- Merge_Seurat_List(list_seurat = object_list)
-} # }
+}
 
 

     

@@ -179,15 +179,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Merge_Sparse_Data_All.html b/docs/reference/Merge_Sparse_Data_All.html
index 33ff2a7ae..dc2b5fdb3 100644
--- a/docs/reference/Merge_Sparse_Data_All.html
+++ b/docs/reference/Merge_Sparse_Data_All.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -132,28 +132,28 @@ 
Merge a list of Sparse Matrices

 
     

     
Arguments

-
-
-
matrix_list

+    
matrix_list

 
list of matrices to merge.

 
 
-
add_cell_ids

+
add_cell_ids

 
a vector of sample ids to add as prefix to cell barcode during merge.

 
 
-
prefix

+
prefix

 
logical.  Whether add_cell_ids should be added as prefix to current cell barcodes/names
 or as suffix to current cell barcodes/names.  Default is TRUE, add as prefix.

 
 
-
cell_id_delimiter

+
cell_id_delimiter

 
The delimiter to use when adding cell id prefix/suffix.  Default is "_".

 
 

     

     
Value

-    
A sparse Matrix

+    
+
+
A sparse Matrix

     

     

     
References

@@ -164,11 +164,11 @@ 
References

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 data_list <- Read10X_GEO(...)
 merged <- Merge_Sparse_Data_All(matrix_list = data_list, add_cell_ids = names(data_list),
 prefix = TRUE, cell_id_delimiter = "_")
-} # }
+}
 
 

     

@@ -184,15 +184,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Merge_Sparse_Multimodal_All.html b/docs/reference/Merge_Sparse_Multimodal_All.html
index d37e4929b..33526bbdc 100644
--- a/docs/reference/Merge_Sparse_Multimodal_All.html
+++ b/docs/reference/Merge_Sparse_Multimodal_All.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -132,37 +132,37 @@ 
Merge a list of Sparse Matrices contain multi-modal data.

 
     

     
Arguments

-
-
-
matrix_list

+    
matrix_list

 
list of matrices to merge.

 
 
-
add_cell_ids

+
add_cell_ids

 
a vector of sample ids to add as prefix to cell barcode during merge.

 
 
-
prefix

+
prefix

 
logical.  Whether add_cell_ids should be added as prefix to current cell barcodes/names
 or as suffix to current cell barcodes/names.  Default is TRUE, add as prefix.

 
 
-
cell_id_delimiter

+
cell_id_delimiter

 
The delimiter to use when adding cell id prefix/suffix.  Default is "_".

 
 

     

     
Value

-    
A list containing one sparse matrix for each modality

+    
+
+
A list containing one sparse matrix for each modality

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 data_list <- Read10X_GEO(...)
 merged_list <- Merge_Sparse_Multimodal_All(matrix_list = data_list, add_cell_ids = names(data_list),
 prefix = TRUE, cell_id_delimiter = "_")
-} # }
+}
 
 

     

@@ -178,15 +178,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Meta_Highlight_Plot.html b/docs/reference/Meta_Highlight_Plot.html
index a76fc7be3..e14d9e134 100644
--- a/docs/reference/Meta_Highlight_Plot.html
+++ b/docs/reference/Meta_Highlight_Plot.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -144,81 +144,81 @@ 
Meta Highlight Plot

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
meta_data_column

+
meta_data_column

 
Name of the column in seurat_object@meta.data slot to pull value from for highlighting.

 
 
-
meta_data_highlight

+
meta_data_highlight

 
Name of variable(s) within meta_data_name to highlight in the plot.

 
 
-
highlight_color

+
highlight_color

 
Color to highlight cells (default "navy").

 
 
-
background_color

+
background_color

 
non-highlighted cell colors.

 
 
-
pt.size

+
pt.size

 
point size for both highlighted cluster and background.

 
 
-
aspect_ratio

+
aspect_ratio

 
Control the aspect ratio (y:x axes ratio length).  Must be numeric value;
 Default is NULL.

 
 
-
figure_plot

+
figure_plot

 
logical.  Whether to remove the axes and plot with legend on left of plot denoting
 axes labels.  (Default is FALSE).  Requires split_seurat = TRUE.

 
 
-
raster

+
raster

 
Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 200,000 cells.

 
 
-
raster.dpi

+
raster.dpi

 
Pixel resolution for rasterized plots, passed to geom_scattermore().
 Default is c(512, 512).

 
 
-
label

+
label

 
Whether to label the highlighted meta data variable(s).  Default is FALSE.

 
 
-
split.by

+
split.by

 
Variable in @meta.data to split the plot by.

 
 
-
split_seurat

+
split_seurat

 
logical.  Whether or not to display split plots like Seurat (shared y axis) or as
 individual plots in layout.  Default is FALSE.

 
 
-
reduction

+
reduction

 
Dimensionality Reduction to use (if NULL then defaults to Object default).

 
 
-
ggplot_default_colors

+
ggplot_default_colors

 
logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

 
 
-
...

+
...

 
Extra parameters passed toDimPlot.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

@@ -245,15 +245,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Meta_Numeric.html b/docs/reference/Meta_Numeric.html
index 5e0fe90b8..d6f4ef826 100644
--- a/docs/reference/Meta_Numeric.html
+++ b/docs/reference/Meta_Numeric.html
@@ -4,7 +4,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -129,22 +129,22 @@ 
Check if meta data columns are numeric

 
     

     
Arguments

-
-
-
data

+    
data

 
a data.frame contain meta.data.

 
 

     

     
Value

-    
vector of meta data columns that are numeric.

+    
+
+
vector of meta data columns that are numeric.

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 numeric_meta_columns <- Meta_Numeric(data = meta_data)
-} # }
+}
 
 

     

@@ -160,15 +160,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Meta_Present.html b/docs/reference/Meta_Present.html
index 3448efa0f..eb6f9eac5 100644
--- a/docs/reference/Meta_Present.html
+++ b/docs/reference/Meta_Present.html
@@ -4,7 +4,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -135,39 +135,39 @@ 
Check if meta data are present

 
     

     
Arguments

-
-
-
object

+    
object

 
Seurat or Liger object name.

 
 
-
meta_col_names

+
meta_col_names

 
vector of column names to check.

 
 
-
print_msg

+
print_msg

 
logical. Whether message should be printed if all features are found.  Default is TRUE.

 
 
-
omit_warn

+
omit_warn

 
logical. Whether to print message about features that are not found in current object. Default is TRUE.

 
 
-
return_none

+
return_none

 
logical. Whether list of found vs. bad features should still be returned if no
 meta_col_names are found.  Default is FALSE.

 
 

     

     
Value

-    
vector of meta data columns that are present

+    
+
+
vector of meta data columns that are present

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 meta_variables <- Meta_Present(object = obj_name, meta_col_names = "percent_mito", print_msg = TRUE)
-} # }
+}
 
 

     

@@ -183,15 +183,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Meta_Remove_Seurat.html b/docs/reference/Meta_Remove_Seurat.html
index f93852379..f6217b742 100644
--- a/docs/reference/Meta_Remove_Seurat.html
+++ b/docs/reference/Meta_Remove_Seurat.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -132,36 +132,36 @@ 
Remove meta data columns containing Seurat Defaults

 
     

     
Arguments

-
-
-
meta_data

+    
meta_data

 
data.frame containing meta data.

 
 
-
seurat_object

+
seurat_object

 
object name.

 
 
-
barcodes_to_rownames

+
barcodes_to_rownames

 
logical, are barcodes present as column and should they be moved to
 rownames (to be compatible with Seurat::AddMetaData).  Default is FALSE.

 
 
-
barcodes_colname

+
barcodes_colname

 
name of barcodes column in meta_data.  Required if barcodes_to_rownames = TRUE.

 
 

     

     
Value

-    
data.frame with only new columns.

+    
+
+
data.frame with only new columns.

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 new_meta <- Meta_Remove_Seurat(meta_data = meta_data_df, seurat_object = object)
 object <- AddMetaData(object = object, metadata = new_meta)
-} # }
+}
 
 

     

@@ -177,15 +177,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Move_Legend.html b/docs/reference/Move_Legend.html
index 6918c1f45..ad0fd9146 100644
--- a/docs/reference/Move_Legend.html
+++ b/docs/reference/Move_Legend.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -127,19 +127,19 @@ 
Move Legend Position

 
     

     
Arguments

-
-
-
position

+    
position

 
valid position to move legend.  Default is "right".

 
 
-
...

+
...

 
extra arguments passed to ggplot2::theme().

 
 

     

     
Value

-    
Returns a list-like object of class theme.

+    
+
+
Returns a list-like object of class theme.

     

 
     

@@ -165,15 +165,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/NavyAndOrange.html b/docs/reference/NavyAndOrange.html
index 6675595b4..ccc52bc93 100644
--- a/docs/reference/NavyAndOrange.html
+++ b/docs/reference/NavyAndOrange.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -127,15 +127,15 @@ 
Navy and Orange Dual Color Palette

 
     

     
Arguments

-
-
-
flip_order

+    
flip_order

 
Whether to flip the order of colors.

 
 

     

     
Value

-    
Navy orange palette

+    
+
+
Navy orange palette

     

 
     

@@ -158,15 +158,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/PC_Plotting.html b/docs/reference/PC_Plotting.html
index 1015dce85..7e3fca2e0 100644
--- a/docs/reference/PC_Plotting.html
+++ b/docs/reference/PC_Plotting.html
@@ -4,7 +4,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -129,19 +129,19 @@ 
PC Plots

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat Object.

 
 
-
dim_number

+
dim_number

 
A single dim to plot (integer).

 
 

     

     
Value

-    
A plot of PC heatmap and gene loadings for single

+    
+
+
A plot of PC heatmap and gene loadings for single

     

     

     
See also

@@ -171,15 +171,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/PalettePlot.html b/docs/reference/PalettePlot.html
index ab977253e..bc5015a10 100644
--- a/docs/reference/PalettePlot.html
+++ b/docs/reference/PalettePlot.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -127,20 +127,20 @@ 
Plot color palette in viewer

 
     

     
Arguments

-
-
-
pal

+    
pal

 
a vector of colors (either named colors of hex codes).

 
 
-
label_color_num

+
label_color_num

 
logical, whether or not to numerically label the colors in output plot.
 Default is TRUE is number of colors in pal is less than 75 and FALSE is greater than 75.

 
 

     

     
Value

-    
Plot of all colors in supplied palette/vector

+    
+
+
Plot of all colors in supplied palette/vector

     

     

     
References

@@ -168,15 +168,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Percent_Expressing.html b/docs/reference/Percent_Expressing.html
index 8828299bb..ce04cca10 100644
--- a/docs/reference/Percent_Expressing.html
+++ b/docs/reference/Percent_Expressing.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -136,44 +136,44 @@ 
Calculate percent of expressing cells

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
features

+
features

 
Feature(s) to plot.

 
 
-
threshold

+
threshold

 
Expression threshold to use for calculation of percent expressing (default is 0).

 
 
-
group_by

+
group_by

 
Factor to group the cells by.

 
 
-
split_by

+
split_by

 
Factor to split the groups by.

 
 
-
entire_object

+
entire_object

 
logical (default = FALSE).  Whether to calculate percent of expressing cells
 across the entire object as opposed to by cluster or by group_by variable.

 
 
-
layer

+
layer

 
Which layer to pull expression data from?  Default is "data".

 
 
-
assay

+
assay

 
Assay to pull feature data from.  Default is active assay.

 
 

     

     
Value

-    
A data.frame

+    
+
+
A data.frame

     

     

     
References

@@ -184,9 +184,9 @@ 
References

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 percent_stats <- Percent_Expressing(seurat_object = object, features = "Cx3cr1", threshold = 0)
-} # }
+}
 
 

     

@@ -202,15 +202,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Plot_Cells_per_Sample.html b/docs/reference/Plot_Cells_per_Sample.html
index 1027ad690..90ebffb6a 100644
--- a/docs/reference/Plot_Cells_per_Sample.html
+++ b/docs/reference/Plot_Cells_per_Sample.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -139,63 +139,63 @@ 
Plot Number of Cells/Nuclei per Sample

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
sample_col

+
sample_col

 
Specify which column in meta.data specifies sample ID (i.e. orig.ident).

 
 
-
group_by

+
group_by

 
Column in meta.data slot to group results by (i.e. "Treatment").

 
 
-
colors_use

+
colors_use

 
List of colors or color palette to use.

 
 
-
dot_size

+
dot_size

 
size of the dots plotted if group_by is not NULL.  Default is 1.

 
 
-
plot_title

+
plot_title

 
Plot title.

 
 
-
y_axis_label

+
y_axis_label

 
Label for y axis.

 
 
-
x_axis_label

+
x_axis_label

 
Label for x axis.

 
 
-
legend_title

+
legend_title

 
Label for plot legend.

 
 
-
x_lab_rotate

+
x_lab_rotate

 
logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.

 
 
-
color_seed

+
color_seed

 
random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 Plot_Cells_per_Sample(seurat_object = obj, sample_col = "orig.ident", group_by = "Treatment")
-} # }
+}
 
 

     

@@ -211,15 +211,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Plot_Density_Custom.html b/docs/reference/Plot_Density_Custom.html
index e183a34db..0734d404e 100644
--- a/docs/reference/Plot_Density_Custom.html
+++ b/docs/reference/Plot_Density_Custom.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -138,61 +138,61 @@ 
Nebulosa Density Plot

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
features

+
features

 
Features to plot.

 
 
-
joint

+
joint

 
logical. Whether to return joint density plot. Default is FALSE.

 
 
-
viridis_palette

+
viridis_palette

 
default viridis palette to use (must be one of: "viridis", "magma", "cividis",
 "inferno", "plasma").  Default is "magma".

 
 
-
custom_palette

+
custom_palette

 
non-default color palette to be used in place of default viridis options.

 
 
-
pt.size

+
pt.size

 
Adjust point size for plotting.

 
 
-
aspect_ratio

+
aspect_ratio

 
Control the aspect ratio (y:x axes ratio length).  Must be numeric value;
 Default is NULL.

 
 
-
reduction

+
reduction

 
Dimensionality Reduction to use (if NULL then defaults to Object default).

 
 
-
combine

+
combine

 
Create a single plot? If FALSE, a list with ggplot objects is returned.

 
 
-
...

+
...

 
Extra parameters passed to plot_density.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 library(Seurat)
 Plot_Density_Custom(seurat_object = pbmc_small, features = "CD3E")
-} # }
+}
 
 

     

@@ -208,15 +208,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Plot_Density_Joint_Only.html b/docs/reference/Plot_Density_Joint_Only.html
index 749f49d25..a971a6c3a 100644
--- a/docs/reference/Plot_Density_Joint_Only.html
+++ b/docs/reference/Plot_Density_Joint_Only.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -136,53 +136,53 @@ 
Nebulosa Joint Density Plot

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
features

+
features

 
Features to plot.

 
 
-
viridis_palette

+
viridis_palette

 
default viridis palette to use (must be one of: "viridis", "magma", "cividis",
 "inferno", "plasma").  Default is "magma".

 
 
-
custom_palette

+
custom_palette

 
non-default color palette to be used in place of default viridis options.

 
 
-
pt.size

+
pt.size

 
Adjust point size for plotting.

 
 
-
aspect_ratio

+
aspect_ratio

 
Control the aspect ratio (y:x axes ratio length).  Must be numeric value;
 Default is NULL.

 
 
-
reduction

+
reduction

 
Dimensionality Reduction to use (if NULL then defaults to Object default).

 
 
-
...

+
...

 
Extra parameters passed to plot_density.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 library(Seurat)
 Plot_Density_Joint_Only(seurat_object = pbmc_small, features = c("CD8A", "CD3E"))
-} # }
+}
 
 

     

@@ -198,15 +198,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Plot_Median_Genes.html b/docs/reference/Plot_Median_Genes.html
index 28f700d56..a365b286b 100644
--- a/docs/reference/Plot_Median_Genes.html
+++ b/docs/reference/Plot_Median_Genes.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -139,56 +139,56 @@ 
Plot Median Genes per Cell per Sample

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
sample_col

+
sample_col

 
Specify which column in meta.data specifies sample ID (i.e. orig.ident).

 
 
-
group_by

+
group_by

 
Column in meta.data slot to group results by (i.e. "Treatment").

 
 
-
colors_use

+
colors_use

 
List of colors or color palette to use.  Only applicable if group_by is not NULL.

 
 
-
dot_size

+
dot_size

 
size of the dots plotted if group_by is not NULL.  Default is 1.

 
 
-
plot_title

+
plot_title

 
Plot title.

 
 
-
y_axis_label

+
y_axis_label

 
Label for y axis.

 
 
-
x_axis_label

+
x_axis_label

 
Label for x axis.

 
 
-
legend_title

+
legend_title

 
Label for plot legend.

 
 
-
x_lab_rotate

+
x_lab_rotate

 
logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.

 
 
-
color_seed

+
color_seed

 
random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

@@ -217,15 +217,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Plot_Median_Mito.html b/docs/reference/Plot_Median_Mito.html
index cdfaabeee..e58417d75 100644
--- a/docs/reference/Plot_Median_Mito.html
+++ b/docs/reference/Plot_Median_Mito.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -139,67 +139,67 @@ 
Plot Median Percent Mito per Cell per Sample

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
sample_col

+
sample_col

 
Specify which column in meta.data specifies sample ID (i.e. orig.ident).

 
 
-
group_by

+
group_by

 
Column in meta.data slot to group results by (i.e. "Treatment").

 
 
-
colors_use

+
colors_use

 
List of colors or color palette to use.  Only applicable if group_by is not NULL.

 
 
-
dot_size

+
dot_size

 
size of the dots plotted if group_by is not NULL.  Default is 1.

 
 
-
plot_title

+
plot_title

 
Plot title.

 
 
-
y_axis_label

+
y_axis_label

 
Label for y axis.

 
 
-
x_axis_label

+
x_axis_label

 
Label for x axis.

 
 
-
legend_title

+
legend_title

 
Label for plot legend.

 
 
-
x_lab_rotate

+
x_lab_rotate

 
logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.

 
 
-
color_seed

+
color_seed

 
random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 # Add mito
 obj <- Add_Mito_Ribo_Seurat(seurat_object = obj, species = "human")
 
 # Plot
 Plot_Median_Mito(seurat_object = obj, sample_col = "orig.ident",  group_by = "sample_id")
-} # }
+}
 
 

     

@@ -215,15 +215,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Plot_Median_Other.html b/docs/reference/Plot_Median_Other.html
index 041e9884a..5eea9ae7e 100644
--- a/docs/reference/Plot_Median_Other.html
+++ b/docs/reference/Plot_Median_Other.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -140,65 +140,65 @@ 
Plot Median other variable per Cell per Sample

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
median_var

+
median_var

 
Variable in meta.data slot to calculate and plot median values for.

 
 
-
sample_col

+
sample_col

 
Specify which column in meta.data specifies sample ID (i.e. orig.ident).

 
 
-
group_by

+
group_by

 
Column in meta.data slot to group results by (i.e. "Treatment").

 
 
-
colors_use

+
colors_use

 
List of colors or color palette to use.  Only applicable if group_by is not NULL.

 
 
-
dot_size

+
dot_size

 
size of the dots plotted if group_by is not NULL.  Default is 1.

 
 
-
plot_title

+
plot_title

 
Plot title.

 
 
-
y_axis_label

+
y_axis_label

 
Label for y axis.

 
 
-
x_axis_label

+
x_axis_label

 
Label for x axis.

 
 
-
legend_title

+
legend_title

 
Label for plot legend.

 
 
-
x_lab_rotate

+
x_lab_rotate

 
logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.

 
 
-
color_seed

+
color_seed

 
random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 library(Seurat)
 cd_features <- list(c('CD79B', 'CD79A', 'CD19', 'CD180', 'CD200', 'CD3D', 'CD2','CD3E',
 'CD7','CD8A', 'CD14', 'CD1C', 'CD68', 'CD9', 'CD247'))
@@ -208,7 +208,7 @@ 
Examples

 
 Plot_Median_Other(seurat_object = pbmc_small, median_var = "CD_Features1",
 sample_col = "orig.ident", group_by = "Treatment")
-} # }
+}
 
 

     

@@ -224,15 +224,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Plot_Median_UMIs.html b/docs/reference/Plot_Median_UMIs.html
index 6f2d58471..40bf88fee 100644
--- a/docs/reference/Plot_Median_UMIs.html
+++ b/docs/reference/Plot_Median_UMIs.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -139,56 +139,56 @@ 
Plot Median UMIs per Cell per Sample

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
sample_col

+
sample_col

 
Specify which column in meta.data specifies sample ID (i.e. orig.ident).

 
 
-
group_by

+
group_by

 
Column in meta.data slot to group results by (i.e. "Treatment").

 
 
-
colors_use

+
colors_use

 
List of colors or color palette to use.  Only applicable if group_by is not NULL.

 
 
-
dot_size

+
dot_size

 
size of the dots plotted if group_by is not NULL.  Default is 1.

 
 
-
plot_title

+
plot_title

 
Plot title.

 
 
-
y_axis_label

+
y_axis_label

 
Label for y axis.

 
 
-
x_axis_label

+
x_axis_label

 
Label for x axis.

 
 
-
legend_title

+
legend_title

 
Label for plot legend.

 
 
-
x_lab_rotate

+
x_lab_rotate

 
logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.

 
 
-
color_seed

+
color_seed

 
random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

@@ -217,15 +217,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Proportion_Plot.html b/docs/reference/Proportion_Plot.html
index 4d074aabd..f05d73252 100644
--- a/docs/reference/Proportion_Plot.html
+++ b/docs/reference/Proportion_Plot.html
@@ -4,7 +4,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -140,55 +140,55 @@ 
Cell Proportion Plot

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
plot_type

+
plot_type

 
whether to plot a pie chart or bar chart; value must be one of "bar" or "pie". Default
 is "bar"

 
 
-
plot_scale

+
plot_scale

 
whether to plot bar chart as total cell counts or percents, value must be one of "percent" or
 "count". Default is "percent".

 
 
-
group_by_var

+
group_by_var

 
meta data column to classify samples (default = "ident" and will use active.ident.

 
 
-
split.by

+
split.by

 
meta data variable to use to split plots.  Default is NULL which will plot across entire object.

 
 
-
num_columns

+
num_columns

 
number of columns in plot.  Only valid if split.by is not NULL.

 
 
-
x_lab_rotate

+
x_lab_rotate

 
Rotate x-axis labels 45 degrees (Default is FALSE). Only valid if plot_type = "bar".

 
 
-
colors_use

+
colors_use

 
color palette to use for plotting.

 
 
-
ggplot_default_colors

+
ggplot_default_colors

 
logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

 
 
-
color_seed

+
color_seed

 
random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.

 
 

     

     
Value

-    
ggplot2 or patchwork object

+    
+
+
ggplot2 or patchwork object

     

 
     

@@ -211,15 +211,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Pull_Cluster_Annotation.html b/docs/reference/Pull_Cluster_Annotation.html
index 947242190..659738c9e 100644
--- a/docs/reference/Pull_Cluster_Annotation.html
+++ b/docs/reference/Pull_Cluster_Annotation.html
@@ -4,7 +4,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -133,29 +133,29 @@ 
Pull cluster information from annotation csv file.

 
     

     
Arguments

-
-
-
annotation

+    
annotation

 
name of the data.frame/tibble or path to CSV file containing cluster annotation.

 
 
-
cluster_name_col

+
cluster_name_col

 
name of column containing cluster names/numbers (default is "cluster").

 
 
-
cell_type_col

+
cell_type_col

 
name of column contain the cell type annotation (default is "cell_type").

 
 

     

     
Value

-    
a list of named vectors for every cell type in the cell_type_col column of the annotation table and
+    
+
+
a list of named vectors for every cell type in the cell_type_col column of the annotation table and
 vectors new cluster names (for use with Rename_Clusters function or manual identity renaming).

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 # If pulling from a data.frame/tibble
 cluster_annotation <- Pull_Cluster_Annotation(annotation = annotation_df,
 cluster_name_col = "cluster", cell_type_col = "cell_type")
@@ -163,7 +163,7 @@ 
Examples

 # If pulling from csv file
 cluster_annotation <- Pull_Cluster_Annotation(annotation = "file_path/file_name.csv",
 cluster_name_col = "cluster", cell_type_col = "cell_type")
-} # }
+}
 
 

     

@@ -179,15 +179,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Pull_Directory_List.html b/docs/reference/Pull_Directory_List.html
index 46a6309fe..6fb3403dc 100644
--- a/docs/reference/Pull_Directory_List.html
+++ b/docs/reference/Pull_Directory_List.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -127,23 +127,23 @@ 
Pull Directory List

 
     

     
Arguments

-
-
-
base_path

+    
base_path

 
path to the parent directory which contains all of the subdirectories of interest.

 
 

     

     
Value

-    
A vector of sub-directories within base_path.

+    
+
+
A vector of sub-directories within base_path.

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 data_dir <- 'path/to/data/directory'
 library_list <- Pull_Directory_List(base_path = data_dir)
-} # }
+}
 
 

     

@@ -159,15 +159,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/QC_Histogram.html b/docs/reference/QC_Histogram.html
index df8ed3e5c..c14863820 100644
--- a/docs/reference/QC_Histogram.html
+++ b/docs/reference/QC_Histogram.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -140,68 +140,68 @@ 
QC Histogram Plots

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
features

+
features

 
Feature from meta.data, assay features, or feature name shortcut to plot.

 
 
-
low_cutoff

+
low_cutoff

 
Plot line a potential low threshold for filtering.

 
 
-
high_cutoff

+
high_cutoff

 
Plot line a potential high threshold for filtering.

 
 
-
cutoff_line_width

+
cutoff_line_width

 
numerical value for thickness of cutoff lines, default is NULL.

 
 
-
split.by

+
split.by

 
Feature to split plots by (i.e. "orig.ident").

 
 
-
bins

+
bins

 
number of bins to plot default is 250.

 
 
-
colors_use

+
colors_use

 
color to fill histogram bars, default is "dodgerblue".

 
 
-
num_columns

+
num_columns

 
Number of columns in plot layout.

 
 
-
plot_title

+
plot_title

 
optional, vector to use for plot title.  Default is the name of the
 variable being plotted.

 
 
-
assay

+
assay

 
assay to pull features from, default is active assay.

 
 
-
print_defaults

+
print_defaults

 
return list of accepted default shortcuts to provide to features instead
 of full name.

 
 

     

     
Value

-    
A patchwork object

+    
+
+
A patchwork object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 QC_Histogram(seurat_object = object, features = "nFeature_RNA")
-} # }
+}
 
 

     

@@ -217,15 +217,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/QC_Plot_GenevsFeature.html b/docs/reference/QC_Plot_GenevsFeature.html
index a65dfce00..ca9caf5fd 100644
--- a/docs/reference/QC_Plot_GenevsFeature.html
+++ b/docs/reference/QC_Plot_GenevsFeature.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -146,95 +146,95 @@ 
QC Plots Genes vs Misc

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
feature1

+
feature1

 
First feature to plot.

 
 
-
x_axis_label

+
x_axis_label

 
Label for x axis.

 
 
-
y_axis_label

+
y_axis_label

 
Label for y axis.

 
 
-
low_cutoff_gene

+
low_cutoff_gene

 
Plot line a potential low threshold for filtering genes per cell.

 
 
-
high_cutoff_gene

+
high_cutoff_gene

 
Plot line a potential high threshold for filtering genes per cell.

 
 
-
low_cutoff_feature

+
low_cutoff_feature

 
Plot line a potential low threshold for filtering feature1 per cell.

 
 
-
high_cutoff_feature

+
high_cutoff_feature

 
Plot line a potential high threshold for filtering feature1 per cell.

 
 
-
cutoff_line_width

+
cutoff_line_width

 
numerical value for thickness of cutoff lines, default is NULL.

 
 
-
colors_use

+
colors_use

 
vector of colors to use for plotting by identity.

 
 
-
pt.size

+
pt.size

 
Adjust point size for plotting.

 
 
-
group.by

+
group.by

 
Name of one or more metadata columns to group (color) cells by (for example, orig.ident).
 Default is @active.ident.

 
 
-
raster

+
raster

 
Convert points to raster format.  Default is NULL which will rasterize by default if greater
 than 100,000 cells.

 
 
-
raster.dpi

+
raster.dpi

 
Pixel resolution for rasterized plots, passed to geom_scattermore().
 Default is c(512, 512).

 
 
-
ggplot_default_colors

+
ggplot_default_colors

 
logical.  If colors_use = NULL, Whether or not to return plot using default
 ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

 
 
-
color_seed

+
color_seed

 
random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.

 
 
-
shuffle_seed

+
shuffle_seed

 
Sets the seed if randomly shuffling the order of points (Default is 1).

 
 
-
...

+
...

 
Extra parameters passed to FeatureScatter.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 QC_Plot_GenevsFeature(seurat_object = obj, y_axis_label = "Feature per Cell")
-} # }
+}
 
 

     

@@ -250,15 +250,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/QC_Plot_UMIvsFeature.html b/docs/reference/QC_Plot_UMIvsFeature.html
index 8bbf46b8c..bc179c896 100644
--- a/docs/reference/QC_Plot_UMIvsFeature.html
+++ b/docs/reference/QC_Plot_UMIvsFeature.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -146,95 +146,95 @@ 
QC Plots UMI vs Misc

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
feature1

+
feature1

 
First feature to plot.

 
 
-
x_axis_label

+
x_axis_label

 
Label for x axis.

 
 
-
y_axis_label

+
y_axis_label

 
Label for y axis.

 
 
-
low_cutoff_UMI

+
low_cutoff_UMI

 
Plot line a potential low threshold for filtering UMI per cell.

 
 
-
high_cutoff_UMI

+
high_cutoff_UMI

 
Plot line a potential high threshold for filtering UMI per cell.

 
 
-
low_cutoff_feature

+
low_cutoff_feature

 
Plot line a potential low threshold for filtering feature1 per cell.

 
 
-
high_cutoff_feature

+
high_cutoff_feature

 
Plot line a potential high threshold for filtering feature1 per cell.

 
 
-
cutoff_line_width

+
cutoff_line_width

 
numerical value for thickness of cutoff lines, default is NULL.

 
 
-
colors_use

+
colors_use

 
vector of colors to use for plotting by identity.

 
 
-
pt.size

+
pt.size

 
Adjust point size for plotting.

 
 
-
group.by

+
group.by

 
Name of one or more metadata columns to group (color) cells by (for example, orig.ident).
 Default is @active.ident.

 
 
-
raster

+
raster

 
Convert points to raster format.  Default is NULL which will rasterize by default if greater
 than 100,000 cells.

 
 
-
raster.dpi

+
raster.dpi

 
Pixel resolution for rasterized plots, passed to geom_scattermore().
 Default is c(512, 512).

 
 
-
ggplot_default_colors

+
ggplot_default_colors

 
logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

 
 
-
color_seed

+
color_seed

 
random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.

 
 
-
shuffle_seed

+
shuffle_seed

 
Sets the seed if randomly shuffling the order of points (Default is 1).

 
 
-
...

+
...

 
Extra parameters passed to FeatureScatter.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 QC_Plot_UMIvsFeature(seurat_object = obj, y_axis_label = "Feature per Cell")
-} # }
+}
 
 

     

@@ -250,15 +250,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/QC_Plot_UMIvsGene.html b/docs/reference/QC_Plot_UMIvsGene.html
index 8acc79d75..11976a276 100644
--- a/docs/reference/QC_Plot_UMIvsGene.html
+++ b/docs/reference/QC_Plot_UMIvsGene.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -152,118 +152,118 @@ 
QC Plots Genes vs UMIs

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
x_axis_label

+
x_axis_label

 
Label for x axis.

 
 
-
y_axis_label

+
y_axis_label

 
Label for y axis.

 
 
-
low_cutoff_gene

+
low_cutoff_gene

 
Plot line a potential low threshold for filtering genes per cell.

 
 
-
high_cutoff_gene

+
high_cutoff_gene

 
Plot line a potential high threshold for filtering genes per cell.

 
 
-
low_cutoff_UMI

+
low_cutoff_UMI

 
Plot line a potential low threshold for filtering UMIs per cell.

 
 
-
high_cutoff_UMI

+
high_cutoff_UMI

 
Plot line a potential high threshold for filtering UMIs per cell.

 
 
-
cutoff_line_width

+
cutoff_line_width

 
numerical value for thickness of cutoff lines, default is NULL.

 
 
-
colors_use

+
colors_use

 
vector of colors to use for plotting by identity.

 
 
-
meta_gradient_name

+
meta_gradient_name

 
Name of continuous meta data variable to color points in plot by.
 (MUST be continuous variable i.e. "percent_mito").

 
 
-
meta_gradient_color

+
meta_gradient_color

 
The gradient color palette to use for plotting of meta variable (default is
 viridis "Plasma" palette with dark colors high).

 
 
-
meta_gradient_na_color

+
meta_gradient_na_color

 
Color to use for plotting values when a meta_gradient_low_cutoff is
 set (default is "lightgray").

 
 
-
meta_gradient_low_cutoff

+
meta_gradient_low_cutoff

 
Value to use as threshold for plotting.  meta_gradient_name values
 below this value will be plotted using meta_gradient_na_color.

 
 
-
cells

+
cells

 
Cells to include on the scatter plot (default is all cells).

 
 
-
combination

+
combination

 
logical (default FALSE).  Whether or not to return a plot layout with both the
 plot colored by identity and the meta data gradient plot.

 
 
-
ident_legend

+
ident_legend

 
logical, whether to plot the legend containing identities (left plot) when
 combination = TRUE.  Default is TRUE.

 
 
-
pt.size

+
pt.size

 
Passes size of points to both FeatureScatter and geom_point.

 
 
-
group.by

+
group.by

 
Name of one or more metadata columns to group (color) cells by (for example, orig.ident).
 Default is @active.ident.

 
 
-
raster

+
raster

 
Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 100,000 cells.

 
 
-
raster.dpi

+
raster.dpi

 
Pixel resolution for rasterized plots, passed to geom_scattermore().
 Default is c(512, 512).

 
 
-
ggplot_default_colors

+
ggplot_default_colors

 
logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

 
 
-
color_seed

+
color_seed

 
Random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.

 
 
-
shuffle_seed

+
shuffle_seed

 
Sets the seed if randomly shuffling the order of points (Default is 1).

 
 
-
...

+
...

 
Extra parameters passed to FeatureScatter.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

@@ -287,15 +287,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/QC_Plots_Combined_Vln.html b/docs/reference/QC_Plots_Combined_Vln.html
index 379d6f4ff..2feb45cd2 100644
--- a/docs/reference/QC_Plots_Combined_Vln.html
+++ b/docs/reference/QC_Plots_Combined_Vln.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -146,95 +146,95 @@ 
QC Plots Genes, UMIs, & % Mito

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
group.by

+
group.by

 
Name of one or more metadata columns to group (color) cells by (for example, orig.ident);
 default is the current active.ident of the object.

 
 
-
feature_cutoffs

+
feature_cutoffs

 
Numeric vector of length 1 or 2 to plot lines for  potential low/high threshold for filtering.

 
 
-
UMI_cutoffs

+
UMI_cutoffs

 
Numeric vector of length 1 or 2 to plot lines for  potential low/high threshold for filtering.

 
 
-
mito_cutoffs

+
mito_cutoffs

 
Numeric vector of length 1 or 2 to plot lines for  potential low/high threshold for filtering.

 
 
-
mito_name

+
mito_name

 
The column name containing percent mitochondrial counts information.  Default value is
 "percent_mito" which is default value created when using Add_Mito_Ribo().

 
 
-
cutoff_line_width

+
cutoff_line_width

 
numerical value for thickness of cutoff lines, default is NULL.

 
 
-
pt.size

+
pt.size

 
Point size for plotting

 
 
-
plot_median

+
plot_median

 
logical, whether to plot median for each ident on the plot (Default is FALSE).

 
 
-
median_size

+
median_size

 
Shape size for the median is plotted.

 
 
-
plot_boxplot

+
plot_boxplot

 
logical, whether to plot boxplot inside of violin (Default is FALSE).

 
 
-
colors_use

+
colors_use

 
vector of colors to use for plot.

 
 
-
x_lab_rotate

+
x_lab_rotate

 
Rotate x-axis labels 45 degrees (Default is TRUE).

 
 
-
y_axis_log

+
y_axis_log

 
logical. Whether to change y axis to log10 scale (Default is FALSE).

 
 
-
raster

+
raster

 
Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 100,000 total points plotted (# Cells x # of features).

 
 
-
ggplot_default_colors

+
ggplot_default_colors

 
logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

 
 
-
color_seed

+
color_seed

 
random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.

 
 
-
...

+
...

 
Extra parameters passed to VlnPlot.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 QC_Plots_Combined_Vln(seurat_object = object)
-} # }
+}
 
 

     

@@ -250,15 +250,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/QC_Plots_Complexity.html b/docs/reference/QC_Plots_Complexity.html
index 38f90027e..36ad5b430 100644
--- a/docs/reference/QC_Plots_Complexity.html
+++ b/docs/reference/QC_Plots_Complexity.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -148,95 +148,95 @@ 
QC Plots Cell "Complexity"

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
feature

+
feature

 
Feature from Meta Data to plot.

 
 
-
group.by

+
group.by

 
Name of one or more metadata columns to group (color) cells by (for example, orig.ident);
 default is the current active.ident of the object.

 
 
-
x_axis_label

+
x_axis_label

 
Label for x axis.

 
 
-
y_axis_label

+
y_axis_label

 
Label for y axis.

 
 
-
plot_title

+
plot_title

 
Plot Title.

 
 
-
low_cutoff

+
low_cutoff

 
Plot line a potential low threshold for filtering.

 
 
-
high_cutoff

+
high_cutoff

 
Plot line a potential high threshold for filtering.

 
 
-
cutoff_line_width

+
cutoff_line_width

 
numerical value for thickness of cutoff lines, default is NULL.

 
 
-
pt.size

+
pt.size

 
Point size for plotting

 
 
-
plot_median

+
plot_median

 
logical, whether to plot median for each ident on the plot (Default is FALSE).

 
 
-
plot_boxplot

+
plot_boxplot

 
logical, whether to plot boxplot inside of violin (Default is FALSE).

 
 
-
median_size

+
median_size

 
Shape size for the median is plotted.

 
 
-
colors_use

+
colors_use

 
vector of colors to use for plot.

 
 
-
x_lab_rotate

+
x_lab_rotate

 
Rotate x-axis labels 45 degrees (Default is TRUE).

 
 
-
y_axis_log

+
y_axis_log

 
logical. Whether to change y axis to log10 scale (Default is FALSE).

 
 
-
raster

+
raster

 
Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 100,000 total points plotted (# Cells x # of features).

 
 
-
ggplot_default_colors

+
ggplot_default_colors

 
logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

 
 
-
color_seed

+
color_seed

 
random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.

 
 
-
...

+
...

 
Extra parameters passed to VlnPlot.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

@@ -261,15 +261,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/QC_Plots_Feature.html b/docs/reference/QC_Plots_Feature.html
index b9e1bd23f..cf65cf723 100644
--- a/docs/reference/QC_Plots_Feature.html
+++ b/docs/reference/QC_Plots_Feature.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -148,104 +148,104 @@ 
QC Plots Feature

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
feature

+
feature

 
Feature from Meta Data to plot.

 
 
-
group.by

+
group.by

 
Name of one or more metadata columns to group (color) cells by (for example, orig.ident);
 default is the current active.ident of the object.

 
 
-
x_axis_label

+
x_axis_label

 
Label for x axis.

 
 
-
y_axis_label

+
y_axis_label

 
Label for y axis.

 
 
-
plot_title

+
plot_title

 
Plot Title.

 
 
-
low_cutoff

+
low_cutoff

 
Plot line a potential low threshold for filtering.

 
 
-
high_cutoff

+
high_cutoff

 
Plot line a potential high threshold for filtering.

 
 
-
cutoff_line_width

+
cutoff_line_width

 
numerical value for thickness of cutoff lines, default is NULL.

 
 
-
pt.size

+
pt.size

 
Point size for plotting.

 
 
-
plot_median

+
plot_median

 
logical, whether to plot median for each ident on the plot (Default is FALSE).

 
 
-
median_size

+
median_size

 
Shape size for the median is plotted.

 
 
-
plot_boxplot

+
plot_boxplot

 
logical, whether to plot boxplot inside of violin (Default is FALSE).

 
 
-
colors_use

+
colors_use

 
vector of colors to use for plot.

 
 
-
x_lab_rotate

+
x_lab_rotate

 
Rotate x-axis labels 45 degrees (Default is TRUE).

 
 
-
y_axis_log

+
y_axis_log

 
logical. Whether to change y axis to log10 scale (Default is FALSE).

 
 
-
raster

+
raster

 
Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 100,000 total points plotted (# Cells x # of features).

 
 
-
ggplot_default_colors

+
ggplot_default_colors

 
logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

 
 
-
color_seed

+
color_seed

 
random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.

 
 
-
...

+
...

 
Extra parameters passed to VlnPlot.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 QC_Plots_Feature(seurat_object = object, feature = "FEATURE_NAME",
 y_axis_label = "FEATURE per Cell", plot_title = "FEATURE per Cell", high_cutoff = 10,
 low_cutoff = 2)
-} # }
+}
 
 

     

@@ -261,15 +261,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/QC_Plots_Genes.html b/docs/reference/QC_Plots_Genes.html
index 6366302e3..4184b07a8 100644
--- a/docs/reference/QC_Plots_Genes.html
+++ b/docs/reference/QC_Plots_Genes.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -147,91 +147,91 @@ 
QC Plots Genes

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
plot_title

+
plot_title

 
Plot Title.

 
 
-
group.by

+
group.by

 
Name of one or more metadata columns to group (color) cells by (for example, orig.ident);
 default is the current active.ident of the object.

 
 
-
x_axis_label

+
x_axis_label

 
Label for x axis.

 
 
-
y_axis_label

+
y_axis_label

 
Label for y axis.

 
 
-
low_cutoff

+
low_cutoff

 
Plot line a potential low threshold for filtering.

 
 
-
high_cutoff

+
high_cutoff

 
Plot line a potential high threshold for filtering.

 
 
-
cutoff_line_width

+
cutoff_line_width

 
numerical value for thickness of cutoff lines, default is NULL.

 
 
-
pt.size

+
pt.size

 
Point size for plotting.

 
 
-
plot_median

+
plot_median

 
logical, whether to plot median for each ident on the plot (Default is FALSE).

 
 
-
plot_boxplot

+
plot_boxplot

 
logical, whether to plot boxplot inside of violin (Default is FALSE).

 
 
-
median_size

+
median_size

 
Shape size for the median is plotted.

 
 
-
colors_use

+
colors_use

 
vector of colors to use for plot.

 
 
-
x_lab_rotate

+
x_lab_rotate

 
Rotate x-axis labels 45 degrees (Default is TRUE).

 
 
-
y_axis_log

+
y_axis_log

 
logical. Whether to change y axis to log10 scale (Default is FALSE).

 
 
-
raster

+
raster

 
Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 100,000 total points plotted (# Cells x # of features).

 
 
-
ggplot_default_colors

+
ggplot_default_colors

 
logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

 
 
-
color_seed

+
color_seed

 
random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.

 
 
-
...

+
...

 
Extra parameters passed to VlnPlot.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

@@ -255,15 +255,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/QC_Plots_Mito.html b/docs/reference/QC_Plots_Mito.html
index bb3c2a8bd..f95c31388 100644
--- a/docs/reference/QC_Plots_Mito.html
+++ b/docs/reference/QC_Plots_Mito.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -148,103 +148,103 @@ 
QC Plots Mito

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
mito_name

+
mito_name

 
The column name containing percent mitochondrial counts information.  Default value is
 "percent_mito" which is default value created when using Add_Mito_Ribo().

 
 
-
plot_title

+
plot_title

 
Plot Title.

 
 
-
group.by

+
group.by

 
Name of one or more metadata columns to group (color) cells by (for example, orig.ident);
 default is the current active.ident of the object.

 
 
-
x_axis_label

+
x_axis_label

 
Label for x axis.

 
 
-
y_axis_label

+
y_axis_label

 
Label for y axis.

 
 
-
low_cutoff

+
low_cutoff

 
Plot line a potential low threshold for filtering.

 
 
-
high_cutoff

+
high_cutoff

 
Plot line a potential high threshold for filtering.

 
 
-
cutoff_line_width

+
cutoff_line_width

 
numerical value for thickness of cutoff lines, default is NULL.

 
 
-
pt.size

+
pt.size

 
Point size for plotting.

 
 
-
plot_median

+
plot_median

 
logical, whether to plot median for each ident on the plot (Default is FALSE).

 
 
-
median_size

+
median_size

 
Shape size for the median is plotted.

 
 
-
plot_boxplot

+
plot_boxplot

 
logical, whether to plot boxplot inside of violin (Default is FALSE).

 
 
-
colors_use

+
colors_use

 
vector of colors to use for plot.

 
 
-
x_lab_rotate

+
x_lab_rotate

 
Rotate x-axis labels 45 degrees (Default is TRUE).

 
 
-
y_axis_log

+
y_axis_log

 
logical. Whether to change y axis to log10 scale (Default is FALSE).

 
 
-
raster

+
raster

 
Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 100,000 total points plotted (# Cells x # of features).

 
 
-
ggplot_default_colors

+
ggplot_default_colors

 
logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

 
 
-
color_seed

+
color_seed

 
random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.

 
 
-
...

+
...

 
Extra parameters passed to VlnPlot.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 QC_Plots_Mito(seurat_object = object, plot_title = "Percent Mito per Cell", high_cutoff = 10)
-} # }
+}
 
 

     

@@ -260,15 +260,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/QC_Plots_UMIs.html b/docs/reference/QC_Plots_UMIs.html
index 339bc3bd8..d6f5d03b8 100644
--- a/docs/reference/QC_Plots_UMIs.html
+++ b/docs/reference/QC_Plots_UMIs.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -147,91 +147,91 @@ 
QC Plots UMIs

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
plot_title

+
plot_title

 
Plot Title.

 
 
-
group.by

+
group.by

 
Name of one or more metadata columns to group (color) cells by (for example, orig.ident);
 default is the current active.ident of the object.

 
 
-
x_axis_label

+
x_axis_label

 
Label for x axis.

 
 
-
y_axis_label

+
y_axis_label

 
Label for y axis.

 
 
-
low_cutoff

+
low_cutoff

 
Plot line a potential low threshold for filtering.

 
 
-
high_cutoff

+
high_cutoff

 
Plot line a potential high threshold for filtering.

 
 
-
cutoff_line_width

+
cutoff_line_width

 
numerical value for thickness of cutoff lines, default is NULL.

 
 
-
pt.size

+
pt.size

 
Point size for plotting.

 
 
-
plot_median

+
plot_median

 
logical, whether to plot median for each ident on the plot (Default is FALSE).

 
 
-
median_size

+
median_size

 
Shape size for the median is plotted.

 
 
-
plot_boxplot

+
plot_boxplot

 
logical, whether to plot boxplot inside of violin (Default is FALSE).

 
 
-
colors_use

+
colors_use

 
vector of colors to use for plot.

 
 
-
x_lab_rotate

+
x_lab_rotate

 
Rotate x-axis labels 45 degrees (Default is TRUE).

 
 
-
y_axis_log

+
y_axis_log

 
logical. Whether to change y axis to log10 scale (Default is FALSE).

 
 
-
raster

+
raster

 
Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 100,000 total points plotted (# Cells x # of features).

 
 
-
ggplot_default_colors

+
ggplot_default_colors

 
logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

 
 
-
color_seed

+
color_seed

 
random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.

 
 
-
...

+
...

 
Extra parameters passed to VlnPlot.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

@@ -255,15 +255,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Random_Cells_Downsample.html b/docs/reference/Random_Cells_Downsample.html
index 98bebd287..f7d06991b 100644
--- a/docs/reference/Random_Cells_Downsample.html
+++ b/docs/reference/Random_Cells_Downsample.html
@@ -4,7 +4,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -136,41 +136,41 @@ 
Randomly downsample by identity

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object

 
 
-
num_cells

+
num_cells

 
number of cells per ident to use in down-sampling.  This value must be less than or
 equal to the size of ident with fewest cells.  Alternatively, can set to "min" which will
 use the maximum number of barcodes based on size of smallest group.

 
 
-
group.by

+
group.by

 
The ident to use to group cells.  Default is "ident" which use current active.ident.  .

 
 
-
return_list

+
return_list

 
logical, whether or not to return the results as list instead of vector, default is
 FALSE.

 
 
-
allow_lower

+
allow_lower

 
logical, if number of cells in identity is lower than num_cells keep the
 maximum number of cells, default is FALSE.  If FALSE will report error message if num_cells is
 too high, if TRUE will subset cells with more than num_cells to that value and those with less
 than num_cells will not be downsampled.

 
 
-
seed

+
seed

 
random seed to use for downsampling.  Default is 123.

 
 

     

     
Value

-    
either a vector or list of cell barcodes

+    
+
+
either a vector or list of cell barcodes

     

 
     

@@ -223,15 +223,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Read10X_GEO.html b/docs/reference/Read10X_GEO.html
index a7ed19c3c..978f5f90a 100644
--- a/docs/reference/Read10X_GEO.html
+++ b/docs/reference/Read10X_GEO.html
@@ -4,7 +4,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -140,49 +140,47 @@ 
Load in NCBI GEO data from 10X

 
     

     
Arguments

-
-
-
data_dir

+    
data_dir

 
Directory containing the matrix.mtx, genes.tsv (or features.tsv), and barcodes.tsv
 files provided by 10X.

 
 
-
sample_list

+
sample_list

 
A vector of file prefixes/names if specific samples are desired.  Default is NULL and
 will load all samples in given directory.

 
 
-
sample_names

+
sample_names

 
a set of sample names to use for each sample entry in returned list.  If NULL will
 set names to the file name of each sample.

 
 
-
gene.column

+
gene.column

 
Specify which column of genes.tsv or features.tsv to use for gene names; default is 2.

 
 
-
cell.column

+
cell.column

 
Specify which column of barcodes.tsv to use for cell names; default is 1.

 
 
-
unique.features

+
unique.features

 
Make feature names unique (default TRUE).

 
 
-
strip.suffix

+
strip.suffix

 
Remove trailing "-1" if present in all cell barcodes.

 
 
-
parallel

+
parallel

 
logical (default FALSE).  Whether to use multiple cores when reading in data.
 Only possible on Linux based systems.

 
 
-
num_cores

+
num_cores

 
if parallel = TRUE indicates the number of cores to use for multicore processing.

 
 
-
merge

+
merge

 
logical (default FALSE) whether or not to merge samples into a single matrix or return
 list of matrices.  If TRUE each sample entry in list will have cell barcode prefix added.  The prefix
 will be taken from sample_names.

@@ -190,7 +188,9 @@ 
Arguments

 

     

     
Value

-    
If features.csv indicates the data has multiple data types, a list
+    
+
+
If features.csv indicates the data has multiple data types, a list
 containing a sparse matrix of the data from each type will be returned.
 Otherwise a sparse matrix containing the expression data will be returned.

     

@@ -204,12 +204,12 @@ 
References

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 data_dir <- 'path/to/data/directory'
 expression_matrices <- Read10X_GEO(data_dir = data_dir)
 # To create object from single file
 seurat_object = CreateSeuratObject(counts = expression_matrices[[1]])
-} # }
+}
 
 

     

@@ -225,15 +225,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Read10X_Multi_Directory.html b/docs/reference/Read10X_Multi_Directory.html
index 5848eaa1f..a82f0c555 100644
--- a/docs/reference/Read10X_Multi_Directory.html
+++ b/docs/reference/Read10X_Multi_Directory.html
@@ -5,7 +5,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -142,64 +142,64 @@ 
Load 10X count matrices from multiple directories

 
     

     
Arguments

-
-
-
base_path

+    
base_path

 
path to the parent directory which contains all of the subdirectories of interest.

 
 
-
secondary_path

+
secondary_path

 
path from the parent directory to count matrix files for each sample.

 
 
-
default_10X_path

+
default_10X_path

 
logical (default TRUE) sets the secondary path variable to the default 10X
 directory structure.

 
 
-
cellranger_multi

+
cellranger_multi

 
logical, whether samples were processed with Cell Ranger multi, default is FALSE.

 
 
-
sample_list

+
sample_list

 
a vector of sample directory names if only specific samples are desired.  If NULL will
 read in subdirectories in parent directory.

 
 
-
sample_names

+
sample_names

 
a set of sample names to use for each sample entry in returned list.  If NULL will
 set names to the subdirectory name of each sample.

 
 
-
parallel

+
parallel

 
logical (default FALSE) whether or not to use multi core processing to read in matrices.

 
 
-
num_cores

+
num_cores

 
how many cores to use for parallel processing.

 
 
-
merge

+
merge

 
logical (default FALSE) whether or not to merge samples into a single matrix or return
 list of matrices.  If TRUE each sample entry in list will have cell barcode prefix added.  The prefix
 will be taken from sample_names.

 
 
-
...

+
...

 
Extra parameters passed to Read10X.

 
 

     

     
Value

-    
a list of sparse matrices (merge = FALSE) or a single sparse matrix (merge = TRUE).

+    
+
+
a list of sparse matrices (merge = FALSE) or a single sparse matrix (merge = TRUE).

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 base_path <- 'path/to/data/directory'
 expression_matrices <- Read10X_Multi_Directory(base_path = base_path)
-} # }
+}
 
 

     

@@ -215,15 +215,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Read10X_h5_GEO.html b/docs/reference/Read10X_h5_GEO.html
index 6e0b824df..4743120bd 100644
--- a/docs/reference/Read10X_h5_GEO.html
+++ b/docs/reference/Read10X_h5_GEO.html
@@ -4,7 +4,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -138,60 +138,60 @@ 
Load in NCBI GEO data from 10X in HDF5 file format

 
     

     
Arguments

-
-
-
data_dir

+    
data_dir

 
Directory containing the .h5 files provided by 10X.

 
 
-
sample_list

+
sample_list

 
A vector of file prefixes/names if specific samples are desired.  Default is NULL and
 will load all samples in given directory.

 
 
-
sample_names

+
sample_names

 
a set of sample names to use for each sample entry in returned list.  If NULL
 will set names to the file name of each sample.

 
 
-
shared_suffix

+
shared_suffix

 
a suffix and file extension shared by all samples.

 
 
-
parallel

+
parallel

 
logical (default FALSE).  Whether to use multiple cores when reading in data.
 Only possible on Linux based systems.

 
 
-
num_cores

+
num_cores

 
if parallel = TRUE indicates the number of cores to use for multicore processing.

 
 
-
merge

+
merge

 
logical (default FALSE) whether or not to merge samples into a single matrix or return
 list of matrices.  If TRUE each sample entry in list will have cell barcode prefix added.  The prefix
 will be taken from sample_names.

 
 
-
...

+
...

 
Additional arguments passed to Read10X_h5

 
 

     

     
Value

-    
If the data has multiple data types, a list
+    
+
+
If the data has multiple data types, a list
 containing a sparse matrix of the data from each type will be returned.
 Otherwise a sparse matrix containing the expression data will be returned.

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 data_dir <- 'path/to/data/directory'
 expression_matrices <- Read10X_h5_GEO(data_dir = data_dir)
 # To create object from single file
 seurat_object = CreateSeuratObject(counts = expression_matrices[[1]])
-} # }
+}
 
 

     

@@ -207,15 +207,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Read10X_h5_Multi_Directory.html b/docs/reference/Read10X_h5_Multi_Directory.html
index 43f5a1b08..8d94bc21f 100644
--- a/docs/reference/Read10X_h5_Multi_Directory.html
+++ b/docs/reference/Read10X_h5_Multi_Directory.html
@@ -5,7 +5,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -145,81 +145,81 @@ 
Load 10X h5 count matrices from multiple directories

 
     

     
Arguments

-
-
-
base_path

+    
base_path

 
path to the parent directory which contains all of the subdirectories of interest.

 
 
-
secondary_path

+
secondary_path

 
path from the parent directory to count matrix files for each sample.

 
 
-
default_10X_path

+
default_10X_path

 
logical (default TRUE) sets the secondary path variable to the default 10X
 directory structure.

 
 
-
cellranger_multi

+
cellranger_multi

 
logical, whether samples were processed with Cell Ranger multi, default is FALSE.

 
 
-
h5_filename

+
h5_filename

 
name of h5 file (including .h5 suffix).  If all h5 files have same name (i.e. Cell Ranger output)
 then use full file name.  By default function uses Cell Ranger name: "filtered_feature_bc_matrix.h5".
 If h5 files have sample specific prefixes (i.e. from Cell Bender) then use only the shared part of file
 name (e.g., "_filtered_out.h5").

 
 
-
sample_list

+
sample_list

 
a vector of sample directory names if only specific samples are desired.  If NULL will
 read in subdirectories in parent directory.

 
 
-
sample_names

+
sample_names

 
a set of sample names to use for each sample entry in returned list.  If NULL will
 set names to the subdirectory name of each sample.

 
 
-
replace_suffix

+
replace_suffix

 
logical (default FALSE).  Whether or not to replace the barcode suffixes of matrices
 using Replace_Suffix.

 
 
-
new_suffix_list

+
new_suffix_list

 
a vector of new suffixes to replace existing suffixes if replace_suffix = TRUE.
 See Replace_Suffix for more information.  To remove all suffixes set new_suffix_list = "".

 
 
-
parallel

+
parallel

 
logical (default FALSE) whether or not to use multi core processing to read in matrices.

 
 
-
num_cores

+
num_cores

 
how many cores to use for parallel processing.

 
 
-
merge

+
merge

 
logical (default FALSE) whether or not to merge samples into a single matrix or return
 list of matrices.  If TRUE each sample entry in list will have cell barcode prefix added.  The prefix
 will be taken from sample_names.

 
 
-
...

+
...

 
Extra parameters passed to Read10X_h5.

 
 

     

     
Value

-    
a list of sparse matrices (merge = FALSE) or a single sparse matrix (merge = TRUE).

+    
+
+
a list of sparse matrices (merge = FALSE) or a single sparse matrix (merge = TRUE).

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 base_path <- 'path/to/data/directory'
 expression_matrices <- Read10X_h5_Multi_Directory(base_path = base_path)
-} # }
+}
 
 

     

@@ -235,15 +235,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Read_CellBender_h5_Mat.html b/docs/reference/Read_CellBender_h5_Mat.html
index b47dd3d6f..d683b80bd 100644
--- a/docs/reference/Read_CellBender_h5_Mat.html
+++ b/docs/reference/Read_CellBender_h5_Mat.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -133,33 +133,33 @@ 
Load CellBender h5 matrices (corrected)

 
     

     
Arguments

-
-
-
file_name

+    
file_name

 
Path to h5 file.

 
 
-
use.names

+
use.names

 
Label row names with feature names rather than ID numbers (default TRUE).

 
 
-
unique.features

+
unique.features

 
Make feature names unique (default TRUE).

 
 
-
h5_group_name

+
h5_group_name

 
Name of the group within H5 file that contains count data.  This is only
 required if H5 file contains multiple subgroups and non-default names.  Default is NULL.

 
 
-
feature_slot_name

+
feature_slot_name

 
Name of the slot contain feature names/ids.  Must be one of:
 "features"(Cell Ranger v3+) or "genes" (Cell Ranger v1/v2 or STARsolo).  Default is "features".

 
 

     

     
Value

-    
sparse matrix

+    
+
+
sparse matrix

     

     

     
References

@@ -169,9 +169,9 @@ 
References

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 mat <- Read_CellBender_h5_Mat(file_name = "/SampleA_out_filtered.h5")
-} # }
+}
 
 

     

@@ -187,15 +187,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Read_CellBender_h5_Multi_Directory.html b/docs/reference/Read_CellBender_h5_Multi_Directory.html
index d5dd94fc3..b1ae494b4 100644
--- a/docs/reference/Read_CellBender_h5_Multi_Directory.html
+++ b/docs/reference/Read_CellBender_h5_Multi_Directory.html
@@ -4,7 +4,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -144,85 +144,85 @@ 
Load CellBender h5 matrices (corrected) from multiple directories

 
     

     
Arguments

-
-
-
base_path

+    
base_path

 
path to the parent directory which contains all of the subdirectories of interest.

 
 
-
secondary_path

+
secondary_path

 
path from the parent directory to count matrix files for each sample.

 
 
-
filtered_h5

+
filtered_h5

 
logical (default TRUE).  Will set the shared file name suffix custom_name is NULL.

 
 
-
custom_name

+
custom_name

 
if file name was customized in CellBender then this parameter should contain the portion
 of file name that is shared across all samples.  Must included the ".h5" extension as well.

 
 
-
sample_list

+
sample_list

 
a vector of sample directory names if only specific samples are desired.  If NULL will
 read in subdirectories in parent directory.

 
 
-
sample_names

+
sample_names

 
a set of sample names to use for each sample entry in returned list.  If NULL will
 set names to the subdirectory name of each sample.  NOTE: unless sample_list is specified this will
 rename files in the order they are read which will be alphabetical.

 
 
-
h5_group_name

+
h5_group_name

 
Name of the group within H5 file that contains count data.  This is only
 required if H5 file contains multiple subgroups and non-default names.  Default is NULL.

 
 
-
feature_slot_name

+
feature_slot_name

 
Name of the slot contain feature names/ids.  Must be one of:
 "features"(Cell Ranger v3+) or "genes" (Cell Ranger v1/v2 or STARsolo).  Default is "features".

 
 
-
replace_suffix

+
replace_suffix

 
logical (default FALSE).  Whether or not to replace the barcode suffixes of matrices
 using Replace_Suffix.

 
 
-
new_suffix_list

+
new_suffix_list

 
a vector of new suffixes to replace existing suffixes if replace_suffix = TRUE.
 See Replace_Suffix for more information.  To remove all suffixes set new_suffix_list = "".

 
 
-
parallel

+
parallel

 
logical (default FALSE) whether or not to use multi core processing to read in matrices.

 
 
-
num_cores

+
num_cores

 
how many cores to use for parallel processing.

 
 
-
merge

+
merge

 
logical (default FALSE) whether or not to merge samples into a single matrix or return
 list of matrices.  If TRUE each sample entry in list will have cell barcode prefix added.  The prefix
 will be taken from sample_names.

 
 
-
...

+
...

 
Extra parameters passed to Read_CellBender_h5_Mat.

 
 

     

     
Value

-    
list of sparse matrices

+    
+
+
list of sparse matrices

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 base_path <- 'path/to/data/directory'
 mat_list <- Read_CellBender_h5_Multi_Directory(base_path = base_path)
-} # }
+}
 
 

     

@@ -238,15 +238,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Read_CellBender_h5_Multi_File.html b/docs/reference/Read_CellBender_h5_Multi_File.html
index 6fa4ec2e7..904486ce5 100644
--- a/docs/reference/Read_CellBender_h5_Multi_File.html
+++ b/docs/reference/Read_CellBender_h5_Multi_File.html
@@ -4,7 +4,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -141,70 +141,70 @@ 
Load CellBender h5 matrices (corrected) from multiple files

 
     

     
Arguments

-
-
-
data_dir

+    
data_dir

 
Directory containing the .h5 files output by CellBender.

 
 
-
filtered_h5

+
filtered_h5

 
logical (default TRUE).  Will set the shared file name suffix if custom_name is NULL.

 
 
-
custom_name

+
custom_name

 
if file name was customized in CellBender then this parameter should contain the portion
 of file name that is shared across all samples.  Must included the ".h5" extension as well.

 
 
-
sample_list

+
sample_list

 
a vector of sample names if only specific samples are desired.  If NULL will
 read in all files within data_dir directory.

 
 
-
sample_names

+
sample_names

 
a set of sample names to use for each sample entry in returned list.  If NULL will
 set names to the subdirectory name of each sample.

 
 
-
h5_group_name

+
h5_group_name

 
Name of the group within H5 file that contains count data.  This is only
 required if H5 file contains multiple subgroups and non-default names.  Default is NULL.

 
 
-
feature_slot_name

+
feature_slot_name

 
Name of the slot contain feature names/ids.  Must be one of:
 "features"(Cell Ranger v3+) or "genes" (Cell Ranger v1/v2 or STARsolo).  Default is "features".

 
 
-
parallel

+
parallel

 
logical (default FALSE) whether or not to use multi core processing to read in matrices

 
 
-
num_cores

+
num_cores

 
how many cores to use for parallel processing.

 
 
-
merge

+
merge

 
logical (default FALSE) whether or not to merge samples into a single matrix or return
 list of matrices.  If TRUE each sample entry in list will have cell barcode prefix added.  The prefix
 will be taken from sample_names.

 
 
-
...

+
...

 
Extra parameters passed to Read_CellBender_h5_Mat.

 
 

     

     
Value

-    
list of sparse matrices

+    
+
+
list of sparse matrices

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 base_path <- 'path/to/data/directory'
 mat_list <- Read_CellBender_h5_Multi_File(data_dir = base_path)
-} # }
+}
 
 

     

@@ -220,15 +220,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Read_GEO_Delim.html b/docs/reference/Read_GEO_Delim.html
index 17d94a235..7e69e39a6 100644
--- a/docs/reference/Read_GEO_Delim.html
+++ b/docs/reference/Read_GEO_Delim.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -138,54 +138,52 @@ 
Load in NCBI GEO data formatted as single file per sample

 
     

     
Arguments

-
-
-
data_dir

+    
data_dir

 
Directory containing the files.

 
 
-
file_suffix

+
file_suffix

 
The file suffix of the individual files.  Must be the same across all files being
 imported.  This is used to detect files to import and their GEO IDs.

 
 
-
move_genes_rownames

+
move_genes_rownames

 
logical.  Whether gene IDs are present in first column or in row names of
 delimited file.  If TRUE will move the first column to row names before creating final matrix.
 Default is TRUE.

 
 
-
sample_list

+
sample_list

 
a vector of samples within directory to read in (can be either with or
 without file_suffix see full_names).  If NULL will read in all subdirectories.

 
 
-
full_names

+
full_names

 
logical (default FALSE).  Whether or not the sample_list vector includes the file suffix.
 If FALSE the function will add suffix based on file_suffix parameter.

 
 
-
sample_names

+
sample_names

 
a set of sample names to use for each sample entry in returned list.
 If NULL will set names to the directory name of each sample.

 
 
-
barcode_suffix_period

+
barcode_suffix_period

 
Is the barcode suffix a period and should it be changed to "-".  Default (FALSE;
 barcodes will be left identical to their format in input files.).  If TRUE "." in barcode suffix will
 be changed to "-".

 
 
-
parallel

+
parallel

 
logical (default FALSE).  Whether to use multiple cores when reading in data.
 Only possible on Linux based systems.

 
 
-
num_cores

+
num_cores

 
if parallel = TRUE indicates the number of cores to use for multicore processing.

 
 
-
merge

+
merge

 
logical (default FALSE) whether or not to merge samples into a single matrix or return
 list of matrices.  If TRUE each sample entry in list will have cell barcode prefix added.  The prefix
 will be taken from sample_names.

@@ -193,15 +191,17 @@ 
Arguments

 

     

     
Value

-    
List of gene x cell matrices in list format named by sample name.

+    
+
+
List of gene x cell matrices in list format named by sample name.

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 data_dir <- 'path/to/data/directory'
 expression_matrices <- Read_GEO_Delim(data_dir = data_dir)
-} # }
+}
 
 

     

@@ -217,15 +217,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Read_Metrics_10X.html b/docs/reference/Read_Metrics_10X.html
index 55b7bff9b..1a3f41c23 100644
--- a/docs/reference/Read_Metrics_10X.html
+++ b/docs/reference/Read_Metrics_10X.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -134,46 +134,46 @@ 
Read Overall Statistics from 10X Cell Ranger Count

 
     

     
Arguments

-
-
-
base_path

+    
base_path

 
path to the parent directory which contains all of the subdirectories of interest or
 alternatively can provide single csv file to read and format identically to reading multiple files.

 
 
-
secondary_path

+
secondary_path

 
path from the parent directory to count "outs/" folder which contains the
 "metrics_summary.csv" file.

 
 
-
default_10X

+
default_10X

 
logical (default TRUE) sets the secondary path variable to the default 10X directory structure.

 
 
-
cellranger_multi

+
cellranger_multi

 
logical, whether or not metrics come from Cell Ranger count or from Cell Ranger multi.  Default is FALSE.

 
 
-
lib_list

+
lib_list

 
a list of sample names (matching directory names) to import.  If NULL will read
 in all samples in parent directory.

 
 
-
lib_names

+
lib_names

 
a set of sample names to use for each sample.  If NULL will set names to the
 directory name of each sample.

 
 

     

     
Value

-    
A data frame or list of data.frames with sample metrics from cell ranger.

+    
+
+
A data frame or list of data.frames with sample metrics from cell ranger.

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 metrics <- Read_Metrics_10X(base_path = "/path/to/directories", default_10X = TRUE)
-} # }
+}
 
 

     

@@ -189,15 +189,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Read_Metrics_CellBender.html b/docs/reference/Read_Metrics_CellBender.html
index 74d1e50f3..d05f2e4c0 100644
--- a/docs/reference/Read_Metrics_CellBender.html
+++ b/docs/reference/Read_Metrics_CellBender.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -127,33 +127,33 @@ 
Read Overall Statistics from CellBender

 
     

     
Arguments

-
-
-
base_path

+    
base_path

 
path to the parent directory which contains all of the sub-directories of interest or
 path to single metrics csv file.

 
 
-
lib_list

+
lib_list

 
a list of sample names (matching directory names) to import.  If NULL will read
 in all samples in parent directory.

 
 
-
lib_names

+
lib_names

 
a set of sample names to use for each sample.  If NULL will set names to the
 directory name of each sample.

 
 

     

     
Value

-    
A data frame with sample metrics from CellBender.

+    
+
+
A data frame with sample metrics from CellBender.

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 CB_metrics <- Read_Metrics_CellBender(base_path = "/path/to/directories")
-} # }
+}
 
 

     

@@ -169,15 +169,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Reduction_Loading_Present.html b/docs/reference/Reduction_Loading_Present.html
index 8521bc5b0..00e2160ca 100644
--- a/docs/reference/Reduction_Loading_Present.html
+++ b/docs/reference/Reduction_Loading_Present.html
@@ -4,7 +4,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -135,41 +135,41 @@ 
Check if reduction loadings are present

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
object name.

 
 
-
reduction_names

+
reduction_names

 
vector of genes to check.

 
 
-
print_msg

+
print_msg

 
logical. Whether message should be printed if all features are found.  Default is TRUE.

 
 
-
omit_warn

+
omit_warn

 
logical. Whether to print message about features that are not found in current object.
 Default is TRUE.

 
 
-
return_none

+
return_none

 
logical. Whether list of found vs. bad features should still be returned if no
 features are found.  Default is FALSE.

 
 

     

     
Value

-    
A list of length 3 containing 1) found features, 2) not found features.

+    
+
+
A list of length 3 containing 1) found features, 2) not found features.

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 reductions <- Reduction_Loading_Present(seurat_object = obj_name, reduction_name = "PC_1")
 found_reductions <- reductions[[1]]
-} # }
+}
 
 

     

@@ -185,15 +185,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Rename_Clusters.html b/docs/reference/Rename_Clusters.html
index bdc582ad9..94062ac49 100644
--- a/docs/reference/Rename_Clusters.html
+++ b/docs/reference/Rename_Clusters.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -124,7 +124,7 @@ 
Rename Clusters

     

     
Rename_Clusters(object, ...)
 
-# S3 method for class 'liger'
+# S3 method for liger
 Rename_Clusters(
   object,
   new_idents,
@@ -134,7 +134,7 @@ 
Rename Clusters

   ...
 )
 
-# S3 method for class 'Seurat'
+# S3 method for Seurat
 Rename_Clusters(
   object,
   new_idents,
@@ -148,55 +148,55 @@ 
Rename Clusters

 
     

     
Arguments

-
-
-
object

+    
object

 
Object of class Seurat or liger.

 
 
-
...

+
...

 
Arguments passed to other methods

 
 
-
new_idents

+
new_idents

 
vector of new cluster names.  Must be equal to the length of current default identity
 of Object.  Will accept named vector (with old idents as names) or will name the new_idents vector internally.

 
 
-
old_ident_name

+
old_ident_name

 
optional, name to use for storing current object idents in object meta data slot.

 
 
-
new_ident_name

+
new_ident_name

 
optional, name to use for storing new object idents in object meta data slot.

 
 
-
overwrite

+
overwrite

 
logical, whether to overwrite columns in object meta data slot. if they have same
 names as old_ident_name and/or new_ident_name.

 
 
-
meta_col_name

+
meta_col_name

 
[Soft-deprecated]. See old_ident_name.

 
 

     

     
Value

-    
An object of the same class as object with updated default identities.

+    
+
+
An object of the same class as object with updated default identities.

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 # Liger version
 obj <- Rename_Clusters(object = obj_name, new_idents = new_idents_vec,
 old_ident_name = "LIGER_Idents_Round01", new_ident_name = "LIGER_Idents_Round02")
-} # }
+}
 
-if (FALSE) { # \dontrun{
+if (FALSE) {
 obj <- Rename_Clusters(seurat_object = obj_name, new_idents = new_idents_vec,
 old_ident_name = "Seurat_Idents_Round01", new_ident_name = "Round01_Res0.6_Idents")
-} # }
+}
 
 

     

@@ -212,15 +212,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Replace_Suffix.html b/docs/reference/Replace_Suffix.html
index 7f454c397..7e602bd18 100644
--- a/docs/reference/Replace_Suffix.html
+++ b/docs/reference/Replace_Suffix.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -127,18 +127,16 @@ 
Replace barcode suffixes

 
     

     
Arguments

-
-
-
data

+    
data

 
Either matrix/data.frame or list of matrices/data.frames with the cell barcodes in the column names.

 
 
-
current_suffix

+
current_suffix

 
a single value or vector of values representing current barcode suffix.
 If suffix is the same for all matrices/data.frames in list only single value is required.

 
 
-
new_suffix

+
new_suffix

 
a single value or vector of values representing new barcode suffix to be added.
 If desired suffix is the same for all matrices/data.frames in list only single value is required.
 If no suffix is desired set new_suffix = "".`

@@ -146,14 +144,16 @@ 
Arguments

 

     

     
Value

-    
matrix or data.frame with new column names.

+    
+
+
matrix or data.frame with new column names.

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 dge_matrix <- Replace_Suffix(data = dge_matrix, current_suffix = "-1", new_suffix = "-2")
-} # }
+}
 
 

     

@@ -169,15 +169,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Seq_QC_Plot_Alignment_Combined.html b/docs/reference/Seq_QC_Plot_Alignment_Combined.html
index c0a0c560b..21143bfd1 100644
--- a/docs/reference/Seq_QC_Plot_Alignment_Combined.html
+++ b/docs/reference/Seq_QC_Plot_Alignment_Combined.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -136,52 +136,52 @@ 
QC Plots Sequencing metrics (Alignment) (Layout)

 
     

     
Arguments

-
-
-
metrics_dataframe

+    
metrics_dataframe

 
data.frame  contain Cell Ranger QC Metrics (see Read_Metrics_10X).

 
 
-
plot_by

+
plot_by

 
Grouping factor for the plot.  Default is to plot as single group with single point per sample.

 
 
-
colors_use

+
colors_use

 
colors to use for plot if plotting by group.  Defaults to RColorBrewer Dark2 palette if
 less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.

 
 
-
dot_size

+
dot_size

 
size of the dots plotted if plot_by is not sample_id  Default is 1.

 
 
-
x_lab_rotate

+
x_lab_rotate

 
logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.

 
 
-
patchwork_title

+
patchwork_title

 
Title to use for the patchworked plot output.

 
 
-
significance

+
significance

 
logical.  Whether to calculate and plot p-value comparisons when plotting by
 grouping factor.  Default is FALSE.

 
 
-
...

+
...

 
Other variables to pass to ggpubr::stat_compare_means when doing significance testing.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 Seq_QC_Plot_Alignment_Combined(metrics_dataframe = metrics)
-} # }
+}
 
 

     

@@ -197,15 +197,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Seq_QC_Plot_Antisense.html b/docs/reference/Seq_QC_Plot_Antisense.html
index c1f5a1864..873a3d7b7 100644
--- a/docs/reference/Seq_QC_Plot_Antisense.html
+++ b/docs/reference/Seq_QC_Plot_Antisense.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -135,48 +135,48 @@ 
QC Plots Sequencing metrics (Alignment)

 
     

     
Arguments

-
-
-
metrics_dataframe

+    
metrics_dataframe

 
data.frame  contain Cell Ranger QC Metrics (see Read_Metrics_10X).

 
 
-
plot_by

+
plot_by

 
Grouping factor for the plot.  Default is to plot as single group with single point per sample.

 
 
-
colors_use

+
colors_use

 
colors to use for plot if plotting by group.  Defaults to RColorBrewer Dark2 palette if
 less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.

 
 
-
dot_size

+
dot_size

 
size of the dots plotted if plot_by is not sample_id  Default is 1.

 
 
-
x_lab_rotate

+
x_lab_rotate

 
logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.

 
 
-
significance

+
significance

 
logical.  Whether to calculate and plot p-value comparisons when plotting by
 grouping factor.  Default is FALSE.

 
 
-
...

+
...

 
Other variables to pass to ggpubr::stat_compare_means when doing significance testing.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 Seq_QC_Plot_Antisense(metrics_dataframe = metrics)
-} # }
+}
 
 

     

@@ -192,15 +192,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Seq_QC_Plot_Basic_Combined.html b/docs/reference/Seq_QC_Plot_Basic_Combined.html
index 51a36994b..b25b517d8 100644
--- a/docs/reference/Seq_QC_Plot_Basic_Combined.html
+++ b/docs/reference/Seq_QC_Plot_Basic_Combined.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -136,52 +136,52 @@ 
QC Plots Sequencing metrics (Layout)

 
     

     
Arguments

-
-
-
metrics_dataframe

+    
metrics_dataframe

 
data.frame  contain Cell Ranger QC Metrics (see Read_Metrics_10X).

 
 
-
plot_by

+
plot_by

 
Grouping factor for the plot.  Default is to plot as single group with single point per sample.

 
 
-
colors_use

+
colors_use

 
colors to use for plot if plotting by group.  Defaults to RColorBrewer Dark2 palette if
 less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.

 
 
-
dot_size

+
dot_size

 
size of the dots plotted if plot_by is not sample_id  Default is 1.

 
 
-
x_lab_rotate

+
x_lab_rotate

 
logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.

 
 
-
patchwork_title

+
patchwork_title

 
Title to use for the patchworked plot output.

 
 
-
significance

+
significance

 
logical.  Whether to calculate and plot p-value comparisons when plotting by
 grouping factor.  Default is FALSE.

 
 
-
...

+
...

 
Other variables to pass to ggpubr::stat_compare_means when doing significance testing.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 Seq_QC_Plot_Basic_Combined(metrics_dataframe = metrics)
-} # }
+}
 
 

     

@@ -197,15 +197,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Seq_QC_Plot_Exonic.html b/docs/reference/Seq_QC_Plot_Exonic.html
index 72973a22b..f7a4e759b 100644
--- a/docs/reference/Seq_QC_Plot_Exonic.html
+++ b/docs/reference/Seq_QC_Plot_Exonic.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -135,48 +135,48 @@ 
QC Plots Sequencing metrics (Alignment)

 
     

     
Arguments

-
-
-
metrics_dataframe

+    
metrics_dataframe

 
data.frame  contain Cell Ranger QC Metrics (see Read_Metrics_10X).

 
 
-
plot_by

+
plot_by

 
Grouping factor for the plot.  Default is to plot as single group with single point per sample.

 
 
-
colors_use

+
colors_use

 
colors to use for plot if plotting by group.  Defaults to RColorBrewer Dark2 palette if
 less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.

 
 
-
dot_size

+
dot_size

 
size of the dots plotted if plot_by is not sample_id  Default is 1.

 
 
-
x_lab_rotate

+
x_lab_rotate

 
logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.

 
 
-
significance

+
significance

 
logical.  Whether to calculate and plot p-value comparisons when plotting by
 grouping factor.  Default is FALSE.

 
 
-
...

+
...

 
Other variables to pass to ggpubr::stat_compare_means when doing significance testing.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 Seq_QC_Plot_Exonic(metrics_dataframe = metrics)
-} # }
+}
 
 

     

@@ -192,15 +192,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Seq_QC_Plot_Genes.html b/docs/reference/Seq_QC_Plot_Genes.html
index f5f7e64ed..c684587f2 100644
--- a/docs/reference/Seq_QC_Plot_Genes.html
+++ b/docs/reference/Seq_QC_Plot_Genes.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -135,48 +135,48 @@ 
QC Plots Sequencing metrics

 
     

     
Arguments

-
-
-
metrics_dataframe

+    
metrics_dataframe

 
data.frame  contain Cell Ranger QC Metrics (see Read_Metrics_10X).

 
 
-
plot_by

+
plot_by

 
Grouping factor for the plot.  Default is to plot as single group with single point per sample.

 
 
-
colors_use

+
colors_use

 
colors to use for plot if plotting by group.  Defaults to RColorBrewer Dark2 palette if
 less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.

 
 
-
dot_size

+
dot_size

 
size of the dots plotted if plot_by is not sample_id  Default is 1.

 
 
-
x_lab_rotate

+
x_lab_rotate

 
logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.

 
 
-
significance

+
significance

 
logical.  Whether to calculate and plot p-value comparisons when plotting by
 grouping factor.  Default is FALSE.

 
 
-
...

+
...

 
Other variables to pass to ggpubr::stat_compare_means when doing significance testing.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 Seq_QC_Plot_Genes(metrics_dataframe = metrics)
-} # }
+}
 
 

     

@@ -192,15 +192,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Seq_QC_Plot_Genome.html b/docs/reference/Seq_QC_Plot_Genome.html
index 2c23778e8..81c2a20a5 100644
--- a/docs/reference/Seq_QC_Plot_Genome.html
+++ b/docs/reference/Seq_QC_Plot_Genome.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -135,48 +135,48 @@ 
QC Plots Sequencing metrics (Alignment)

 
     

     
Arguments

-
-
-
metrics_dataframe

+    
metrics_dataframe

 
data.frame  contain Cell Ranger QC Metrics (see Read_Metrics_10X).

 
 
-
plot_by

+
plot_by

 
Grouping factor for the plot.  Default is to plot as single group with single point per sample.

 
 
-
colors_use

+
colors_use

 
colors to use for plot if plotting by group.  Defaults to RColorBrewer Dark2 palette if
 less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.

 
 
-
dot_size

+
dot_size

 
size of the dots plotted if plot_by is not sample_id  Default is 1.

 
 
-
x_lab_rotate

+
x_lab_rotate

 
logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.

 
 
-
significance

+
significance

 
logical.  Whether to calculate and plot p-value comparisons when plotting by
 grouping factor.  Default is FALSE.

 
 
-
...

+
...

 
Other variables to pass to ggpubr::stat_compare_means when doing significance testing.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 Seq_QC_Plot_Genome(metrics_dataframe = metrics)
-} # }
+}
 
 

     

@@ -192,15 +192,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Seq_QC_Plot_Intergenic.html b/docs/reference/Seq_QC_Plot_Intergenic.html
index 0547dd2e4..53750e0d2 100644
--- a/docs/reference/Seq_QC_Plot_Intergenic.html
+++ b/docs/reference/Seq_QC_Plot_Intergenic.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -135,48 +135,48 @@ 
QC Plots Sequencing metrics (Alignment)

 
     

     
Arguments

-
-
-
metrics_dataframe

+    
metrics_dataframe

 
data.frame  contain Cell Ranger QC Metrics (see Read_Metrics_10X).

 
 
-
plot_by

+
plot_by

 
Grouping factor for the plot.  Default is to plot as single group with single point per sample.

 
 
-
colors_use

+
colors_use

 
colors to use for plot if plotting by group.  Defaults to RColorBrewer Dark2 palette if
 less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.

 
 
-
dot_size

+
dot_size

 
size of the dots plotted if plot_by is not sample_id  Default is 1.

 
 
-
x_lab_rotate

+
x_lab_rotate

 
logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.

 
 
-
significance

+
significance

 
logical.  Whether to calculate and plot p-value comparisons when plotting by
 grouping factor.  Default is FALSE.

 
 
-
...

+
...

 
Other variables to pass to ggpubr::stat_compare_means when doing significance testing.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 Seq_QC_Plot_Intergeneic(metrics_dataframe = metrics)
-} # }
+}
 
 

     

@@ -192,15 +192,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Seq_QC_Plot_Intronic.html b/docs/reference/Seq_QC_Plot_Intronic.html
index b2e021a10..7475d9cad 100644
--- a/docs/reference/Seq_QC_Plot_Intronic.html
+++ b/docs/reference/Seq_QC_Plot_Intronic.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -135,48 +135,48 @@ 
QC Plots Sequencing metrics (Alignment)

 
     

     
Arguments

-
-
-
metrics_dataframe

+    
metrics_dataframe

 
data.frame  contain Cell Ranger QC Metrics (see Read_Metrics_10X).

 
 
-
plot_by

+
plot_by

 
Grouping factor for the plot.  Default is to plot as single group with single point per sample.

 
 
-
colors_use

+
colors_use

 
colors to use for plot if plotting by group.  Defaults to RColorBrewer Dark2 palette if
 less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.

 
 
-
dot_size

+
dot_size

 
size of the dots plotted if plot_by is not sample_id  Default is 1.

 
 
-
x_lab_rotate

+
x_lab_rotate

 
logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.

 
 
-
significance

+
significance

 
logical.  Whether to calculate and plot p-value comparisons when plotting by
 grouping factor.  Default is FALSE.

 
 
-
...

+
...

 
Other variables to pass to ggpubr::stat_compare_means when doing significance testing.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 Seq_QC_Plot_Intronic(metrics_dataframe = metrics)
-} # }
+}
 
 

     

@@ -192,15 +192,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Seq_QC_Plot_Number_Cells.html b/docs/reference/Seq_QC_Plot_Number_Cells.html
index 7894a4293..7faf27d66 100644
--- a/docs/reference/Seq_QC_Plot_Number_Cells.html
+++ b/docs/reference/Seq_QC_Plot_Number_Cells.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -135,48 +135,48 @@ 
QC Plots Sequencing metrics

 
     

     
Arguments

-
-
-
metrics_dataframe

+    
metrics_dataframe

 
data.frame  contain Cell Ranger QC Metrics (see Read_Metrics_10X).

 
 
-
plot_by

+
plot_by

 
Grouping factor for the plot.  Default is to plot as single group with single point per sample.

 
 
-
colors_use

+
colors_use

 
colors to use for plot if plotting by group.  Defaults to RColorBrewer Dark2 palette if
 less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.

 
 
-
dot_size

+
dot_size

 
size of the dots plotted if plot_by is not sample_id  Default is 1.

 
 
-
x_lab_rotate

+
x_lab_rotate

 
logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.

 
 
-
significance

+
significance

 
logical.  Whether to calculate and plot p-value comparisons when plotting by
 grouping factor.  Default is FALSE.

 
 
-
...

+
...

 
Other variables to pass to ggpubr::stat_compare_means when doing significance testing.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 Seq_QC_Plot_Number_Cells(metrics_dataframe = metrics)
-} # }
+}
 
 

     

@@ -192,15 +192,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Seq_QC_Plot_Reads_in_Cells.html b/docs/reference/Seq_QC_Plot_Reads_in_Cells.html
index a4f7d7097..ce2bce38f 100644
--- a/docs/reference/Seq_QC_Plot_Reads_in_Cells.html
+++ b/docs/reference/Seq_QC_Plot_Reads_in_Cells.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -135,48 +135,48 @@ 
QC Plots Sequencing metrics

 
     

     
Arguments

-
-
-
metrics_dataframe

+    
metrics_dataframe

 
data.frame  contain Cell Ranger QC Metrics (see Read_Metrics_10X).

 
 
-
plot_by

+
plot_by

 
Grouping factor for the plot.  Default is to plot as single group with single point per sample.

 
 
-
colors_use

+
colors_use

 
colors to use for plot if plotting by group.  Defaults to RColorBrewer Dark2 palette if
 less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.

 
 
-
dot_size

+
dot_size

 
size of the dots plotted if plot_by is not sample_id  Default is 1.

 
 
-
x_lab_rotate

+
x_lab_rotate

 
logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.

 
 
-
significance

+
significance

 
logical.  Whether to calculate and plot p-value comparisons when plotting by
 grouping factor.  Default is FALSE.

 
 
-
...

+
...

 
Other variables to pass to ggpubr::stat_compare_means when doing significance testing.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 Seq_QC_Plot_Reads_in_Cells(metrics_dataframe = metrics)
-} # }
+}
 
 

     

@@ -192,15 +192,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Seq_QC_Plot_Reads_per_Cell.html b/docs/reference/Seq_QC_Plot_Reads_per_Cell.html
index 10fe6663f..8d4f3d4a5 100644
--- a/docs/reference/Seq_QC_Plot_Reads_per_Cell.html
+++ b/docs/reference/Seq_QC_Plot_Reads_per_Cell.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -135,48 +135,48 @@ 
QC Plots Sequencing metrics

 
     

     
Arguments

-
-
-
metrics_dataframe

+    
metrics_dataframe

 
data.frame  contain Cell Ranger QC Metrics (see Read_Metrics_10X).

 
 
-
plot_by

+
plot_by

 
Grouping factor for the plot.  Default is to plot as single group with single point per sample.

 
 
-
colors_use

+
colors_use

 
colors to use for plot if plotting by group.  Defaults to RColorBrewer Dark2 palette if
 less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.

 
 
-
dot_size

+
dot_size

 
size of the dots plotted if plot_by is not sample_id  Default is 1.

 
 
-
x_lab_rotate

+
x_lab_rotate

 
logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.

 
 
-
significance

+
significance

 
logical.  Whether to calculate and plot p-value comparisons when plotting by
 grouping factor.  Default is FALSE.

 
 
-
...

+
...

 
Other variables to pass to ggpubr::stat_compare_means when doing significance testing.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 Seq_QC_Plot_Reads_per_Cell(metrics_dataframe = metrics)
-} # }
+}
 
 

     

@@ -192,15 +192,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Seq_QC_Plot_Saturation.html b/docs/reference/Seq_QC_Plot_Saturation.html
index 5d01eaf25..0a9064259 100644
--- a/docs/reference/Seq_QC_Plot_Saturation.html
+++ b/docs/reference/Seq_QC_Plot_Saturation.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -135,48 +135,48 @@ 
QC Plots Sequencing metrics

 
     

     
Arguments

-
-
-
metrics_dataframe

+    
metrics_dataframe

 
data.frame  contain Cell Ranger QC Metrics (see Read_Metrics_10X).

 
 
-
plot_by

+
plot_by

 
Grouping factor for the plot.  Default is to plot as single group with single point per sample.

 
 
-
colors_use

+
colors_use

 
colors to use for plot if plotting by group.  Defaults to RColorBrewer Dark2 palette if
 less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.

 
 
-
dot_size

+
dot_size

 
size of the dots plotted if plot_by is not sample_id  Default is 1.

 
 
-
x_lab_rotate

+
x_lab_rotate

 
logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.

 
 
-
significance

+
significance

 
logical.  Whether to calculate and plot p-value comparisons when plotting by
 grouping factor.  Default is FALSE.

 
 
-
...

+
...

 
Other variables to pass to ggpubr::stat_compare_means when doing significance testing.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 Seq_QC_Plot_Saturation(metrics_dataframe = metrics)
-} # }
+}
 
 

     

@@ -192,15 +192,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Seq_QC_Plot_Total_Genes.html b/docs/reference/Seq_QC_Plot_Total_Genes.html
index f3aebe608..f9f0eab59 100644
--- a/docs/reference/Seq_QC_Plot_Total_Genes.html
+++ b/docs/reference/Seq_QC_Plot_Total_Genes.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -135,48 +135,48 @@ 
QC Plots Sequencing metrics

 
     

     
Arguments

-
-
-
metrics_dataframe

+    
metrics_dataframe

 
data.frame  contain Cell Ranger QC Metrics (see Read_Metrics_10X).

 
 
-
plot_by

+
plot_by

 
Grouping factor for the plot.  Default is to plot as single group with single point per sample.

 
 
-
colors_use

+
colors_use

 
colors to use for plot if plotting by group.  Defaults to RColorBrewer Dark2 palette if
 less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.

 
 
-
dot_size

+
dot_size

 
size of the dots plotted if plot_by is not sample_id  Default is 1.

 
 
-
x_lab_rotate

+
x_lab_rotate

 
logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.

 
 
-
significance

+
significance

 
logical.  Whether to calculate and plot p-value comparisons when plotting by
 grouping factor.  Default is FALSE.

 
 
-
...

+
...

 
Other variables to pass to ggpubr::stat_compare_means when doing significance testing.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 Seq_QC_Plot_Total_Genes(metrics_dataframe = metrics)
-} # }
+}
 
 

     

@@ -192,15 +192,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Seq_QC_Plot_Transcriptome.html b/docs/reference/Seq_QC_Plot_Transcriptome.html
index b230cabda..d3ab5b0d9 100644
--- a/docs/reference/Seq_QC_Plot_Transcriptome.html
+++ b/docs/reference/Seq_QC_Plot_Transcriptome.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -135,48 +135,48 @@ 
QC Plots Sequencing metrics (Alignment)

 
     

     
Arguments

-
-
-
metrics_dataframe

+    
metrics_dataframe

 
data.frame  contain Cell Ranger QC Metrics (see Read_Metrics_10X).

 
 
-
plot_by

+
plot_by

 
Grouping factor for the plot.  Default is to plot as single group with single point per sample.

 
 
-
colors_use

+
colors_use

 
colors to use for plot if plotting by group.  Defaults to RColorBrewer Dark2 palette if
 less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.

 
 
-
dot_size

+
dot_size

 
size of the dots plotted if plot_by is not sample_id  Default is 1.

 
 
-
x_lab_rotate

+
x_lab_rotate

 
logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.

 
 
-
significance

+
significance

 
logical.  Whether to calculate and plot p-value comparisons when plotting by
 grouping factor.  Default is FALSE.

 
 
-
...

+
...

 
Other variables to pass to ggpubr::stat_compare_means when doing significance testing.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 Seq_QC_Plot_Transcriptome(metrics_dataframe = metrics)
-} # }
+}
 
 

     

@@ -192,15 +192,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Seq_QC_Plot_UMIs.html b/docs/reference/Seq_QC_Plot_UMIs.html
index 6043fe7f9..f04508eed 100644
--- a/docs/reference/Seq_QC_Plot_UMIs.html
+++ b/docs/reference/Seq_QC_Plot_UMIs.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -135,48 +135,48 @@ 
QC Plots Sequencing metrics

 
     

     
Arguments

-
-
-
metrics_dataframe

+    
metrics_dataframe

 
data.frame contain Cell Ranger QC Metrics (see Read_Metrics_10X).

 
 
-
plot_by

+
plot_by

 
Grouping factor for the plot.  Default is to plot as single group with single point per sample.

 
 
-
colors_use

+
colors_use

 
colors to use for plot if plotting by group.  Defaults to RColorBrewer Dark2 palette if
 less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.

 
 
-
dot_size

+
dot_size

 
size of the dots plotted if plot_by is not sample_id  Default is 1.

 
 
-
x_lab_rotate

+
x_lab_rotate

 
logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.

 
 
-
significance

+
significance

 
logical.  Whether to calculate and plot p-value comparisons when plotting by
 grouping factor.  Default is FALSE.

 
 
-
...

+
...

 
Other variables to pass to ggpubr::stat_compare_means when doing significance testing.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 Seq_QC_Plot_UMIs(metrics_dataframe = metrics)
-} # }
+}
 
 

     

@@ -192,15 +192,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Setup_scRNAseq_Project.html b/docs/reference/Setup_scRNAseq_Project.html
index 6cac78e97..253a649d8 100644
--- a/docs/reference/Setup_scRNAseq_Project.html
+++ b/docs/reference/Setup_scRNAseq_Project.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -131,32 +131,32 @@ 
Setup project directory structure

 
     

     
Arguments

-
-
-
custom_dir_file

+    
custom_dir_file

 
file to file containing desired directory structure.  Default is NULL and
 will provide generic built-in directory structure.

 
 
-
cluster_annotation_path

+
cluster_annotation_path

 
path to place cluster annotation file using Create_Cluster_Annotation_File.

 
 
-
cluster_annotation_file_name

+
cluster_annotation_file_name

 
name to use for annotation file if created (optional).

 
 

     

     
Value

-    
no return value.  Creates system folders.

+    
+
+
no return value.  Creates system folders.

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 # If using built-in directory structure.
 Setup_scRNAseq_Project()
-} # }
+}
 
 

     

@@ -172,15 +172,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Single_Color_Palette.html b/docs/reference/Single_Color_Palette.html
index 1825503f1..aad220c36 100644
--- a/docs/reference/Single_Color_Palette.html
+++ b/docs/reference/Single_Color_Palette.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -127,24 +127,24 @@ 
Single Color Palettes for Plotting

 
     

     
Arguments

-
-
-
pal_color

+    
pal_color

 
color palette to select (Options are: 'reds', 'blues',
 'greens', 'purples', 'oranges', 'grays').

 
 
-
num_colors

+
num_colors

 
set number of colors (max = 7).

 
 
-
seed_use

+
seed_use

 
set seed for reproducibility (default: 123).

 
 

     

     
Value

-    
A vector of colors

+    
+
+
A vector of colors

     

     

     
References

@@ -172,15 +172,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/SpatialDimPlot_scCustom.html b/docs/reference/SpatialDimPlot_scCustom.html
index fad41ce07..de009df07 100644
--- a/docs/reference/SpatialDimPlot_scCustom.html
+++ b/docs/reference/SpatialDimPlot_scCustom.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -148,103 +148,103 @@ 
SpatialDimPlot with modified default settings

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
group.by

+
group.by

 
Name of meta.data column to group the data by

 
 
-
images

+
images

 
Name of the images to use in the plot(s)

 
 
-
colors_use

+
colors_use

 
color palette to use for plotting.  By default if number of levels plotted is less than
 or equal to 36 it will use "polychrome" and if greater than 36 will use "varibow" with shuffle = TRUE
 both from DiscretePalette_scCustomize.

 
 
-
crop

+
crop

 
Crop the plot in to focus on points plotted. Set to FALSE to show
 entire background image.

 
 
-
label

+
label

 
Whether to label the clusters

 
 
-
label.size

+
label.size

 
Sets the size of the labels

 
 
-
label.color

+
label.color

 
Sets the color of the label text

 
 
-
label.box

+
label.box

 
Whether to put a box around the label text (geom_text vs
 geom_label)

 
 
-
repel

+
repel

 
Repels the labels to prevent overlap

 
 
-
ncol

+
ncol

 
Number of columns if plotting multiple plots

 
 
-
pt.size.factor

+
pt.size.factor

 
Scale the size of the spots.

 
 
-
alpha

+
alpha

 
Controls opacity of spots. Provide as a vector specifying the
 min and max for SpatialFeaturePlot. For SpatialDimPlot, provide a single
 alpha value for each plot.

 
 
-
image.alpha

+
image.alpha

 
Adjust the opacity of the background images. Set to 0 to
 remove.

 
 
-
stroke

+
stroke

 
Control the width of the border around the spots

 
 
-
interactive

+
interactive

 
Launch an interactive SpatialDimPlot or SpatialFeaturePlot
 session, see ISpatialDimPlot or
 ISpatialFeaturePlot for more details

 
 
-
combine

+
combine

 
Combine plots into a single gg object; note that if TRUE;
 themeing will not work when plotting multiple features/groupings

 
 
-
ggplot_default_colors

+
ggplot_default_colors

 
logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

 
 
-
color_seed

+
color_seed

 
random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.

 
 
-
...

+
...

 
Extra parameters passed to DimPlot.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

     

     
References

@@ -254,9 +254,9 @@ 
References

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 SpatialDimPlot_scCustom(seurat_object = seurat_object)
-} # }
+}
 
 

     

@@ -272,15 +272,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Split_Layers.html b/docs/reference/Split_Layers.html
index 7b93c2e38..8d24be88a 100644
--- a/docs/reference/Split_Layers.html
+++ b/docs/reference/Split_Layers.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -127,27 +127,25 @@ 
Split Seurat object into layers

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
assay

+
assay

 
name(s) of assays to convert.  Defaults to current active assay.

 
 
-
split.by

+
split.by

 
Variable in meta.data to use for splitting layers.

 
 

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 # Split object by "treatment"
 obj <- Split_Layers(object = obj, assay = "RNA", split.by = "treatment")
-} # }
+}
 
 

     

@@ -163,15 +161,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Split_Vector.html b/docs/reference/Split_Vector.html
index b5197b6c2..7152afb36 100644
--- a/docs/reference/Split_Vector.html
+++ b/docs/reference/Split_Vector.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -127,29 +127,29 @@ 
Split vector into list

 
     

     
Arguments

-
-
-
x

+    
x

 
vector to split

 
 
-
chunk_size

+
chunk_size

 
size of chunks for vector to be split into, default is NULL.  Only valid if
 num_chunk is NULL.

 
 
-
num_chunk

+
num_chunk

 
number of chunks to split the vector into, default is NULL.  Only valid if
 chunk_size is NULL.

 
 
-
verbose

+
verbose

 
logical, print details of vector and split, default is FALSE.

 
 

     

     
Value

-    
list with vector of X length

+    
+
+
list with vector of X length

     

     

     
References

@@ -177,15 +177,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Stacked_VlnPlot.html b/docs/reference/Stacked_VlnPlot.html
index 834e37d84..b0c64b9ad 100644
--- a/docs/reference/Stacked_VlnPlot.html
+++ b/docs/reference/Stacked_VlnPlot.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -145,87 +145,87 @@ 
Stacked Violin Plot

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
features

+
features

 
Features to plot.

 
 
-
group.by

+
group.by

 
Group (color) cells in different ways (for example, orig.ident).

 
 
-
split.by

+
split.by

 
A variable to split the violin plots by,

 
 
-
idents

+
idents

 
Which classes to include in the plot (default is all).

 
 
-
x_lab_rotate

+
x_lab_rotate

 
logical or numeric.  If logical whether to rotate x-axis labels 45 degrees
 (Default is FALSE).  If numeric must be either 45 or 90.  Setting 45 is equivalent to setting TRUE.

 
 
-
plot_legend

+
plot_legend

 
logical.  Adds plot legend containing idents to the returned plot.

 
 
-
colors_use

+
colors_use

 
specify color palette to used in VlnPlot.  By default if
 number of levels plotted is less than or equal to 36 it will use "polychrome" and if greater than 36
 will use "varibow" with shuffle = TRUE both from DiscretePalette_scCustomize.

 
 
-
color_seed

+
color_seed

 
random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.

 
 
-
ggplot_default_colors

+
ggplot_default_colors

 
logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

 
 
-
plot_spacing

+
plot_spacing

 
Numerical value specifying the vertical spacing between each plot in the stack.
 Default is 0.15 ("cm").  Spacing dependent on unit provided to spacing_unit.

 
 
-
spacing_unit

+
spacing_unit

 
Unit to use in specifying vertical spacing between plots.  Default is "cm".

 
 
-
vln_linewidth

+
vln_linewidth

 
Adjust the linewidth of violin outline.  Must be numeric.

 
 
-
pt.size

+
pt.size

 
Adjust point size for plotting.  Default for Stacked_VlnPlot is 0 to avoid issues with
 rendering so many points in vector form.  Alternatively, see raster parameter.

 
 
-
raster

+
raster

 
Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 100,000 total points plotted (# Cells x # of features).

 
 
-
add.noise

+
add.noise

 
logical, determine if adding a small noise for plotting (Default is TRUE).

 
 
-
...

+
...

 
Extra parameters passed to VlnPlot.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

     

     
References

@@ -263,15 +263,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Store_Misc_Info_Seurat.html b/docs/reference/Store_Misc_Info_Seurat.html
index bbc074942..f27d8d649 100644
--- a/docs/reference/Store_Misc_Info_Seurat.html
+++ b/docs/reference/Store_Misc_Info_Seurat.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -134,39 +134,39 @@ 
Store misc data in Seurat object

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
object name.

 
 
-
data_to_store

+
data_to_store

 
data to be stored in @misc slot.  Can be single piece of data or list.
 If list of data see list_as_list parameter for control over data storage.

 
 
-
data_name

+
data_name

 
name to give the entry in @misc slot.  Must be of equal length of the number
 of data items being stored.

 
 
-
list_as_list

+
list_as_list

 
logical.  If data_to_store is a list, this dictates whether to store in @misc slot
 as list (TRUE) or whether to store each entry in the list separately (FALSE).  Default is FALSE.

 
 
-
overwrite

+
overwrite

 
Logical.  Whether to overwrite existing items with the same name.  Default is FALSE, meaning
 that function will abort if item with data_name is present in misc slot.

 
 
-
verbose

+
verbose

 
logical, whether to print messages when running function, default is TRUE.

 
 

     

     
Value

-    
Seurat Object with new entries in the @misc slot.

+    
+
+
Seurat Object with new entries in the @misc slot.

     

 
     

@@ -193,15 +193,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Store_Palette_Seurat.html b/docs/reference/Store_Palette_Seurat.html
index c4261cb22..75f463c37 100644
--- a/docs/reference/Store_Palette_Seurat.html
+++ b/docs/reference/Store_Palette_Seurat.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -134,39 +134,39 @@ 
Store color palette in Seurat object

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
object name.

 
 
-
palette

+
palette

 
vector or list of vectors containing color palettes to store.  If list of palettes
 see list_as_list parameter for control over data storage.

 
 
-
palette_name

+
palette_name

 
name to give the palette(s) in @misc slot.  Must be of equal length to the number
 of data items being stored.

 
 
-
list_as_list

+
list_as_list

 
logical.  If data_to_store is a list, this dictates whether to store in @misc slot
 as list (TRUE) or whether to store each entry in the list separately (FALSE).  Default is FALSE.

 
 
-
overwrite

+
overwrite

 
Logical.  Whether to overwrite existing items with the same name.  Default is FALSE, meaning
 that function will abort if item with data_name is present in misc slot.

 
 
-
verbose

+
verbose

 
logical, whether to print messages when running function, default is TRUE.

 
 

     

     
Value

-    
Seurat Object with new entries in the @misc slot.

+    
+
+
Seurat Object with new entries in the @misc slot.

     

 
     

@@ -193,15 +193,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Subset_LIGER.html b/docs/reference/Subset_LIGER.html
index 2c2131a9f..006cec4f7 100644
--- a/docs/reference/Subset_LIGER.html
+++ b/docs/reference/Subset_LIGER.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -134,40 +134,40 @@ 
Subset LIGER object

 
     

     
Arguments

-
-
-
liger_object

+    
liger_object

 
LIGER object name.

 
 
-
cluster

+
cluster

 
Name(s) of cluster to subset from object.

 
 
-
cluster_col

+
cluster_col

 
name of @cellMeta column containing cluster names, default is "leiden_cluster".

 
 
-
ident

+
ident

 
variable within ident_col to use in sub-setting object.

 
 
-
ident_col

+
ident_col

 
column in @cellMeta that contains values provided to ident.

 
 
-
invert

+
invert

 
logical, whether to subset the inverse of the clusters or idents provided, default is FALSE.

 
 

     

     
Value

-    
liger object

+    
+
+
liger object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 # subset clusters 3 and 5
 sub_liger <- subset_liger(liger_object = liger_object, cluster = c(3, 5))
 
@@ -181,7 +181,7 @@ 
Examples

 
 # Remove cluster 9
 sub_liger <- subset_liger(liger_object = liger_object, cluster = 9, invert = TRUE)
-} # }
+}
 
 

     

@@ -197,15 +197,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Top_Genes_Factor.html b/docs/reference/Top_Genes_Factor.html
index 59b833377..642f2c108 100644
--- a/docs/reference/Top_Genes_Factor.html
+++ b/docs/reference/Top_Genes_Factor.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -127,30 +127,30 @@ 
Extract top loading genes for LIGER factor

 
     

     
Arguments

-
-
-
liger_object

+    
liger_object

 
LIGER object name.

 
 
-
liger_factor

+
liger_factor

 
LIGER factor number to pull genes from.

 
 
-
num_genes

+
num_genes

 
number of top loading genes to return as vector.

 
 

     

     
Value

-    
A LIGER Object

+    
+
+
A LIGER Object

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 top_genes_factor10 <- Top_Genes_Factor(liger_object = object, num_genes = 10)
-} # }
+}
 
 

     

@@ -166,15 +166,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/UnRotate_X.html b/docs/reference/UnRotate_X.html
index 3c569f37a..e7a57e106 100644
--- a/docs/reference/UnRotate_X.html
+++ b/docs/reference/UnRotate_X.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -127,15 +127,15 @@ 
Unrotate x axis on VlnPlot

 
     

     
Arguments

-
-
-
...

+    
...

 
extra arguments passed to ggplot2::theme().

 
 

     

     
Value

-    
Returns a list-like object of class theme.

+    
+
+
Returns a list-like object of class theme.

     

 
     

@@ -159,15 +159,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Updated_HGNC_Symbols.html b/docs/reference/Updated_HGNC_Symbols.html
index 2a1cf013f..784c10c66 100644
--- a/docs/reference/Updated_HGNC_Symbols.html
+++ b/docs/reference/Updated_HGNC_Symbols.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -132,9 +132,7 @@ 
Update HGNC Gene Symbols

 
     

     
Arguments

-
-
-
input_data

+    
input_data

 
Data source containing gene names.  Accepted formats are:
  • charcter vector
    • 
 
  • Seurat Objects
    • 
 
  • data.frame: genes as rownames
    • 
@@ -143,34 +141,36 @@ 
    Arguments
    
 

 
 
-
update_symbol_data

+
update_symbol_data

 
logical, whether to update cached HGNC data, default is NULL.
 If NULL BiocFileCache will check and prompt for update if cache is stale.
 If FALSE the BiocFileCache stale check will be skipped and current cache will be used.
 If TRUE the BiocFileCache stale check will be skipped and HGNC data will be downloaded.

 
 
-
case_check_as_warn

+
case_check_as_warn

 
logical, whether case checking of features should cause abort or
 only warn, default is FALSE (abort).  Set to TRUE if atypical names (i.e. old LOC naming) are
 present in input_data.

 
 
-
verbose

+
verbose

 
logical, whether to print results detailing numbers of symbols, found, updated,
 and not found; default is TRUE.

 
 

     

     
Value

-    
data.frame containing columns: input_features, Approved_Symbol (already approved; output unchanged), Not_Found_Symbol (symbol not in HGNC; output unchanged), Updated_Symbol (new symbol from HGNC; output updated).

+    
+
+
data.frame containing columns: input_features, Approved_Symbol (already approved; output unchanged), Not_Found_Symbol (symbol not in HGNC; output unchanged), Updated_Symbol (new symbol from HGNC; output updated).

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 new_names <- Updated_HGNC_Symbols(input_data = Seurat_Object)
-} # }
+}
 
 

     

@@ -186,15 +186,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Updated_MGI_Symbols.html b/docs/reference/Updated_MGI_Symbols.html
index 16d38c03c..a82aff87b 100644
--- a/docs/reference/Updated_MGI_Symbols.html
+++ b/docs/reference/Updated_MGI_Symbols.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -127,9 +127,7 @@ 
Update MGI Gene Symbols

 
     

     
Arguments

-
-
-
input_data

+    
input_data

 
Data source containing gene names.  Accepted formats are:
  • charcter vector
    • 
 
  • Seurat Objects
    • 
 
  • data.frame: genes as rownames
    • 
@@ -138,28 +136,30 @@ 
    Arguments
    
 

 
 
-
update_symbol_data

+
update_symbol_data

 
logical, whether to update cached MGI data, default is NULL.
 If NULL BiocFileCache will check and prompt for update if cache is stale.
 If FALSE the BiocFileCache stale check will be skipped and current cache will be used.
 If TRUE the BiocFileCache stale check will be skipped and MGI data will be downloaded.

 
 
-
verbose

+
verbose

 
logical, whether to print results detailing numbers of symbols, found, updated,
 and not found; default is TRUE.

 
 

     

     
Value

-    
data.frame containing columns: input_features, Approved_Symbol (already approved; output unchanged), Not_Found_Symbol (symbol not in MGI; output unchanged), Updated_Symbol (new symbol from MGI; output updated).

+    
+
+
data.frame containing columns: input_features, Approved_Symbol (already approved; output unchanged), Not_Found_Symbol (symbol not in MGI; output unchanged), Updated_Symbol (new symbol from MGI; output updated).

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 new_names <- Updated_MGI_Symbols(input_data = Seurat_Object)
-} # }
+}
 
 

     

@@ -175,15 +175,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/VariableFeaturePlot_scCustom.html b/docs/reference/VariableFeaturePlot_scCustom.html
index bffca73f2..feaaec538 100644
--- a/docs/reference/VariableFeaturePlot_scCustom.html
+++ b/docs/reference/VariableFeaturePlot_scCustom.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -139,58 +139,58 @@ 
Custom Labeled Variable Features Plot

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
num_features

+
num_features

 
Number of top variable features to highlight by color/label.

 
 
-
custom_features

+
custom_features

 
A vector of custom feature names to label on plot instead of labeling top
 variable genes.

 
 
-
label

+
label

 
logical. Whether to label the top features.  Default is TRUE.

 
 
-
pt.size

+
pt.size

 
Adjust point size for plotting.

 
 
-
colors_use

+
colors_use

 
colors to use for plotting.  Default is "black" and "red".

 
 
-
repel

+
repel

 
logical (default TRUE).  Whether or not to repel the feature labels on plot.

 
 
-
y_axis_log

+
y_axis_log

 
logical. Whether to change y axis to log10 scale (Default is FALSE).

 
 
-
assay

+
assay

 
Assay to pull variable features from.

 
 
-
selection.method

+
selection.method

 
If more then one method use to calculate variable features specify which
 method to use for plotting.  See selection.method parameter in VariableFeaturePlot
 for list of options.

 
 
-
...

+
...

 
Extra parameters passed to VariableFeaturePlot.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

 
     

@@ -214,15 +214,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/Variable_Features_ALL_LIGER.html b/docs/reference/Variable_Features_ALL_LIGER.html
index d17192135..176f398dd 100644
--- a/docs/reference/Variable_Features_ALL_LIGER.html
+++ b/docs/reference/Variable_Features_ALL_LIGER.html
@@ -4,7 +4,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -138,49 +138,49 @@ 
Perform variable gene selection over whole dataset

 
     

     
Arguments

-
-
-
liger_object

+    
liger_object

 
LIGER object name.

 
 
-
num_genes

+
num_genes

 
Number of genes to find. Optimizes the value of var.thresh  to get
 this number of genes, (Default is NULL).

 
 
-
var.thresh

+
var.thresh

 
Variance threshold. Main threshold used to identify variable genes.
 Genes with expression variance greater than threshold (relative to mean) are selected.
 (higher threshold -> fewer selected genes).

 
 
-
alpha.thresh

+
alpha.thresh

 
Alpha threshold. Controls upper bound for expected mean gene
 expression (lower threshold -> higher upper bound). (default 0.99)

 
 
-
tol

+
tol

 
Tolerance to use for optimization if num.genes values passed in (default 0.0001).
 Only applicable for rliger < 2.0.0.

 
 
-
do.plot

+
do.plot

 
Display log plot of gene variance vs. gene expression. Selected genes are
 plotted in green. (Default FALSE)

 
 
-
pt.size

+
pt.size

 
Point size for plot.

 
 
-
chunk

+
chunk

 
size of chunks in hdf5 file. (Default 1000)

 
 

     

     
Value

-    
A LIGER Object with variable genes in correct slot.

+    
+
+
A LIGER Object with variable genes in correct slot.

     

     

     
References

@@ -191,9 +191,9 @@ 
References

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 liger_obj <- Variable_Features_ALL_LIGER(liger_object = liger_obj, num_genes = 2000)
-} # }
+}
 
 

     

@@ -209,15 +209,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/VlnPlot_scCustom.html b/docs/reference/VlnPlot_scCustom.html
index ddb49acb0..f31ac5938 100644
--- a/docs/reference/VlnPlot_scCustom.html
+++ b/docs/reference/VlnPlot_scCustom.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -144,81 +144,81 @@ 
VlnPlot with modified default settings

 
     

     
Arguments

-
-
-
seurat_object

+    
seurat_object

 
Seurat object name.

 
 
-
features

+
features

 
Feature(s) to plot.

 
 
-
colors_use

+
colors_use

 
color palette to use for plotting.  By default if number of levels plotted is less than
 or equal to 36 it will use "polychrome" and if greater than 36 will use "varibow" with shuffle = TRUE
 both from DiscretePalette_scCustomize.

 
 
-
pt.size

+
pt.size

 
Adjust point size for plotting.

 
 
-
group.by

+
group.by

 
Name of one or more metadata columns to group (color) cells by (for example, orig.ident);
 default is the current active.ident of the object.

 
 
-
split.by

+
split.by

 
Feature to split plots by (i.e. "orig.ident").

 
 
-
plot_median

+
plot_median

 
logical, whether to plot median for each ident on the plot (Default is FALSE).

 
 
-
plot_boxplot

+
plot_boxplot

 
logical, whether to plot boxplot inside of violin (Default is FALSE).

 
 
-
median_size

+
median_size

 
Shape size for the median is plotted.

 
 
-
idents

+
idents

 
Which classes to include in the plot (default is all).

 
 
-
num_columns

+
num_columns

 
Number of columns in plot layout.  Only valid if split.by != NULL.

 
 
-
raster

+
raster

 
Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 100,000 total points plotted (# Cells x # of features).

 
 
-
add.noise

+
add.noise

 
logical, determine if adding a small noise for plotting (Default is TRUE).

 
 
-
ggplot_default_colors

+
ggplot_default_colors

 
logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.

 
 
-
color_seed

+
color_seed

 
random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.

 
 
-
...

+
...

 
Extra parameters passed to VlnPlot.

 
 

     

     
Value

-    
A ggplot object

+    
+
+
A ggplot object

     

     

     
References

@@ -246,15 +246,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/WhichCells.html b/docs/reference/WhichCells.html
index 2b5f1f9a2..790e5e999 100644
--- a/docs/reference/WhichCells.html
+++ b/docs/reference/WhichCells.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -122,7 +122,7 @@ 
Extract Cells for particular identity

     

 
     

-    
# S3 method for class 'liger'
+    
# S3 method for liger
 WhichCells(
   object,
   idents = NULL,
@@ -135,48 +135,48 @@ 
Extract Cells for particular identity

 
     

     
Arguments

-
-
-
object

+    
object

 
LIGER object name.

 
 
-
idents

+
idents

 
identities to extract cell barcodes.

 
 
-
ident_col

+
ident_col

 
name of meta data column to use when subsetting cells by identity values.
 Default is NULL, which will use the objects default clustering as the ident_col.

 
 
-
by_dataset

+
by_dataset

 
logical, whether to return vector with cell barcodes for all idents in or
 to return list (1 entry per dataset with vector of cells) (default is FALSE; return vector).

 
 
-
invert

+
invert

 
logical, invert the selection of cells (default is FALSE).

 
 
-
...

+
...

 
Arguments passed to other methods

 
 

     

     
Value

-    
vector or list depending on by_dataset parameter

+    
+
+
vector or list depending on by_dataset parameter

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 # Extract cells from ident =1 in current default clustering
 ident1_cells <- WhichCells(object = liger_object, idents = 1)
 
 # Extract all cells from "stim" treatment from object
 stim_cells <- WhichCells(object = liger_object, idents = "stim", ident_col = "Treatment")
-} # }
+}
 
 

     

@@ -192,15 +192,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/as.LIGER.html b/docs/reference/as.LIGER.html
index c6f9c4cfb..627fcd20b 100644
--- a/docs/reference/as.LIGER.html
+++ b/docs/reference/as.LIGER.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -124,7 +124,7 @@ 
Convert objects to LIGER objects

     

     
as.LIGER(x, ...)
 
-# S3 method for class 'Seurat'
+# S3 method for Seurat
 as.LIGER(
   x,
   group.by = "orig.ident",
@@ -140,7 +140,7 @@ 
Convert objects to LIGER objects

   ...
 )
 
-# S3 method for class 'list'
+# S3 method for list
 as.LIGER(
   x,
   group.by = "orig.ident",
@@ -158,71 +158,73 @@ 
Convert objects to LIGER objects

 
     

     
Arguments

-
-
-
x

+    
x

 
An object to convert to class liger

 
 
-
...

+
...

 
Arguments passed to other methods

 
 
-
group.by

+
group.by

 
Variable in meta data which contains variable to split data by, (default is "orig.ident").

 
 
-
layers_name

+
layers_name

 
name of meta.data column used to split layers if setting group.by = "layers".

 
 
-
assay

+
assay

 
Assay containing raw data to use, (default is "RNA").

 
 
-
remove_missing

+
remove_missing

 
logical, whether to remove missing genes with no counts when converting to
 LIGER object (default is FALSE).

 
 
-
renormalize

+
renormalize

 
logical, whether to perform normalization after LIGER object creation (default is TRUE).

 
 
-
use_seurat_var_genes

+
use_seurat_var_genes

 
logical, whether to transfer variable features from Seurat object to
 new LIGER object (default is FALSE).

 
 
-
use_seurat_dimreduc

+
use_seurat_dimreduc

 
logical, whether to transfer dimensionality reduction coordinates from
 Seurat to new LIGER object (default is FALSE).

 
 
-
reduction

+
reduction

 
Name of Seurat reduction to transfer if use_seurat_dimreduc = TRUE.

 
 
-
keep_meta

+
keep_meta

 
logical, whether to transfer columns in Seurat meta.data slot to LIGER cell.data
 slot (default is TRUE).

 
 
-
verbose

+
verbose

 
logical, whether to print status messages during object conversion (default is TRUE).

 
 
-
dataset_names

+
dataset_names

 
optional, vector of names to use for naming datasets.

 
 
-
var_genes_method

+
var_genes_method

 
how variable genes should be selected from Seurat objects if use_seurat_var_genes = TRUE.  Can be either "intersect" or "union", (default is "intersect").

 
 

     

     
Value

-    
a liger object generated from x

+    
+
+
a liger object generated from x

+
+
     

     

     
References

@@ -231,13 +233,13 @@ 
References

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 liger_object <- as.LIGER(x = seurat_object)
-} # }
+}
 
-if (FALSE) { # \dontrun{
+if (FALSE) {
 liger_object <- as.LIGER(x = seurat_object_list)
-} # }
+}
 
 

     

@@ -253,15 +255,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/as.Seurat.html b/docs/reference/as.Seurat.html
index 30278ef2c..173740365 100644
--- a/docs/reference/as.Seurat.html
+++ b/docs/reference/as.Seurat.html
@@ -5,7 +5,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -126,7 +126,7 @@ 
Convert objects to Seurat objects

     

 
     

-    
# S3 method for class 'liger'
+    
# S3 method for liger
 as.Seurat(
   x,
   nms = names(x@H),
@@ -146,72 +146,74 @@ 
Convert objects to Seurat objects

 
     

     
Arguments

-
-
-
x

+    
x

 
liger object.

 
 
-
nms

+
nms

 
By default, labels cell names with dataset of origin (this is to account for cells in
 different datasets which may have same name). Other names can be passed here as vector, must have
 same length as the number of datasets. (default names(H)).

 
 
-
renormalize

+
renormalize

 
Whether to log-normalize raw data using Seurat defaults (default TRUE).

 
 
-
use.liger.genes

+
use.liger.genes

 
Whether to carry over variable genes (default TRUE).

 
 
-
by.dataset

+
by.dataset

 
Include dataset of origin in cluster identity in Seurat object (default FALSE).

 
 
-
keep_meta

+
keep_meta

 
logical. Whether to transfer additional metadata (nGene/nUMI/dataset already transferred)
 to new Seurat Object.  Default is TRUE.

 
 
-
reduction_label

+
reduction_label

 
Name of dimensionality reduction technique used.  Enables accurate transfer
 or name to Seurat object instead of defaulting to "tSNE".

 
 
-
seurat_assay

+
seurat_assay

 
Name to set for assay in Seurat Object.  Default is "RNA".

 
 
-
assay_type

+
assay_type

 
what type of Seurat assay to create in new object (Assay vs Assay5).
 Default is NULL which will default to the current user settings.
 See Convert_Assay parameter convert_to for acceptable values.

 
 
-
add_barcode_names

+
add_barcode_names

 
logical, whether to add dataset names to the cell barcodes when
 creating Seurat object, default is FALSE.

 
 
-
barcode_prefix

+
barcode_prefix

 
logical, if add_barcode_names = TRUE should the names be added as
 prefix to current cell barcodes/names or a suffix (default is TRUE; prefix).

 
 
-
barcode_cell_id_delimiter

+
barcode_cell_id_delimiter

 
The delimiter to use when adding dataset id to barcode
 prefix/suffix.  Default is "_".

 
 
-
...

+
...

 
unused.

 
 

     

     
Value

-    
Seurat object with raw.data, scale.data, reduction_label, iNMF, and ident slots set.

+    
+
+
Seurat object with raw.data, scale.data, reduction_label, iNMF, and ident slots set.

+
+
 
Seurat object.

     

     

@@ -227,9 +229,9 @@ 
References

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 seurat_object <- as.Seurat(x = liger_object)
-} # }
+}
 
 

     

@@ -245,15 +247,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/as.anndata.html b/docs/reference/as.anndata.html
index 12d33a49a..8f07db1f4 100644
--- a/docs/reference/as.anndata.html
+++ b/docs/reference/as.anndata.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -124,7 +124,7 @@ 
Convert objects to anndata objects

     

     
as.anndata(x, ...)
 
-# S3 method for class 'Seurat'
+# S3 method for Seurat
 as.anndata(
   x,
   file_path,
@@ -137,7 +137,7 @@ 
Convert objects to anndata objects

   ...
 )
 
-# S3 method for class 'liger'
+# S3 method for liger
 as.anndata(
   x,
   file_path,
@@ -154,73 +154,73 @@ 
Convert objects to anndata objects

 
     

     
Arguments

-
-
-
x

+    
x

 
Seurat or LIGER object

 
 
-
...

+
...

 
Arguments passed to other methods

 
 
-
file_path

+
file_path

 
directory file path and/or file name prefix.  Defaults to current wd.

 
 
-
file_name

+
file_name

 
file name.

 
 
-
assay

+
assay

 
Assay containing data to use, (default is object default assay).

 
 
-
main_layer

+
main_layer

 
the layer of data to become default layer in anndata object (default is "data").

 
 
-
other_layers

+
other_layers

 
other data layers to transfer to anndata object (default is "counts").

 
 
-
transer_dimreduc

+
transer_dimreduc

 
logical, whether to transfer dimensionality reduction coordinates from
 Seurat to anndata object (default is TRUE).

 
 
-
verbose

+
verbose

 
logical, whether to print status messages during object conversion (default is TRUE).

 
 
-
transfer_norm.data

+
transfer_norm.data

 
logical, whether to transfer the norm.data in addition to
 raw.data, default is FALSE.

 
 
-
reduction_label

+
reduction_label

 
What to label the visualization dimensionality reduction.
 LIGER does not store name of technique and therefore needs to be set manually.

 
 
-
add_barcode_names

+
add_barcode_names

 
logical, whether to add dataset names to the cell barcodes when
 merging object data, default is FALSE.

 
 
-
barcode_prefix

+
barcode_prefix

 
logical, if add_barcode_names = TRUE should the names be added as
 prefix to current cell barcodes/names or a suffix (default is TRUE; prefix).

 
 
-
barcode_cell_id_delimiter

+
barcode_cell_id_delimiter

 
The delimiter to use when adding dataset id to barcode
 prefix/suffix.  Default is "_".

 
 

     

     
Value

-    
an anndata object generated from x, saved at path provided.

+    
+
+
an anndata object generated from x, saved at path provided.

     

     

     
References

@@ -230,13 +230,13 @@ 
References

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 as.anndata(x = seurat_object, file_path = "/folder_name", file_name = "anndata_converted.h5ad")
-} # }
+}
 
-if (FALSE) { # \dontrun{
+if (FALSE) {
 as.anndata(x = liger_object, file_path = "/folder_name", file_name = "anndata_converted.h5ad")
-} # }
+}
 
 

     

@@ -252,15 +252,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/deprecated.html b/docs/reference/deprecated.html
index de93ab6e3..963690149 100644
--- a/docs/reference/deprecated.html
+++ b/docs/reference/deprecated.html
@@ -10,7 +10,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -166,15 +166,15 @@ 
Deprecated functions 
-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/ensembl_hemo_id.html b/docs/reference/ensembl_hemo_id.html
index 4172941ac..f99739031 100644
--- a/docs/reference/ensembl_hemo_id.html
+++ b/docs/reference/ensembl_hemo_id.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -167,15 +167,15 @@ 
Source

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/ensembl_ieg_list.html b/docs/reference/ensembl_ieg_list.html
index 455e5ac47..25f2ab32c 100644
--- a/docs/reference/ensembl_ieg_list.html
+++ b/docs/reference/ensembl_ieg_list.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -156,15 +156,15 @@ 
Source

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/ensembl_mito_id.html b/docs/reference/ensembl_mito_id.html
index 3d55a4183..3140c39b6 100644
--- a/docs/reference/ensembl_mito_id.html
+++ b/docs/reference/ensembl_mito_id.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -167,15 +167,15 @@ 
Source

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/ensembl_ribo_id.html b/docs/reference/ensembl_ribo_id.html
index acd85eac7..a3962a92d 100644
--- a/docs/reference/ensembl_ribo_id.html
+++ b/docs/reference/ensembl_ribo_id.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -170,15 +170,15 @@ 
Source

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/ieg_gene_list.html b/docs/reference/ieg_gene_list.html
index 96c111215..bb5cbd098 100644
--- a/docs/reference/ieg_gene_list.html
+++ b/docs/reference/ieg_gene_list.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -156,15 +156,15 @@ 
Source

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 2ebea5584..bfb3409e3 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -1,9 +1,9 @@
 
-Package index • scCustomizeFunction reference • scCustomize
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -860,15 +860,15 @@ 
Data 

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/msigdb_qc_ensembl_list.html b/docs/reference/msigdb_qc_ensembl_list.html
index c6587b496..c1602bcef 100644
--- a/docs/reference/msigdb_qc_ensembl_list.html
+++ b/docs/reference/msigdb_qc_ensembl_list.html
@@ -5,7 +5,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -213,15 +213,15 @@ 
Source

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/msigdb_qc_gene_list.html b/docs/reference/msigdb_qc_gene_list.html
index 3be6e387a..d7c1d367d 100644
--- a/docs/reference/msigdb_qc_gene_list.html
+++ b/docs/reference/msigdb_qc_gene_list.html
@@ -4,7 +4,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -211,15 +211,15 @@ 
Source

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/plotFactors_scCustom.html b/docs/reference/plotFactors_scCustom.html
index 3658aa909..24fe10cef 100644
--- a/docs/reference/plotFactors_scCustom.html
+++ b/docs/reference/plotFactors_scCustom.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -149,106 +149,106 @@ 
Customized version of plotFactors

 
     

     
Arguments

-
-
-
liger_object

+    
liger_object

 
liger liger_object.  Need to perform clustering and factorization before calling this function

 
 
-
num_genes

+
num_genes

 
Number of genes to display for each factor (Default 8).

 
 
-
colors_use_factors

+
colors_use_factors

 
colors to use for plotting factor loadings  By default datasets will be
 plotted using "varibow" with shuffle = TRUE from both from DiscretePalette_scCustomize.

 
 
-
colors_use_dimreduc

+
colors_use_dimreduc

 
colors to use for plotting factor loadings on dimensionality reduction
 coordinates (tSNE/UMAP).  Default is c('lemonchiffon', 'red'),

 
 
-
pt.size_factors

+
pt.size_factors

 
Adjust point size for plotting in the factor plots.

 
 
-
pt.size_dimreduc

+
pt.size_dimreduc

 
Adjust point size for plotting in dimensionality reduction plots.

 
 
-
reduction

+
reduction

 
Name of dimensionality reduction to use for plotting.  Default is "UMAP".
 Only for newer style liger objects.

 
 
-
reduction_label

+
reduction_label

 
What to label the x and y axes of resulting plots.  LIGER does not store name of
 technique and therefore needs to be set manually.  Default is "UMAP".
 Only for older style liger objects.

 
 
-
plot_legend

+
plot_legend

 
logical, whether to plot the legend on factor loading plots, default is TRUE.
 Helpful if number of datasets is large to avoid crowding the plot with legend.

 
 
-
raster

+
raster

 
Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 200,000 cells.

 
 
-
raster.dpi

+
raster.dpi

 
Pixel resolution for rasterized plots, passed to geom_scattermore().
 Default is c(512, 512).

 
 
-
order

+
order

 
logical. Whether to plot higher loading cells on top of cells with lower loading values in the
 dimensionality reduction plots (Default = FALSE).

 
 
-
plot_dimreduc

+
plot_dimreduc

 
logical.  Whether to plot factor loadings on dimensionality reduction coordinates.  Default is TRUE.

 
 
-
save_plots

+
save_plots

 
logical.  Whether to save plots.  Default is TRUE

 
 
-
file_path

+
file_path

 
directory file path and/or file name prefix.  Defaults to current wd.

 
 
-
file_name

+
file_name

 
name suffix to append after sample name.

 
 
-
return_plots

+
return_plots

 
logical. Whether or not to return plots to the environment.  (Default is FALSE)

 
 
-
cells.highlight

+
cells.highlight

 
Names of specific cells to highlight in plot (black) (default NULL).

 
 
-
reorder_datasets

+
reorder_datasets

 
New order to plot datasets in for the factor plots if different from current
 factor level order in cell.data slot. Only for older style liger objects.

 
 
-
ggplot_default_colors

+
ggplot_default_colors

 
logical.  If colors_use_factors = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "varibow" palette.

 
 
-
color_seed

+
color_seed

 
random seed for the palette shuffle if colors_use_factors = NULL.  Default = 123.

 
 

     

     
Value

-    
A list of ggplot/patchwork objects and/or PDF file.

+    
+
+
A list of ggplot/patchwork objects and/or PDF file.

     

     

     
References

@@ -261,10 +261,10 @@ 
Author

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 plotFactors_scCustom(liger_object = liger_obj, return_plots = FALSE, plot_dimreduc = TRUE,
 raster = FALSE, save_plots = TRUE)
-} # }
+}
 
 

     

@@ -280,15 +280,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index 7a256757d..9a001a1e0 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -10,7 +10,7 @@
 
 
 
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+    
 
     

       

   

 

 
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+      
 
       

   

@@ -157,15 +157,15 @@ 
Note

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/scCustomize-package.html b/docs/reference/scCustomize-package.html
index 0810cdcdc..02fd2faaf 100644
--- a/docs/reference/scCustomize-package.html
+++ b/docs/reference/scCustomize-package.html
@@ -4,7 +4,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -126,7 +126,7 @@ 
scCustomize: Custom Visualizations & Functions for Streamlined Analyses
 
     

     
Package options

-
+    
 
 
 
scCustomize uses the following options() to configure behavior:

@@ -199,15 +199,15 @@ 
Author

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/scCustomize_Palette.html b/docs/reference/scCustomize_Palette.html
index f1aa9fdfd..a4277ffc0 100644
--- a/docs/reference/scCustomize_Palette.html
+++ b/docs/reference/scCustomize_Palette.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -131,26 +131,26 @@ 
Color Palette Selection for scCustomize

 
     

     
Arguments

-
-
-
num_groups

+    
num_groups

 
number of groups to be plotted. If ggplot_default_colors = FALSE then by default:
  • If number of levels plotted equal to 2 then colors will be NavyAndOrange().
    • 
 
  • If number of levels plotted greater than 2 but less than or equal to 36 it will use "polychrome" from DiscretePalette_scCustomize().
    • 
 
  • If greater than 36 will use "varibow" with shuffle = TRUE from DiscretePalette_scCustomize.
    • 
 

 
 
-
ggplot_default_colors

+
ggplot_default_colors

 
logical.  Whether to use default ggplot hue palette or not.

 
 
-
color_seed

+
color_seed

 
random seed to use for shuffling the "varibow" palette.

 
 

     

     
Value

-    
vector of colors to use for plotting.

+    
+
+
vector of colors to use for plotting.

     

 
     

@@ -173,15 +173,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/seq_zeros.html b/docs/reference/seq_zeros.html
index 5292f0b96..057574dfb 100644
--- a/docs/reference/seq_zeros.html
+++ b/docs/reference/seq_zeros.html
@@ -4,7 +4,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -129,21 +129,21 @@ 
Create sequence with zeros

 
     

     
Arguments

-
-
-
seq_length

+    
seq_length

 
a seqeunce or numbers of numbers to create sequence.
 Users can provide sequence (1:XX) or number of values to add in sequence (will
 be used as second number in seq_len; 1:XX).

 
 
-
num_zeros

+
num_zeros

 
number of zeros to prefix sequence, default is  (e.g, 01, 02, 03, ...)

 
 

     

     
Value

-    
vector of numbers in sequence

+    
+
+
vector of numbers in sequence

     

     

     
References

@@ -183,15 +183,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/theme_ggprism_mod.html b/docs/reference/theme_ggprism_mod.html
index 1511397ce..a7d36bb26 100644
--- a/docs/reference/theme_ggprism_mod.html
+++ b/docs/reference/theme_ggprism_mod.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -136,46 +136,46 @@ 
Modified ggprism theme

 
     

     
Arguments

-
-
-
palette

+    
palette

 
string. Palette name, use
 names(ggprism_data$themes) to show all valid palette names.

 
 
-
base_size

+
base_size

 
numeric. Base font size, given in "pt".

 
 
-
base_family

+
base_family

 
string. Base font family, default is "sans".

 
 
-
base_fontface

+
base_fontface

 
string. Base font face, default is "bold".

 
 
-
base_line_size

+
base_line_size

 
numeric. Base linewidth for line elements

 
 
-
base_rect_size

+
base_rect_size

 
numeric. Base linewidth for rect elements

 
 
-
axis_text_angle

+
axis_text_angle

 
integer. Angle of axis text in degrees.
 One of: 0, 45, 90, 270.

 
 
-
border

+
border

 
logical. Should a border be drawn around the plot?
 Clipping will occur unless e.g. coord_cartesian(clip = "off") is used.

 
 

     

     
Value

-    
Returns a list-like object of class theme.

+    
+
+
Returns a list-like object of class theme.

     

     

     
References

@@ -208,15 +208,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/reference/viridis_shortcut.html b/docs/reference/viridis_shortcut.html
index 4745ce1b3..2f556e0c6 100644
--- a/docs/reference/viridis_shortcut.html
+++ b/docs/reference/viridis_shortcut.html
@@ -3,7 +3,7 @@
 
 
 
-
+    
 
     

       

   

 

 
-
+      
 
       

   

@@ -152,15 +152,17 @@ 
Format

     

     

     
Value

-    
A color palette for plotting

+    
+
+
A color palette for plotting

     

 
     

     
Examples

-    
if (FALSE) { # \dontrun{
+    
if (FALSE) {
 FeaturePlot_scCustom(object = seurat_object, features = "Cx3cr1",
 colors_use = viridis_plasma_dark_high, na_color = "lightgray")
-} # }
+}
 
 

     

@@ -176,15 +178,15 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.1.0.

+  
Site built with pkgdown 2.0.9.

 

 
       

 
+  
 
 
-
-
+  
 
   
 
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index 2a88cf2e9..1a058f808 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -1,191 +1,720 @@
-
-https://samuel-marsh.github.io/scCustomize/404.html
-https://samuel-marsh.github.io/scCustomize/LICENSE.html
-https://samuel-marsh.github.io/scCustomize/articles/Cell_Bender_Functions.html
-https://samuel-marsh.github.io/scCustomize/articles/Color_Palettes.html
-https://samuel-marsh.github.io/scCustomize/articles/FAQ.html
-https://samuel-marsh.github.io/scCustomize/articles/Gene_Expression_Plotting.html
-https://samuel-marsh.github.io/scCustomize/articles/Helpers_and_Utilities.html
-https://samuel-marsh.github.io/scCustomize/articles/Installation.html
-https://samuel-marsh.github.io/scCustomize/articles/Iterative_Plotting.html
-https://samuel-marsh.github.io/scCustomize/articles/LIGER_Functions.html
-https://samuel-marsh.github.io/scCustomize/articles/Markers_and_Cluster_Annotation.html
-https://samuel-marsh.github.io/scCustomize/articles/Misc_Functions.html
-https://samuel-marsh.github.io/scCustomize/articles/Object_Conversion.html
-https://samuel-marsh.github.io/scCustomize/articles/Object_QC_Functions.html
-https://samuel-marsh.github.io/scCustomize/articles/QC_Plots.html
-https://samuel-marsh.github.io/scCustomize/articles/Read_and_Write_Functions.html
-https://samuel-marsh.github.io/scCustomize/articles/Sequencing_QC_Plots.html
-https://samuel-marsh.github.io/scCustomize/articles/Spatial_Plotting.html
-https://samuel-marsh.github.io/scCustomize/articles/Statistics.html
-https://samuel-marsh.github.io/scCustomize/articles/Update_Gene_Symbols.html
-https://samuel-marsh.github.io/scCustomize/articles/index.html
-https://samuel-marsh.github.io/scCustomize/authors.html
-https://samuel-marsh.github.io/scCustomize/index.html
-https://samuel-marsh.github.io/scCustomize/news/index.html
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-https://samuel-marsh.github.io/scCustomize/reference/Add_Cell_Complexity.html
-https://samuel-marsh.github.io/scCustomize/reference/Add_Cell_QC_Metrics.html
-https://samuel-marsh.github.io/scCustomize/reference/Add_Hemo.html
-https://samuel-marsh.github.io/scCustomize/reference/Add_Mito_Ribo.html
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-https://samuel-marsh.github.io/scCustomize/reference/Barcode_Plot.html
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-https://samuel-marsh.github.io/scCustomize/reference/Seq_QC_Plot_Saturation.html
-https://samuel-marsh.github.io/scCustomize/reference/Seq_QC_Plot_Total_Genes.html
-https://samuel-marsh.github.io/scCustomize/reference/Seq_QC_Plot_Transcriptome.html
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+    https://samuel-marsh.github.io/scCustomize/reference/Seq_QC_Plot_Reads_in_Cells.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/Seq_QC_Plot_Reads_per_Cell.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/Seq_QC_Plot_Saturation.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/Seq_QC_Plot_Total_Genes.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/Seq_QC_Plot_Transcriptome.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/Seq_QC_Plot_UMIs.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/Setup_scRNAseq_Project.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/Single_Color_Palette.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/SpatialDimPlot_scCustom.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/Split_FeatureScatter.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/Split_Layers.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/Split_Vector.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/Stacked_VlnPlot.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/Store_Misc_Info_Seurat.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/Store_Palette_Seurat.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/Subset_LIGER.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/Top_Genes_Factor.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/UnRotate_X.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/Updated_HGNC_Symbols.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/Updated_MGI_Symbols.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/VariableFeaturePlot_scCustom.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/Variable_Features_ALL_LIGER.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/VlnPlot_scCustom.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/WhichCells.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/as.LIGER.Seurat.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/as.LIGER.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/as.LIGER.list.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/as.Seurat.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/as.anndata.Seurat.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/as.anndata.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/as.anndata.liger.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/deprecated.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/ensembl_hemo_id.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/ensembl_ieg_list.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/ensembl_mito_id.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/ensembl_ribo_id.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/ieg_gene_list.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/index.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/msigdb_qc_ensembl_list.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/msigdb_qc_gene_list.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/plotFactors_scCustom.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/reexports.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/scCustomize-package.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/scCustomize.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/scCustomize_Palette.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/seq_zeros.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/theme_ggprism_mod.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/viridis_dark_high.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/viridis_inferno_dark_high.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/viridis_inferno_light_high.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/viridis_light_high.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/viridis_magma_dark_high.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/viridis_magma_light_high.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/viridis_plasma_light_high.html
+  
+  
+    https://samuel-marsh.github.io/scCustomize/reference/viridis_shortcut.html
+  
 
-
diff --git a/inst/pkgdown.yml b/inst/pkgdown.yml
index 52153f2c1..0ffa5e706 100644
--- a/inst/pkgdown.yml
+++ b/inst/pkgdown.yml
@@ -1,26 +1,27 @@
 pandoc: '3.2'
-pkgdown: 2.1.0
+pkgdown: 2.0.9
 pkgdown_sha: ~
 articles:
-  articles/Cell_Bender_Functions: Cell_Bender_Functions.html
-  articles/Color_Palettes: Color_Palettes.html
-  articles/FAQ: FAQ.html
-  articles/Gene_Expression_Plotting: Gene_Expression_Plotting.html
-  articles/Helpers_and_Utilities: Helpers_and_Utilities.html
-  articles/Installation: Installation.html
-  articles/Iterative_Plotting: Iterative_Plotting.html
-  articles/LIGER_Functions: LIGER_Functions.html
-  articles/Markers_and_Cluster_Annotation: Markers_and_Cluster_Annotation.html
-  articles/Misc_Functions: Misc_Functions.html
-  articles/Object_Conversion: Object_Conversion.html
-  articles/Object_QC_Functions: Object_QC_Functions.html
-  articles/QC_Plots: QC_Plots.html
-  articles/Read_and_Write_Functions: Read_and_Write_Functions.html
-  articles/Sequencing_QC_Plots: Sequencing_QC_Plots.html
-  articles/Spatial_Plotting: Spatial_Plotting.html
-  articles/Statistics: Statistics.html
-  articles/Update_Gene_Symbols: Update_Gene_Symbols.html
-last_built: 2024-12-05T19:28Z
+  Cell_Bender_Functions: Cell_Bender_Functions.html
+  Color_Palettes: Color_Palettes.html
+  FAQ: FAQ.html
+  Gene_Expression_Plotting: Gene_Expression_Plotting.html
+  Helpers_and_Utilities: Helpers_and_Utilities.html
+  Installation: Installation.html
+  Iterative_Plotting: Iterative_Plotting.html
+  LIGER_Functions: LIGER_Functions.html
+  Markers_and_Cluster_Annotation: Markers_and_Cluster_Annotation.html
+  Misc_Functions: Misc_Functions.html
+  Object_Conversion: Object_Conversion.html
+  Object_QC_Functions: Object_QC_Functions.html
+  QC_Plots: QC_Plots.html
+  Read_and_Write_Functions: Read_and_Write_Functions.html
+  Sequencing_QC_Plots: Sequencing_QC_Plots.html
+  Spatial_Plotting: Spatial_Plotting.html
+  Statistics: Statistics.html
+  Update_Gene_Symbols: Update_Gene_Symbols.html
+last_built: 2024-12-06T15:33Z
 urls:
   reference: https://samuel-marsh.github.io/scCustomize/reference
   article: https://samuel-marsh.github.io/scCustomize/articles
+