diff --git a/.github/workflows/check-standard.yaml b/.github/workflows/check-standard.yaml index 1f2ff43..40b71af 100644 --- a/.github/workflows/check-standard.yaml +++ b/.github/workflows/check-standard.yaml @@ -23,12 +23,65 @@ jobs: - {os: ubuntu-latest, r: 'release'} env: - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - R_KEEP_PKG_SOURCE: yes - R_REMOTES_NO_ERRORS_FROM_WARNINGS: true - _R_CHECK_CRAN_INCOMING_REMOTE_: false - _R_CHECK_FORCE_SUGGESTS_: false - + # environment setting created by JEFWorks-Lab + # GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + # R_KEEP_PKG_SOURCE: yes + # R_REMOTES_NO_ERRORS_FROM_WARNINGS: true + # _R_CHECK_CRAN_INCOMING_REMOTE_: false + # _R_CHECK_FORCE_SUGGESTS_: false + + # Bioconductor recommended environment (https://contributions.bioconductor.org/general.html) + # https://www.rdocumentation.org/packages/base/versions/3.5.1/topics/Startup + # https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Checking-and-building-packages + # https://cran.r-project.org/doc/manuals/r-devel/R-ints.html#Tools + _R_CHECK_FORCE_SUGGESTS_: true + _R_CHECK_RD_LINE_WIDTHS_: true + _R_CHECK_EXECUTABLES_: false + _R_CHECK_EXECUTABLES_EXCLUSIONS_: false + _R_CHECK_FF_DUP_: true + _R_CHECK_VC_DIR_: true + _R_CHECK_PKG_SIZES_: true + _R_CHECK_PKG_SIZES_THRESHOLD_: 5 + _R_CHECK_REPLACING_IMPORTS_: true + _R_CHECK_TIMINGS_: "0" + _R_CHECK_INSTALL_DEPENDS_: true + _R_CHECK_SUGGESTS_ONLY_: true + _R_CHECK_NO_RECOMMENDED_: true + _R_CHECK_CODE_ASSIGN_TO_GLOBALENV_: true + _R_CHECK_CODE_ATTACH_: true + _R_CHECK_CODE_DATA_INTO_GLOBALENV_: true + _R_CHECK_DOT_FIRSTLIB_: true + _R_CHECK_DEPRECATED_DEFUNCT_: true + _R_CHECK_TOPLEVELFILES_: true + _R_CHECK_LIMIT_CORES_: true + _R_CHECK_CODE_USAGE_VIA_NAMESPACES_: true + _R_CHECK_S3_METHODS_NOT_REGISTERED_: true + _R_CHECK_OVERWRITE_REGISTERED_S3_METHODS_: true + _R_S3_METHOD_LOOKUP_BASEENV_AFTER_GLOBALENV_: true + _R_CHECK_TESTS_NLINES_: 20 + _R_CHECK_NATIVE_ROUTINE_REGISTRATION_: true + _R_CHECK_NO_STOP_ON_TEST_ERROR_: true + _R_CHECK_PRAGMAS_: true + _R_CHECK_COMPILATION_FLAGS_: true + _R_CHECK_R_DEPENDS_: "warn" + _R_CHECK_SERIALIZATION_: true + _R_CHECK_R_ON_PATH_: true + _R_CHECK_PACKAGES_USED_IN_TESTS_USE_SUBDIRS_: true + _R_CHECK_SHLIB_OPENMP_FLAGS_: true + _R_CHECK_CONNECTIONS_LEFT_OPEN_: true + _R_CHECK_FUTURE_FILE_TIMESTAMPS_: true + _R_CHECK_LENGTH_1_CONDITION_ : package:_R_CHECK_PACKAGE_NAME_ + _R_CHECK_LENGTH_1_LOGIC2_: package:_R_CHECK_PACKAGE_NAME_ + IS_BIOC_BUILD_MACHINE: true + _R_CHECK_NEWS_IN_PLAIN_TEXT_: true + R_DEFAULT_INTERNET_TIMEOUT: 600 + BIOCPARALLEL_WORKER_NUMBER: 4 + OMP_THREAD_LIMIT: 2 + OMP_NUM_THREADS: 2 + KMP_DEVICE_THREAD_LIMIT: 2 + KMP_TEAMS_THREAD_LIMIT: 2 + _R_COMPARE_LANG_OBJECTS: eqonly + steps: - uses: actions/checkout@v3 diff --git a/DESCRIPTION b/DESCRIPTION index 354d90c..e5cbccb 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -49,6 +49,7 @@ Imports: BiocParallel, ggplot2, Matrix, + methods, rearrr, sf, SpatialExperiment, diff --git a/docs/articles/formatting-SpatialExperiment-for-SEraster.html b/docs/articles/formatting-SpatialExperiment-for-SEraster.html index df479bd..52190ae 100644 --- a/docs/articles/formatting-SpatialExperiment-for-SEraster.html +++ b/docs/articles/formatting-SpatialExperiment-for-SEraster.html @@ -100,7 +100,8 @@

Formatting a Spatial mouse POA regions for various sexes, behavioral conditions, and bregma sections. The full dataset can be downloaded from Dryad. We only use the dataset for a bregma -0.29 slice from a female naive -animal (Animal ID = 1).

+animal (Animal ID = 1, Animal Sex = “Female”, Behavior = “Naive”, Bregma += “-0.29”).

Load libraries

@@ -179,29 +180,13 @@

Load libraries#> expand library(ggplot2) #> Warning: package 'ggplot2' was built under R version 4.3.2 -library(gridExtra) -#> -#> Attaching package: 'gridExtra' -#> The following object is masked from 'package:Biobase': -#> -#> combine -#> The following object is masked from 'package:BiocGenerics': -#> -#> combine

+library(ggrastr)
-

Load dataset +

Load the subsetted dataset 

-data <- read.csv('~/Downloads/Moffitt_and_Bambah-Mukku_et_al_merfish_all_cells.csv')
-

Subset the dataset to specific female, behavioral condition, and -bregma section.

-
-animal <- 1
-sex <- "Female"
-behavior <- "Naive"
-bregma <- "-0.29"
-data_sub <- data[(data$Animal_ID == animal & data$Animal_sex == sex & data$Behavior == behavior & data$Bregma == bregma),]
+data_sub <- readRDS(file = "merfish_mousePOA_raw.RDS")
 dim(data_sub)
 #> [1] 6509  170
@@ -219,7 +204,7 @@

Process datasetcolData slot. Thus, here, we extract genes-by-cells matrix, spatial coordinates matrix, and data frame with cell-type labels.

-
+
 ## genes-by-cells matrix
 # extract the genes-by-cells matrix as a sparse matrix (dgCMatrix)
 mat <- as(t(data_sub[,10:ncol(data_sub)]), "CsparseMatrix")
@@ -245,7 +230,7 @@ 
Process dataset## standardize cell IDs for the extracted objects
 colnames(mat) <- rownames(pos) <- rownames(meta) <- data_sub$Cell_ID

 
Remove genes and cells with NaN values.

-
+
 ## filter genes with NaN values
 bad_genes <- names(which(rowSums(is.nan(mat)) > 0)) 
 mat <- mat[setdiff(rownames(mat),bad_genes),]
@@ -257,32 +242,32 @@ 
Process datasetmeta <- meta[setdiff(rownames(pos),bad_cells),]

 
Plot total gene expression at single-cell resolution for
 verification.

-
+
 df_plt <- data.frame(pos, total_gexp = colSums(mat))
 
 ggplot(df_plt, aes(x = x, y = y, color = total_gexp)) +
   coord_fixed() +
-  geom_point(size = 1.5, stroke = 0) +
+  rasterise(geom_point(size = 1.5, stroke = 0)) +
   scale_color_viridis_c(name = "total gene expression") +
   theme_bw() +
   theme(panel.grid = element_blank(),
         axis.title = element_blank(),
         axis.text = element_blank(),
         axis.ticks = element_blank())

-

+

 
Plot cell-type labels at single-cell resolution for verification.

-
+
 df_plt <- data.frame(pos, celltype = meta$celltype)
 
 ggplot(df_plt, aes(x = x, y = y, color = celltype)) +
   coord_fixed() +
-  geom_point(size = 1.5, stroke = 0) +
+  rasterise(geom_point(size = 1.5, stroke = 0)) +
   theme_bw() +
   theme(panel.grid = element_blank(),
         axis.title = element_blank(),
         axis.text = element_blank(),
         axis.ticks = element_blank())

-

+

 

 

 
Format SpatialExperiment object
@@ -292,14 +277,14 @@ 
Format SpatialExperiment object
-
+
 spe <- SpatialExperiment::SpatialExperiment(
   assays = list(volnorm = mat),
   spatialCoords = as.matrix(pos),
   colData = meta
 )

 
Session Info
-
+
 sessionInfo()
 #> R version 4.3.1 (2023-06-16)
 #> Platform: x86_64-apple-darwin20 (64-bit)
@@ -320,7 +305,7 @@ 
Format SpatialExperiment object#> [8] base     
 #> 
 #> other attached packages:
-#>  [1] gridExtra_2.3               ggplot2_3.5.1              
+#>  [1] ggrastr_1.0.2               ggplot2_3.5.1              
 #>  [3] Matrix_1.6-5                SpatialExperiment_1.10.0   
 #>  [5] SingleCellExperiment_1.22.0 SummarizedExperiment_1.30.2
 #>  [7] Biobase_2.60.0              GenomicRanges_1.52.1       
@@ -330,46 +315,48 @@ 
Format SpatialExperiment object#> 
 #> loaded via a namespace (and not attached):
 #>  [1] tidyselect_1.2.1          viridisLite_0.4.2        
-#>  [3] dplyr_1.1.4               farver_2.1.2             
-#>  [5] R.utils_2.12.3            bitops_1.0-7             
-#>  [7] fastmap_1.1.1             RCurl_1.98-1.14          
-#>  [9] digest_0.6.35             lifecycle_1.0.4          
-#> [11] magrittr_2.0.3            compiler_4.3.1           
-#> [13] rlang_1.1.3               sass_0.4.9               
-#> [15] tools_4.3.1               utf8_1.2.4               
-#> [17] yaml_2.3.8                knitr_1.45               
-#> [19] labeling_0.4.3            S4Arrays_1.0.6           
-#> [21] dqrng_0.3.2               htmlwidgets_1.6.4        
-#> [23] DelayedArray_0.26.7       abind_1.4-5              
-#> [25] BiocParallel_1.36.0       HDF5Array_1.28.1         
-#> [27] withr_3.0.0               purrr_1.0.2              
-#> [29] desc_1.4.3                R.oo_1.26.0              
-#> [31] grid_4.3.1                fansi_1.0.6              
-#> [33] beachmat_2.16.0           colorspace_2.1-0         
-#> [35] Rhdf5lib_1.22.1           edgeR_3.42.4             
-#> [37] scales_1.3.0              cli_3.6.2                
-#> [39] rmarkdown_2.26            crayon_1.5.2             
-#> [41] ragg_1.3.1                generics_0.1.3           
-#> [43] rstudioapi_0.16.0         rjson_0.2.21             
-#> [45] DelayedMatrixStats_1.22.6 scuttle_1.10.3           
-#> [47] cachem_1.0.8              rhdf5_2.44.0             
-#> [49] zlibbioc_1.46.0           parallel_4.3.1           
-#> [51] XVector_0.40.0            vctrs_0.6.5              
-#> [53] jsonlite_1.8.8            systemfonts_1.0.6        
-#> [55] magick_2.8.3              locfit_1.5-9.9           
-#> [57] limma_3.56.2              jquerylib_0.1.4          
-#> [59] glue_1.7.0                pkgdown_2.0.9            
-#> [61] DropletUtils_1.20.0       codetools_0.2-20         
-#> [63] gtable_0.3.5              munsell_0.5.1            
-#> [65] tibble_3.2.1              pillar_1.9.0             
-#> [67] htmltools_0.5.8.1         rhdf5filters_1.12.1      
-#> [69] GenomeInfoDbData_1.2.10   R6_2.5.1                 
-#> [71] textshaping_0.3.7         sparseMatrixStats_1.12.2 
-#> [73] evaluate_0.23             lattice_0.22-6           
-#> [75] highr_0.10                R.methodsS3_1.8.2        
-#> [77] memoise_2.0.1             bslib_0.7.0              
-#> [79] Rcpp_1.0.12               xfun_0.43                
-#> [81] fs_1.6.4                  pkgconfig_2.0.3

+#>  [3] farver_2.1.2              vipor_0.4.7              
+#>  [5] dplyr_1.1.4               R.utils_2.12.3           
+#>  [7] bitops_1.0-7              fastmap_1.1.1            
+#>  [9] RCurl_1.98-1.14           digest_0.6.35            
+#> [11] lifecycle_1.0.4           Cairo_1.6-2              
+#> [13] magrittr_2.0.3            compiler_4.3.1           
+#> [15] rlang_1.1.3               sass_0.4.9               
+#> [17] tools_4.3.1               utf8_1.2.4               
+#> [19] yaml_2.3.8                knitr_1.45               
+#> [21] labeling_0.4.3            S4Arrays_1.0.6           
+#> [23] dqrng_0.3.2               htmlwidgets_1.6.4        
+#> [25] DelayedArray_0.26.7       abind_1.4-5              
+#> [27] BiocParallel_1.36.0       HDF5Array_1.28.1         
+#> [29] withr_3.0.0               purrr_1.0.2              
+#> [31] desc_1.4.3                R.oo_1.26.0              
+#> [33] grid_4.3.1                fansi_1.0.6              
+#> [35] beachmat_2.16.0           colorspace_2.1-0         
+#> [37] Rhdf5lib_1.22.1           edgeR_3.42.4             
+#> [39] scales_1.3.0              cli_3.6.2                
+#> [41] rmarkdown_2.26            crayon_1.5.2             
+#> [43] ragg_1.3.1                generics_0.1.3           
+#> [45] rstudioapi_0.16.0         rjson_0.2.21             
+#> [47] DelayedMatrixStats_1.22.6 scuttle_1.10.3           
+#> [49] ggbeeswarm_0.7.2          cachem_1.0.8             
+#> [51] rhdf5_2.44.0              zlibbioc_1.46.0          
+#> [53] parallel_4.3.1            XVector_0.40.0           
+#> [55] vctrs_0.6.5               jsonlite_1.8.8           
+#> [57] beeswarm_0.4.0            systemfonts_1.0.6        
+#> [59] magick_2.8.3              locfit_1.5-9.9           
+#> [61] limma_3.56.2              jquerylib_0.1.4          
+#> [63] glue_1.7.0                pkgdown_2.0.9            
+#> [65] DropletUtils_1.20.0       codetools_0.2-20         
+#> [67] gtable_0.3.5              munsell_0.5.1            
+#> [69] tibble_3.2.1              pillar_1.9.0             
+#> [71] htmltools_0.5.8.1         rhdf5filters_1.12.1      
+#> [73] GenomeInfoDbData_1.2.10   R6_2.5.1                 
+#> [75] textshaping_0.3.7         sparseMatrixStats_1.12.2 
+#> [77] evaluate_0.23             lattice_0.22-6           
+#> [79] highr_0.10                R.methodsS3_1.8.2        
+#> [81] memoise_2.0.1             bslib_0.7.0              
+#> [83] Rcpp_1.0.12               xfun_0.43                
+#> [85] fs_1.6.4                  pkgconfig_2.0.3

 

 

 

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