From 4f6bfa72af7289a548c7581fa90477665a330335 Mon Sep 17 00:00:00 2001
From: jiajic <72078254+jiajic@users.noreply.github.com>
Date: Wed, 22 Nov 2023 11:30:59 -0500
Subject: [PATCH 1/6] Update dimension_reduction.R

---
 R/dimension_reduction.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/dimension_reduction.R b/R/dimension_reduction.R
index 79d9be813..1462f24a9 100644
--- a/R/dimension_reduction.R
+++ b/R/dimension_reduction.R
@@ -688,7 +688,7 @@ runPCA_BiocSingular_irlba_projection = function(x,
 #' @param feat_type feature type
 #' @param expression_values expression values to use
 #' @param reduction cells or genes
-#' @param random_subset random subset to perform PCA on
+#' @param random_subset numeric. random subset to perform PCA on
 #' @param name arbitrary name for PCA run
 #' @param feats_to_use subset of features to use for PCA
 #' @param return_gobject boolean: return giotto object (default = TRUE)

From 87dc495b16858372e540dc2aed2e89c0d641d9d6 Mon Sep 17 00:00:00 2001
From: jiajic <72078254+jiajic@users.noreply.github.com>
Date: Tue, 28 Nov 2023 11:51:44 -0500
Subject: [PATCH 2/6] Update differential_expression.R

make sure that scran pkg citation is shown by default
---
 R/differential_expression.R | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/R/differential_expression.R b/R/differential_expression.R
index ca69f1535..044d049b7 100644
--- a/R/differential_expression.R
+++ b/R/differential_expression.R
@@ -38,7 +38,7 @@ findScranMarkers <- function(gobject,
                              group_1_name = NULL,
                              group_2 = NULL,
                              group_2_name = NULL,
-                             verbose = FALSE,
+                             verbose = TRUE,
                              ...) {
 
 
@@ -47,10 +47,12 @@ findScranMarkers <- function(gobject,
 
 
   # print message with information #
-  if(verbose) wrap_msg("using 'Scran' to detect marker genes. If used in published research, please cite:
+  if(isTRUE(verbose)) {
+  wrap_msg("Using 'Scran' to detect marker genes. If used in published research, please cite:
   Lun ATL, McCarthy DJ, Marioni JC (2016).
   'A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor.'
-  F1000Res., 5, 2122. doi: 10.12688/f1000research.9501.2. ")
+  F1000Res., 5, 2122. doi: 10.12688/f1000research.9501.2.")
+  }
 
 
   # Set feat_type and spat_unit

From 8969835b1f1b80adef51de078396f91c9fc2d35f Mon Sep 17 00:00:00 2001
From: jiajic <72078254+jiajic@users.noreply.github.com>
Date: Wed, 29 Nov 2023 12:00:32 -0500
Subject: [PATCH 3/6] version bump

---
 DESCRIPTION | 2 +-
 NEWS.md     | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 39bd5d889..5ae04677d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Giotto
 Title: Spatial Single-Cell Transcriptomics Toolbox
-Version: 3.3.2
+Version: 4.0.0
 Authors@R: c(
 	person("Ruben", "Dries", email = "rubendries@gmail.com",
 		 role = c("aut", "cre")),
diff --git a/NEWS.md b/NEWS.md
index d4f724c0e..d448fd14f 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,6 +1,7 @@
-# Giotto Suite 3.3.2 (Release TBD)
+# Giotto Suite 4.0.0 2023*11*29)
 
 ## Breaking Changes
+* Update to modular package organization with the main packages being `GiottoUtils`, `GiottoClass`, `GiottoVisuals`, and `Giotto` as the analytical umbrella package.
 
 ## Added
 
@@ -15,7 +16,6 @@
 
 ## Changes
 
-* Improved performance of gefToGiotto()
 
 
 # Giotto Suite 3.3.1 (2023*08*02)

From cf537e015f046cb5adcbc3ddbbcbce740f1cda38 Mon Sep 17 00:00:00 2001
From: jiajic <72078254+jiajic@users.noreply.github.com>
Date: Wed, 29 Nov 2023 12:04:19 -0500
Subject: [PATCH 4/6] run document

---
 man/findScranMarkers.Rd           |   2 +-
 man/reexports.Rd                  |   2 +-
 man/runPCAprojection.Rd           |   2 +-
 tests/testthat/test_mini_vizgen.R | 314 ++++++++++++++++++++++++++++++
 4 files changed, 317 insertions(+), 3 deletions(-)
 create mode 100644 tests/testthat/test_mini_vizgen.R

diff --git a/man/findScranMarkers.Rd b/man/findScranMarkers.Rd
index 84f39d7b7..b35d9b18c 100644
--- a/man/findScranMarkers.Rd
+++ b/man/findScranMarkers.Rd
@@ -15,7 +15,7 @@ findScranMarkers(
   group_1_name = NULL,
   group_2 = NULL,
   group_2_name = NULL,
-  verbose = FALSE,
+  verbose = TRUE,
   ...
 )
 }
diff --git a/man/reexports.Rd b/man/reexports.Rd
index 01e774cb3..6c9417f73 100644
--- a/man/reexports.Rd
+++ b/man/reexports.Rd
@@ -206,7 +206,7 @@ These objects are imported from other packages. Follow the links
 below to see their documentation.
 
 \describe{
-  \item{GiottoClass}{\code{\link[GiottoClass]{addCellMetadata}}, \code{\link[GiottoClass]{addGiottoImage}}, \code{\link[GiottoClass]{addGiottoImageMG}}, \code{\link[GiottoClass]{addGiottoLargeImage}}, \code{\link[GiottoClass]{addGiottoPoints}}, \code{\link[GiottoClass]{addGiottoPoints3D}}, \code{\link[GiottoClass]{addGiottoPolygons}}, \code{\link[GiottoClass]{addSpatialCentroidLocations}}, \code{\link[GiottoClass]{addSpatialCentroidLocationsLayer}}, \code{\link[GiottoClass]{aggregateStacks}}, \code{\link[GiottoClass]{aggregateStacksExpression}}, \code{\link[GiottoClass]{aggregateStacksLocations}}, \code{\link[GiottoClass]{aggregateStacksPolygonOverlaps}}, \code{\link[GiottoClass]{aggregateStacksPolygons}}, \code{\link[GiottoClass]{aggregateStacksPolygonsOLD}}, \code{\link[GiottoClass]{anndataToGiotto}}, \code{\link[GiottoClass]{annotateGiotto}}, \code{\link[GiottoClass]{annotateSpatialGrid}}, \code{\link[GiottoClass]{annotateSpatialNetwork}}, \code{\link[GiottoClass]{calculateMetaTable}}, \code{\link[GiottoClass]{calculateMetaTableCells}}, \code{\link[GiottoClass]{calculateOverlapParallel}}, \code{\link[GiottoClass]{calculateOverlapPolygonImages}}, \code{\link[GiottoClass]{calculateOverlapRaster}}, \code{\link[GiottoClass]{calculateOverlapSerial}}, \code{\link[GiottoClass]{changeGiottoInstructions}}, \code{\link[GiottoClass]{changeImageBg}}, \code{\link[GiottoClass]{circleVertices}}, \code{\link[GiottoClass]{combineCellData}}, \code{\link[GiottoClass]{combineFeatureData}}, \code{\link[GiottoClass]{combineFeatureOverlapData}}, \code{\link[GiottoClass]{combineMetadata}}, \code{\link[GiottoClass]{combineSpatialCellFeatureInfo}}, \code{\link[GiottoClass]{combineSpatialCellMetadataInfo}}, \code{\link[GiottoClass]{convertGiottoLargeImageToMG}}, \code{\link[GiottoClass]{createCellMetaObj}}, \code{\link[GiottoClass]{createDimObj}}, \code{\link[GiottoClass]{createExprObj}}, \code{\link[GiottoClass]{createFeatMetaObj}}, \code{\link[GiottoClass]{createGiottoImage}}, \code{\link[GiottoClass]{createGiottoInstructions}}, \code{\link[GiottoClass]{createGiottoLargeImage}}, \code{\link[GiottoClass]{createGiottoLargeImageList}}, \code{\link[GiottoClass]{createGiottoObject}}, \code{\link[GiottoClass]{createGiottoObjectSubcellular}}, \code{\link[GiottoClass]{createGiottoPoints}}, \code{\link[GiottoClass:createGiottoPolygon]{createGiottoPolygonsFromDfr}}, \code{\link[GiottoClass:createGiottoPolygon]{createGiottoPolygonsFromGeoJSON}}, \code{\link[GiottoClass:createGiottoPolygon]{createGiottoPolygonsFromMask}}, \code{\link[GiottoClass]{createMetafeats}}, \code{\link[GiottoClass]{createNearestNetObj}}, \code{\link[GiottoClass]{createSpatEnrObj}}, \code{\link[GiottoClass]{createSpatialDefaultGrid}}, \code{\link[GiottoClass]{createSpatialDelaunayNetwork}}, \code{\link[GiottoClass]{createSpatialFeaturesKNNnetwork}}, \code{\link[GiottoClass]{createSpatialGrid}}, \code{\link[GiottoClass]{createSpatialKNNnetwork}}, \code{\link[GiottoClass]{createSpatialNetwork}}, \code{\link[GiottoClass]{createSpatialWeightMatrix}}, \code{\link[GiottoClass]{createSpatLocsObj}}, \code{\link[GiottoClass]{createSpatNetObj}}, \code{\link[GiottoClass]{cropGiottoLargeImage}}, \code{\link[GiottoClass]{distGiottoImage}}, \code{\link[GiottoClass]{estimateImageBg}}, \code{\link[GiottoClass]{fDataDT}}, \code{\link[GiottoClass:featType-generic]{featType}}, \code{\link[GiottoClass:featureNetwork-class]{featureNetwork}}, \code{\link[GiottoClass]{gefToGiotto}}, \code{\link[GiottoClass]{get_dimReduction}}, \code{\link[GiottoClass]{get_dimReduction}}, \code{\link[GiottoClass]{get_feature_info}}, \code{\link[GiottoClass]{get_feature_info}}, \code{\link[GiottoClass]{get_giottoImage}}, \code{\link[GiottoClass]{get_giottoImage}}, \code{\link[GiottoClass]{get_multiomics}}, \code{\link[GiottoClass]{get_multiomics}}, \code{\link[GiottoClass]{get_NearestNetwork}}, \code{\link[GiottoClass]{get_NearestNetwork}}, \code{\link[GiottoClass]{get_polygon_info}}, \code{\link[GiottoClass]{get_polygon_info}}, \code{\link[GiottoClass]{get_spatial_enrichment}}, \code{\link[GiottoClass]{get_spatial_enrichment}}, \code{\link[GiottoClass]{get_spatial_locations}}, \code{\link[GiottoClass]{get_spatial_locations}}, \code{\link[GiottoClass]{get_spatialGrid}}, \code{\link[GiottoClass]{get_spatialGrid}}, \code{\link[GiottoClass]{get_spatialNetwork}}, \code{\link[GiottoClass]{get_spatialNetwork}}, \code{\link[GiottoClass]{getCellMetadata}}, \code{\link[GiottoClass]{getDimReduction}}, \code{\link[GiottoClass]{getExpression}}, \code{\link[GiottoClass]{getFeatureInfo}}, \code{\link[GiottoClass]{getFeatureMetadata}}, \code{\link[GiottoClass]{getGiottoImage}}, \code{\link[GiottoClass]{getMultiomics}}, \code{\link[GiottoClass]{getNearestNetwork}}, \code{\link[GiottoClass]{getPolygonInfo}}, \code{\link[GiottoClass]{getRainbowColors}}, \code{\link[GiottoClass]{getSpatialEnrichment}}, \code{\link[GiottoClass]{getSpatialEnrichment}}, \code{\link[GiottoClass]{getSpatialGrid}}, \code{\link[GiottoClass]{getSpatialGrid}}, \code{\link[GiottoClass]{getSpatialLocations}}, \code{\link[GiottoClass]{getSpatialLocations}}, \code{\link[GiottoClass]{getSpatialNetwork}}, \code{\link[GiottoClass]{getSpatialNetwork}}, \code{\link[GiottoClass:giotto-class]{giotto}}, \code{\link[GiottoClass:giottoImage-class]{giottoImage}}, \code{\link[GiottoClass:giottoLargeImage-class]{giottoLargeImage}}, \code{\link[GiottoClass]{giottoMasterToSuite}}, \code{\link[GiottoClass:giottoPoints-class]{giottoPoints}}, \code{\link[GiottoClass:giottoPolygon-class]{giottoPolygon}}, \code{\link[GiottoClass]{giottoToAnnData}}, \code{\link[GiottoClass]{giottoToSeurat}}, \code{\link[GiottoClass]{giottoToSpatialExperiment}}, \code{\link[GiottoClass]{hexVertices}}, \code{\link[GiottoClass]{joinGiottoObjects}}, \code{\link[GiottoClass]{loadGiotto}}, \code{\link[GiottoClass]{makePseudoVisium}}, \code{\link[GiottoClass]{objHistory}}, \code{\link[GiottoClass:objName-generic]{objName}}, \code{\link[GiottoClass]{overlapImagesToMatrix}}, \code{\link[GiottoClass]{overlapToMatrix}}, \code{\link[GiottoClass]{overlapToMatrixMultiPoly}}, \code{\link[GiottoClass]{pDataDT}}, \code{\link[GiottoClass]{plotGiottoImage}}, \code{\link[GiottoClass]{polyStamp}}, \code{\link[GiottoClass:prov-generic]{prov}}, \code{\link[GiottoClass:read_cell_metadata]{readCellMetadata}}, \code{\link[GiottoClass]{readDimReducData}}, \code{\link[GiottoClass]{readExprData}}, \code{\link[GiottoClass]{readExprMatrix}}, \code{\link[GiottoClass]{readFeatData}}, \code{\link[GiottoClass:read_feature_metadata]{readFeatMetadata}}, \code{\link[GiottoClass]{readGiottoInstructions}}, \code{\link[GiottoClass]{readNearestNetData}}, \code{\link[GiottoClass]{readPolygonData}}, \code{\link[GiottoClass]{readSpatEnrichData}}, \code{\link[GiottoClass]{readSpatLocsData}}, \code{\link[GiottoClass]{readSpatNetData}}, \code{\link[GiottoClass]{reconnectGiottoImage}}, \code{\link[GiottoClass]{rectVertices}}, \code{\link[GiottoClass]{removeCellAnnotation}}, \code{\link[GiottoClass]{removeFeatAnnotation}}, \code{\link[GiottoClass]{replaceGiottoInstructions}}, \code{\link[GiottoClass]{rescalePolygons}}, \code{\link[GiottoClass]{saveGiotto}}, \code{\link[GiottoClass]{set_dimReduction}}, \code{\link[GiottoClass]{set_expression_values}}, \code{\link[GiottoClass]{set_feature_info}}, \code{\link[GiottoClass]{set_giottoImage}}, \code{\link[GiottoClass]{set_multiomics}}, \code{\link[GiottoClass]{set_NearestNetwork}}, \code{\link[GiottoClass]{set_polygon_info}}, \code{\link[GiottoClass]{set_spatial_enrichment}}, \code{\link[GiottoClass]{set_spatial_locations}}, \code{\link[GiottoClass]{set_spatialGrid}}, \code{\link[GiottoClass]{set_spatialNetwork}}, \code{\link[GiottoClass]{setDimReduction}}, \code{\link[GiottoClass]{setExpression}}, \code{\link[GiottoClass]{setFeatureInfo}}, \code{\link[GiottoClass]{setGiottoImage}}, \code{\link[GiottoClass]{setMultiomics}}, \code{\link[GiottoClass]{setNearestNetwork}}, \code{\link[GiottoClass]{setPolygonInfo}}, \code{\link[GiottoClass]{setSpatialEnrichment}}, \code{\link[GiottoClass]{setSpatialGrid}}, \code{\link[GiottoClass]{setSpatialLocations}}, \code{\link[GiottoClass]{setSpatialNetwork}}, \code{\link[GiottoClass]{seuratToGiotto}}, \code{\link[GiottoClass]{showGiottoCellMetadata}}, \code{\link[GiottoClass]{showGiottoDimRed}}, \code{\link[GiottoClass]{showGiottoExpression}}, \code{\link[GiottoClass]{showGiottoFeatInfo}}, \code{\link[GiottoClass]{showGiottoFeatMetadata}}, \code{\link[GiottoClass]{showGiottoImageNames}}, \code{\link[GiottoClass]{showGiottoInstructions}}, \code{\link[GiottoClass]{showGiottoNearestNetworks}}, \code{\link[GiottoClass]{showGiottoSpatEnrichments}}, \code{\link[GiottoClass]{showGiottoSpatGrids}}, \code{\link[GiottoClass]{showGiottoSpatialInfo}}, \code{\link[GiottoClass]{showGiottoSpatLocs}}, \code{\link[GiottoClass]{showGiottoSpatNetworks}}, \code{\link[GiottoClass]{showGrids}}, \code{\link[GiottoClass]{showNetworks}}, \code{\link[GiottoClass]{showProcessingSteps}}}
+  \item{GiottoClass}{\code{\link[GiottoClass]{addCellMetadata}}, \code{\link[GiottoClass]{addGiottoImage}}, \code{\link[GiottoClass]{addGiottoImageMG}}, \code{\link[GiottoClass]{addGiottoLargeImage}}, \code{\link[GiottoClass]{addGiottoPoints}}, \code{\link[GiottoClass:addGiottoPoints]{addGiottoPoints3D}}, \code{\link[GiottoClass]{addGiottoPolygons}}, \code{\link[GiottoClass]{addSpatialCentroidLocations}}, \code{\link[GiottoClass]{addSpatialCentroidLocationsLayer}}, \code{\link[GiottoClass]{aggregateStacks}}, \code{\link[GiottoClass]{aggregateStacksExpression}}, \code{\link[GiottoClass]{aggregateStacksLocations}}, \code{\link[GiottoClass]{aggregateStacksPolygonOverlaps}}, \code{\link[GiottoClass]{aggregateStacksPolygons}}, \code{\link[GiottoClass]{aggregateStacksPolygonsOLD}}, \code{\link[GiottoClass]{anndataToGiotto}}, \code{\link[GiottoClass]{annotateGiotto}}, \code{\link[GiottoClass]{annotateSpatialGrid}}, \code{\link[GiottoClass]{annotateSpatialNetwork}}, \code{\link[GiottoClass]{calculateMetaTable}}, \code{\link[GiottoClass]{calculateMetaTableCells}}, \code{\link[GiottoClass]{calculateOverlapParallel}}, \code{\link[GiottoClass]{calculateOverlapPolygonImages}}, \code{\link[GiottoClass]{calculateOverlapRaster}}, \code{\link[GiottoClass]{calculateOverlapSerial}}, \code{\link[GiottoClass]{changeGiottoInstructions}}, \code{\link[GiottoClass]{changeImageBg}}, \code{\link[GiottoClass]{circleVertices}}, \code{\link[GiottoClass]{combineCellData}}, \code{\link[GiottoClass]{combineFeatureData}}, \code{\link[GiottoClass]{combineFeatureOverlapData}}, \code{\link[GiottoClass]{combineMetadata}}, \code{\link[GiottoClass]{combineSpatialCellFeatureInfo}}, \code{\link[GiottoClass]{combineSpatialCellMetadataInfo}}, \code{\link[GiottoClass]{convertGiottoLargeImageToMG}}, \code{\link[GiottoClass]{createCellMetaObj}}, \code{\link[GiottoClass]{createDimObj}}, \code{\link[GiottoClass]{createExprObj}}, \code{\link[GiottoClass]{createFeatMetaObj}}, \code{\link[GiottoClass]{createGiottoImage}}, \code{\link[GiottoClass]{createGiottoInstructions}}, \code{\link[GiottoClass]{createGiottoLargeImage}}, \code{\link[GiottoClass]{createGiottoLargeImageList}}, \code{\link[GiottoClass]{createGiottoObject}}, \code{\link[GiottoClass]{createGiottoObjectSubcellular}}, \code{\link[GiottoClass]{createGiottoPoints}}, \code{\link[GiottoClass:createGiottoPolygon]{createGiottoPolygonsFromDfr}}, \code{\link[GiottoClass:createGiottoPolygon]{createGiottoPolygonsFromGeoJSON}}, \code{\link[GiottoClass:createGiottoPolygon]{createGiottoPolygonsFromMask}}, \code{\link[GiottoClass]{createMetafeats}}, \code{\link[GiottoClass]{createNearestNetObj}}, \code{\link[GiottoClass]{createSpatEnrObj}}, \code{\link[GiottoClass]{createSpatialDefaultGrid}}, \code{\link[GiottoClass]{createSpatialDelaunayNetwork}}, \code{\link[GiottoClass]{createSpatialFeaturesKNNnetwork}}, \code{\link[GiottoClass]{createSpatialGrid}}, \code{\link[GiottoClass]{createSpatialKNNnetwork}}, \code{\link[GiottoClass]{createSpatialNetwork}}, \code{\link[GiottoClass]{createSpatialWeightMatrix}}, \code{\link[GiottoClass]{createSpatLocsObj}}, \code{\link[GiottoClass]{createSpatNetObj}}, \code{\link[GiottoClass]{cropGiottoLargeImage}}, \code{\link[GiottoClass]{distGiottoImage}}, \code{\link[GiottoClass]{estimateImageBg}}, \code{\link[GiottoClass]{fDataDT}}, \code{\link[GiottoClass:featType-generic]{featType}}, \code{\link[GiottoClass:featureNetwork-class]{featureNetwork}}, \code{\link[GiottoClass]{gefToGiotto}}, \code{\link[GiottoClass]{get_dimReduction}}, \code{\link[GiottoClass]{get_dimReduction}}, \code{\link[GiottoClass]{get_feature_info}}, \code{\link[GiottoClass]{get_feature_info}}, \code{\link[GiottoClass]{get_giottoImage}}, \code{\link[GiottoClass]{get_giottoImage}}, \code{\link[GiottoClass]{get_multiomics}}, \code{\link[GiottoClass]{get_multiomics}}, \code{\link[GiottoClass]{get_NearestNetwork}}, \code{\link[GiottoClass]{get_NearestNetwork}}, \code{\link[GiottoClass]{get_polygon_info}}, \code{\link[GiottoClass]{get_polygon_info}}, \code{\link[GiottoClass]{get_spatial_enrichment}}, \code{\link[GiottoClass]{get_spatial_enrichment}}, \code{\link[GiottoClass]{get_spatial_locations}}, \code{\link[GiottoClass]{get_spatial_locations}}, \code{\link[GiottoClass]{get_spatialGrid}}, \code{\link[GiottoClass]{get_spatialGrid}}, \code{\link[GiottoClass]{get_spatialNetwork}}, \code{\link[GiottoClass]{get_spatialNetwork}}, \code{\link[GiottoClass]{getCellMetadata}}, \code{\link[GiottoClass]{getDimReduction}}, \code{\link[GiottoClass]{getExpression}}, \code{\link[GiottoClass]{getFeatureInfo}}, \code{\link[GiottoClass]{getFeatureMetadata}}, \code{\link[GiottoClass]{getGiottoImage}}, \code{\link[GiottoClass]{getMultiomics}}, \code{\link[GiottoClass]{getNearestNetwork}}, \code{\link[GiottoClass]{getPolygonInfo}}, \code{\link[GiottoClass]{getRainbowColors}}, \code{\link[GiottoClass]{getSpatialEnrichment}}, \code{\link[GiottoClass]{getSpatialEnrichment}}, \code{\link[GiottoClass]{getSpatialGrid}}, \code{\link[GiottoClass]{getSpatialGrid}}, \code{\link[GiottoClass]{getSpatialLocations}}, \code{\link[GiottoClass]{getSpatialLocations}}, \code{\link[GiottoClass]{getSpatialNetwork}}, \code{\link[GiottoClass]{getSpatialNetwork}}, \code{\link[GiottoClass:giotto-class]{giotto}}, \code{\link[GiottoClass:giottoImage-class]{giottoImage}}, \code{\link[GiottoClass:giottoLargeImage-class]{giottoLargeImage}}, \code{\link[GiottoClass]{giottoMasterToSuite}}, \code{\link[GiottoClass:giottoPoints-class]{giottoPoints}}, \code{\link[GiottoClass:giottoPolygon-class]{giottoPolygon}}, \code{\link[GiottoClass]{giottoToAnnData}}, \code{\link[GiottoClass]{giottoToSeurat}}, \code{\link[GiottoClass]{giottoToSpatialExperiment}}, \code{\link[GiottoClass]{hexVertices}}, \code{\link[GiottoClass]{joinGiottoObjects}}, \code{\link[GiottoClass]{loadGiotto}}, \code{\link[GiottoClass]{makePseudoVisium}}, \code{\link[GiottoClass]{objHistory}}, \code{\link[GiottoClass:objName-generic]{objName}}, \code{\link[GiottoClass]{overlapImagesToMatrix}}, \code{\link[GiottoClass]{overlapToMatrix}}, \code{\link[GiottoClass]{overlapToMatrixMultiPoly}}, \code{\link[GiottoClass]{pDataDT}}, \code{\link[GiottoClass]{plotGiottoImage}}, \code{\link[GiottoClass]{polyStamp}}, \code{\link[GiottoClass:prov-generic]{prov}}, \code{\link[GiottoClass:read_cell_metadata]{readCellMetadata}}, \code{\link[GiottoClass]{readDimReducData}}, \code{\link[GiottoClass]{readExprData}}, \code{\link[GiottoClass]{readExprMatrix}}, \code{\link[GiottoClass]{readFeatData}}, \code{\link[GiottoClass:read_feature_metadata]{readFeatMetadata}}, \code{\link[GiottoClass]{readGiottoInstructions}}, \code{\link[GiottoClass]{readNearestNetData}}, \code{\link[GiottoClass]{readPolygonData}}, \code{\link[GiottoClass]{readSpatEnrichData}}, \code{\link[GiottoClass]{readSpatLocsData}}, \code{\link[GiottoClass]{readSpatNetData}}, \code{\link[GiottoClass]{reconnectGiottoImage}}, \code{\link[GiottoClass]{rectVertices}}, \code{\link[GiottoClass]{removeCellAnnotation}}, \code{\link[GiottoClass]{removeFeatAnnotation}}, \code{\link[GiottoClass]{replaceGiottoInstructions}}, \code{\link[GiottoClass]{rescalePolygons}}, \code{\link[GiottoClass]{saveGiotto}}, \code{\link[GiottoClass]{set_dimReduction}}, \code{\link[GiottoClass]{set_expression_values}}, \code{\link[GiottoClass]{set_feature_info}}, \code{\link[GiottoClass]{set_giottoImage}}, \code{\link[GiottoClass]{set_multiomics}}, \code{\link[GiottoClass]{set_NearestNetwork}}, \code{\link[GiottoClass]{set_polygon_info}}, \code{\link[GiottoClass]{set_spatial_enrichment}}, \code{\link[GiottoClass]{set_spatial_locations}}, \code{\link[GiottoClass]{set_spatialGrid}}, \code{\link[GiottoClass]{set_spatialNetwork}}, \code{\link[GiottoClass]{setDimReduction}}, \code{\link[GiottoClass]{setExpression}}, \code{\link[GiottoClass]{setFeatureInfo}}, \code{\link[GiottoClass]{setGiottoImage}}, \code{\link[GiottoClass]{setMultiomics}}, \code{\link[GiottoClass]{setNearestNetwork}}, \code{\link[GiottoClass]{setPolygonInfo}}, \code{\link[GiottoClass]{setSpatialEnrichment}}, \code{\link[GiottoClass]{setSpatialGrid}}, \code{\link[GiottoClass]{setSpatialLocations}}, \code{\link[GiottoClass]{setSpatialNetwork}}, \code{\link[GiottoClass]{seuratToGiotto}}, \code{\link[GiottoClass]{showGiottoCellMetadata}}, \code{\link[GiottoClass]{showGiottoDimRed}}, \code{\link[GiottoClass]{showGiottoExpression}}, \code{\link[GiottoClass]{showGiottoFeatInfo}}, \code{\link[GiottoClass]{showGiottoFeatMetadata}}, \code{\link[GiottoClass]{showGiottoImageNames}}, \code{\link[GiottoClass]{showGiottoInstructions}}, \code{\link[GiottoClass]{showGiottoNearestNetworks}}, \code{\link[GiottoClass]{showGiottoSpatEnrichments}}, \code{\link[GiottoClass]{showGiottoSpatGrids}}, \code{\link[GiottoClass]{showGiottoSpatialInfo}}, \code{\link[GiottoClass]{showGiottoSpatLocs}}, \code{\link[GiottoClass]{showGiottoSpatNetworks}}, \code{\link[GiottoClass]{showGrids}}, \code{\link[GiottoClass]{showNetworks}}, \code{\link[GiottoClass]{showProcessingSteps}}}
 
   \item{GiottoUtils}{\code{\link[GiottoUtils:pipe]{\%>\%}}}
 
diff --git a/man/runPCAprojection.Rd b/man/runPCAprojection.Rd
index bdf95f934..ae2546d97 100644
--- a/man/runPCAprojection.Rd
+++ b/man/runPCAprojection.Rd
@@ -37,7 +37,7 @@ runPCAprojection(
 
 \item{reduction}{cells or genes}
 
-\item{random_subset}{random subset to perform PCA on}
+\item{random_subset}{numeric. random subset to perform PCA on}
 
 \item{name}{arbitrary name for PCA run}
 
diff --git a/tests/testthat/test_mini_vizgen.R b/tests/testthat/test_mini_vizgen.R
new file mode 100644
index 000000000..fa1a58f85
--- /dev/null
+++ b/tests/testthat/test_mini_vizgen.R
@@ -0,0 +1,314 @@
+# Continuing on from GiottoClass mini vizgen
+
+options('giotto.use_conda' = FALSE)
+g <- GiottoData::loadGiottoMini('vizgen')
+
+# reset portions of object to before aggregate spat_unit filtering and normalization
+
+
+
+# 5. normalize on aggregated layer #####
+# ----------------------------------- ##
+
+# rna data, default.
+# other feature modalities can be processed and filtered in an anologous manner
+vizsubc <- normalizeGiotto(gobject = vizsubc, spat_unit = 'aggregate',
+                           scalefactor = 5000, verbose = T)
+vizsubc <- addStatistics(gobject = vizsubc, spat_unit = 'aggregate')
+vizsubc <- normalizeGiotto(gobject = vizsubc, spat_unit = 'aggregate',
+                           norm_methods = 'pearson_resid', update_slot = 'pearson')
+
+
+# 6. highly variable genes ####
+# ----------------------------- #
+
+# typical way of calculating HVG
+vizsubc <- calculateHVF(gobject = vizsubc, spat_unit = 'aggregate', HVFname = 'hvg_orig')
+
+# new method based on variance of pearson residuals for each gene
+vizsubc <- calculateHVF(gobject = vizsubc,
+                        spat_unit = 'aggregate',
+                        method = 'var_p_resid',
+                        expression_values = 'pearson',
+                        show_plot = T)
+
+
+
+# 7. dimension reduction ####
+# --------------------------- #
+
+# ** 7.1 PCA ####
+
+# we will run pca on the pre-scaled matrix from the pearson residual normalization
+# if features are not specified it will automatically search for the hvf column in the feature metadata
+
+vizsubc <- runPCA(gobject = vizsubc,
+                  spat_unit = 'aggregate',
+                  expression_values = 'pearson',
+                  scale_unit = F, center = F)
+
+screePlot(vizsubc,
+          ncp = 20,
+          spat_unit = 'aggregate')
+
+showGiottoDimRed(vizsubc)
+
+plotPCA(vizsubc,
+        spat_unit = 'aggregate',
+        dim_reduction_name = 'pca',
+        dim1_to_use = 1,
+        dim2_to_use = 2)
+
+
+# ** 7.2 UMAP and TSN ####
+vizsubc <- runUMAP(vizsubc, dimensions_to_use = 1:8, n_threads = 4, spat_unit = 'aggregate')
+plotUMAP(gobject = vizsubc, spat_unit = 'aggregate')
+
+vizsubc <- runtSNE(vizsubc, dimensions_to_use = 1:8, spat_unit = 'aggregate')
+plotTSNE(gobject = vizsubc, spat_unit = 'aggregate')
+
+
+# 8. graph-based clustering ####
+# ---------------------------- #
+vizsubc <- createNearestNetwork(gobject = vizsubc, dimensions_to_use = 1:8, k = 10,
+                                spat_unit = 'aggregate')
+vizsubc <- doLeidenCluster(gobject = vizsubc, resolution = 0.05, n_iterations = 1000,
+                           spat_unit = 'aggregate')
+vizsubc <- doLouvainCluster(gobject = vizsubc, resolution = 5,
+                            spat_unit = 'aggregate')
+
+
+# visualize UMAP / TSNE cluster results
+plotUMAP(gobject = vizsubc,
+         spat_unit = 'aggregate',
+         cell_color = 'leiden_clus',
+         show_NN_network = T,
+         point_size = 2.5)
+
+spatInSituPlotPoints(vizsubc,
+                     show_polygon = TRUE,
+                     spat_unit = 'aggregate',
+                     polygon_feat_type = 'aggregate',
+                     polygon_color = 'white',
+                     polygon_line_size = 0.1,
+                     polygon_fill = 'leiden_clus',
+                     polygon_fill_as_factor = T,
+                     coord_fix_ratio = T)
+
+plotTSNE(gobject = vizsubc,
+         spat_unit = 'aggregate',
+         cell_color = 'louvain_clus',
+         show_NN_network = T,
+         point_size = 2.5)
+
+spatInSituPlotPoints(vizsubc,
+                     show_polygon = TRUE,
+                     spat_unit = 'aggregate',
+                     polygon_feat_type = 'aggregate',
+                     polygon_color = 'white',
+                     polygon_line_size = 0.1,
+                     polygon_fill = 'louvain_clus',
+                     polygon_fill_as_factor = T,
+                     coord_fix_ratio = T)
+
+spatInSituPlotPoints(vizsubc,
+                     spat_unit = 'aggregate',
+                     show_image = T,
+                     largeImage_name = 'dapi_z0',
+                     feats = list('rna' = c("Htr1b", "Ackr1", "Epha7")),
+                     feats_color_code = c("Htr1b" = 'green', 'Ackr1' = 'blue', 'Epha7' = 'red'),
+                     point_size = 0.35,
+                     show_polygon = TRUE,
+                     polygon_feat_type = 'aggregate',
+                     polygon_color = 'white',
+                     polygon_line_size = 0.1,
+                     polygon_fill = 'leiden_clus',
+                     polygon_fill_as_factor = T,
+                     coord_fix_ratio = TRUE)
+
+
+
+
+# 9. spatial network ####
+# --------------------- #
+# defaults to delaunay
+vizsubc = createSpatialNetwork(vizsubc, spat_unit = 'aggregate')
+# kNN with k of 8 nearest
+vizsubc = createSpatialNetwork(vizsubc, spat_unit = 'aggregate', method = 'kNN', k = 8)
+# create spatial weight matrix
+vizsubc = createSpatialWeightMatrix(vizsubc,
+                                    spat_unit = 'aggregate',
+                                    method = 'distance',
+                                    spatial_network_to_use = 'kNN_network',
+                                    return_gobject = TRUE)
+
+pDataDT(vizsubc, 'aggregate')
+spatPlot(gobject = vizsubc,
+         spat_unit = 'aggregate',
+         show_network = T,
+         network_color = 'lightgray',
+         spatial_network_name = 'Delaunay_network',
+         point_size = 2.5,
+         cell_color = 'leiden_clus')
+
+
+## 9.1 spatial genes ####
+km_spatialfeats = binSpect(vizsubc, spat_unit = 'aggregate')
+
+spatFeatPlot2D_single(vizsubc,
+                      spat_unit = 'aggregate',
+                      expression_values = 'scaled',
+                      feats = km_spatialfeats[1:4]$feats,
+                      point_shape = 'border',
+                      point_border_stroke = 0.1,
+                      show_network = F,
+                      network_color = 'lightgrey',
+                      point_size = 2.5,
+                      cow_n_col = 2)
+
+## 9.2 spatial co-expression ####
+# here we use existing detectSpatialCorGenes function to calculate pairwise distances between genes
+ext_spatial_genes = km_spatialfeats[1:200,]$feats
+spat_cor_netw_DT = detectSpatialCorFeats(vizsubc,
+                                         spat_unit = 'aggregate',
+                                         method = 'network',
+                                         spatial_network_name = 'Delaunay_network',
+                                         subset_feats = ext_spatial_genes)
+
+# cluster and visualize spatial co-expression genes
+spat_cor_netw_DT = clusterSpatialCorFeats(spat_cor_netw_DT,
+                                          name = 'spat_netw_clus',
+                                          k = 5)
+
+heatmSpatialCorFeats(vizsubc,
+                     spatCorObject = spat_cor_netw_DT,
+                     use_clus_name = 'spat_netw_clus',
+                     heatmap_legend_param = list(title = NULL),
+                     save_param = list(base_height = 6,
+                                       base_width = 8,
+                                       units = 'cm'))
+
+# create and visualize metafeatures
+testweight = getBalancedSpatCoexpressionFeats(spat_cor_netw_DT, rank = 'weighted', maximum = 30)
+
+vizsubc = createMetafeats(vizsubc,
+                          spat_unit = 'aggregate',
+                          feat_clusters = testweight,
+                          name = 'cluster_metagene')
+
+spatCellPlot(vizsubc,
+             spat_unit = 'aggregate',
+             spat_enr_names = 'cluster_metagene',
+             cell_annotation_values = as.character(c(1:6)),
+             gradient_style = 's',
+             point_size = 1.8,
+             save_param = list(base_width = 15))
+
+
+
+## 9.3 spatial structure ####
+cell_proximities = cellProximityEnrichment(gobject = vizsubc,
+                                           spat_unit = 'aggregate',
+                                           cluster_column = 'leiden_clus',
+                                           spatial_network_name = 'Delaunay_network',
+                                           adjust_method = 'fdr',
+                                           number_of_simulations = 2000)
+## barplot
+cellProximityBarplot(gobject = vizsubc,
+                     CPscore = cell_proximities,
+                     min_orig_ints = 5, min_sim_ints = 5)
+
+## heatmap
+cellProximityHeatmap(gobject = vizsubc,
+                     CPscore = cell_proximities,
+                     order_cell_types = T, scale = T,
+                     color_breaks = c(-1.5, 0, 1.5),
+                     color_names = c('blue', 'white', 'red'))
+
+spatInSituPlotPoints(
+  vizsubc,
+  spat_unit = 'aggregate',
+  show_image = T,
+  largeImage_name = 'dapi_z0',
+  feats = list('rna' = c("Htr1b", "Ackr1", "Epha7")),
+  feats_color_code = c("Htr1b" = 'green', 'Ackr1' = 'blue', 'Epha7' = 'red'),
+  point_size = 0.75,
+  show_polygon = TRUE,
+  polygon_feat_type = 'aggregate',
+  polygon_color = 'white',
+  polygon_line_size = 0.1,
+  polygon_fill = 'leiden_clus',
+  polygon_fill_as_factor = T,
+  coord_fix_ratio = 1
+)
+
+showGiottoSpatialInfo(vizsubc)
+
+
+spatInSituPlotDensity(vizsubc,
+                      polygon_feat_type = 'aggregate',
+                      feats = c("Htr1b", "Ackr1", "Epha7"),
+                      alpha = 0.5,
+                      polygon_color = 'white')
+
+spatInSituPlotHex(vizsubc,
+                  polygon_feat_type = 'aggregate',
+                  feats = c("Htr1b", "Ackr1", "Epha7"))
+
+
+
+# 10. save Giotto object ####
+# ------------------------- #
+format(object.size(vizsubc), units = 'Mb')
+
+# you need to use your local GiottoData repo
+# giottodata_repo = '/Users/rubendries/Packages/R_Packages/GiottoData/inst/Mini_datasets/'
+giottodata_repo = '/Users/rubendries/r_packages/GiottoData//inst/Mini_datasets/'
+
+saveGiotto(vizsubc,
+           foldername = 'VizgenObject',
+           #dir = paste0(system.file(package = 'GiottoData'),'/', 'Mini_datasets/Vizgen/'),
+           dir = paste0(giottodata_repo, '/', 'Vizgen/'),
+           overwrite = TRUE)
+
+pDataDT(vizsubc, spat_unit = 'aggregate')
+pDataDT(vizsubc, spat_unit = 'aggregate')
+
+
+
+## some quick tests ##
+gvizg = loadGiotto(path_to_folder = system.file('/Mini_datasets/Vizgen/VizgenObject/',
+                                                package = 'GiottoData'))
+
+
+# subsetting
+selected_ids = pDataDT(gvizg)$cell_ID[1:100]
+
+# important to specify which spatial_unit to use and which polygon information slots to update
+mySubset <- subsetGiotto(gobject = gvizg,
+                         cell_ids = selected_ids,
+                         spat_unit = 'aggregate',
+                         poly_info = c('aggregate'))
+
+pDataDT(mySubset, 'aggregate')
+fDataDT(mySubset)
+
+spatInSituPlotPoints(mySubset,
+                     spat_unit = 'aggregate',
+                     show_image = T,
+                     largeImage_name = 'dapi_z0',
+                     feats = list('rna' = c("Htr1b", "Ackr1", "Epha7")),
+                     feats_color_code = c("Htr1b" = 'green', 'Ackr1' = 'blue', 'Epha7' = 'red'),
+                     point_size = 0.35,
+                     show_polygon = TRUE,
+                     polygon_feat_type = 'aggregate',
+                     polygon_color = 'white',
+                     polygon_line_size = 0.1,
+                     polygon_fill = 'leiden_clus',
+                     polygon_fill_as_factor = T,
+                     coord_fix_ratio = TRUE)
+
+
+spatPlot(gobject = mySubset, spat_unit = 'aggregate', show_network = T,
+         network_color = 'lightgray', spatial_network_name = 'Delaunay_network',
+         point_size = 2.5, cell_color = 'leiden_clus')

From c2db30dff8225a2b668c1c3e8eb5b96fe2211f57 Mon Sep 17 00:00:00 2001
From: jiajic <72078254+jiajic@users.noreply.github.com>
Date: Wed, 29 Nov 2023 12:06:13 -0500
Subject: [PATCH 5/6] Revert "run document"

This reverts commit cf537e015f046cb5adcbc3ddbbcbce740f1cda38.
---
 man/findScranMarkers.Rd           |   2 +-
 man/reexports.Rd                  |   2 +-
 man/runPCAprojection.Rd           |   2 +-
 tests/testthat/test_mini_vizgen.R | 314 ------------------------------
 4 files changed, 3 insertions(+), 317 deletions(-)
 delete mode 100644 tests/testthat/test_mini_vizgen.R

diff --git a/man/findScranMarkers.Rd b/man/findScranMarkers.Rd
index b35d9b18c..84f39d7b7 100644
--- a/man/findScranMarkers.Rd
+++ b/man/findScranMarkers.Rd
@@ -15,7 +15,7 @@ findScranMarkers(
   group_1_name = NULL,
   group_2 = NULL,
   group_2_name = NULL,
-  verbose = TRUE,
+  verbose = FALSE,
   ...
 )
 }
diff --git a/man/reexports.Rd b/man/reexports.Rd
index 6c9417f73..01e774cb3 100644
--- a/man/reexports.Rd
+++ b/man/reexports.Rd
@@ -206,7 +206,7 @@ These objects are imported from other packages. Follow the links
 below to see their documentation.
 
 \describe{
-  \item{GiottoClass}{\code{\link[GiottoClass]{addCellMetadata}}, \code{\link[GiottoClass]{addGiottoImage}}, \code{\link[GiottoClass]{addGiottoImageMG}}, \code{\link[GiottoClass]{addGiottoLargeImage}}, \code{\link[GiottoClass]{addGiottoPoints}}, \code{\link[GiottoClass:addGiottoPoints]{addGiottoPoints3D}}, \code{\link[GiottoClass]{addGiottoPolygons}}, \code{\link[GiottoClass]{addSpatialCentroidLocations}}, \code{\link[GiottoClass]{addSpatialCentroidLocationsLayer}}, \code{\link[GiottoClass]{aggregateStacks}}, \code{\link[GiottoClass]{aggregateStacksExpression}}, \code{\link[GiottoClass]{aggregateStacksLocations}}, \code{\link[GiottoClass]{aggregateStacksPolygonOverlaps}}, \code{\link[GiottoClass]{aggregateStacksPolygons}}, \code{\link[GiottoClass]{aggregateStacksPolygonsOLD}}, \code{\link[GiottoClass]{anndataToGiotto}}, \code{\link[GiottoClass]{annotateGiotto}}, \code{\link[GiottoClass]{annotateSpatialGrid}}, \code{\link[GiottoClass]{annotateSpatialNetwork}}, \code{\link[GiottoClass]{calculateMetaTable}}, \code{\link[GiottoClass]{calculateMetaTableCells}}, \code{\link[GiottoClass]{calculateOverlapParallel}}, \code{\link[GiottoClass]{calculateOverlapPolygonImages}}, \code{\link[GiottoClass]{calculateOverlapRaster}}, \code{\link[GiottoClass]{calculateOverlapSerial}}, \code{\link[GiottoClass]{changeGiottoInstructions}}, \code{\link[GiottoClass]{changeImageBg}}, \code{\link[GiottoClass]{circleVertices}}, \code{\link[GiottoClass]{combineCellData}}, \code{\link[GiottoClass]{combineFeatureData}}, \code{\link[GiottoClass]{combineFeatureOverlapData}}, \code{\link[GiottoClass]{combineMetadata}}, \code{\link[GiottoClass]{combineSpatialCellFeatureInfo}}, \code{\link[GiottoClass]{combineSpatialCellMetadataInfo}}, \code{\link[GiottoClass]{convertGiottoLargeImageToMG}}, \code{\link[GiottoClass]{createCellMetaObj}}, \code{\link[GiottoClass]{createDimObj}}, \code{\link[GiottoClass]{createExprObj}}, \code{\link[GiottoClass]{createFeatMetaObj}}, \code{\link[GiottoClass]{createGiottoImage}}, \code{\link[GiottoClass]{createGiottoInstructions}}, \code{\link[GiottoClass]{createGiottoLargeImage}}, \code{\link[GiottoClass]{createGiottoLargeImageList}}, \code{\link[GiottoClass]{createGiottoObject}}, \code{\link[GiottoClass]{createGiottoObjectSubcellular}}, \code{\link[GiottoClass]{createGiottoPoints}}, \code{\link[GiottoClass:createGiottoPolygon]{createGiottoPolygonsFromDfr}}, \code{\link[GiottoClass:createGiottoPolygon]{createGiottoPolygonsFromGeoJSON}}, \code{\link[GiottoClass:createGiottoPolygon]{createGiottoPolygonsFromMask}}, \code{\link[GiottoClass]{createMetafeats}}, \code{\link[GiottoClass]{createNearestNetObj}}, \code{\link[GiottoClass]{createSpatEnrObj}}, \code{\link[GiottoClass]{createSpatialDefaultGrid}}, \code{\link[GiottoClass]{createSpatialDelaunayNetwork}}, \code{\link[GiottoClass]{createSpatialFeaturesKNNnetwork}}, \code{\link[GiottoClass]{createSpatialGrid}}, \code{\link[GiottoClass]{createSpatialKNNnetwork}}, \code{\link[GiottoClass]{createSpatialNetwork}}, \code{\link[GiottoClass]{createSpatialWeightMatrix}}, \code{\link[GiottoClass]{createSpatLocsObj}}, \code{\link[GiottoClass]{createSpatNetObj}}, \code{\link[GiottoClass]{cropGiottoLargeImage}}, \code{\link[GiottoClass]{distGiottoImage}}, \code{\link[GiottoClass]{estimateImageBg}}, \code{\link[GiottoClass]{fDataDT}}, \code{\link[GiottoClass:featType-generic]{featType}}, \code{\link[GiottoClass:featureNetwork-class]{featureNetwork}}, \code{\link[GiottoClass]{gefToGiotto}}, \code{\link[GiottoClass]{get_dimReduction}}, \code{\link[GiottoClass]{get_dimReduction}}, \code{\link[GiottoClass]{get_feature_info}}, \code{\link[GiottoClass]{get_feature_info}}, \code{\link[GiottoClass]{get_giottoImage}}, \code{\link[GiottoClass]{get_giottoImage}}, \code{\link[GiottoClass]{get_multiomics}}, \code{\link[GiottoClass]{get_multiomics}}, \code{\link[GiottoClass]{get_NearestNetwork}}, \code{\link[GiottoClass]{get_NearestNetwork}}, \code{\link[GiottoClass]{get_polygon_info}}, \code{\link[GiottoClass]{get_polygon_info}}, \code{\link[GiottoClass]{get_spatial_enrichment}}, \code{\link[GiottoClass]{get_spatial_enrichment}}, \code{\link[GiottoClass]{get_spatial_locations}}, \code{\link[GiottoClass]{get_spatial_locations}}, \code{\link[GiottoClass]{get_spatialGrid}}, \code{\link[GiottoClass]{get_spatialGrid}}, \code{\link[GiottoClass]{get_spatialNetwork}}, \code{\link[GiottoClass]{get_spatialNetwork}}, \code{\link[GiottoClass]{getCellMetadata}}, \code{\link[GiottoClass]{getDimReduction}}, \code{\link[GiottoClass]{getExpression}}, \code{\link[GiottoClass]{getFeatureInfo}}, \code{\link[GiottoClass]{getFeatureMetadata}}, \code{\link[GiottoClass]{getGiottoImage}}, \code{\link[GiottoClass]{getMultiomics}}, \code{\link[GiottoClass]{getNearestNetwork}}, \code{\link[GiottoClass]{getPolygonInfo}}, \code{\link[GiottoClass]{getRainbowColors}}, \code{\link[GiottoClass]{getSpatialEnrichment}}, \code{\link[GiottoClass]{getSpatialEnrichment}}, \code{\link[GiottoClass]{getSpatialGrid}}, \code{\link[GiottoClass]{getSpatialGrid}}, \code{\link[GiottoClass]{getSpatialLocations}}, \code{\link[GiottoClass]{getSpatialLocations}}, \code{\link[GiottoClass]{getSpatialNetwork}}, \code{\link[GiottoClass]{getSpatialNetwork}}, \code{\link[GiottoClass:giotto-class]{giotto}}, \code{\link[GiottoClass:giottoImage-class]{giottoImage}}, \code{\link[GiottoClass:giottoLargeImage-class]{giottoLargeImage}}, \code{\link[GiottoClass]{giottoMasterToSuite}}, \code{\link[GiottoClass:giottoPoints-class]{giottoPoints}}, \code{\link[GiottoClass:giottoPolygon-class]{giottoPolygon}}, \code{\link[GiottoClass]{giottoToAnnData}}, \code{\link[GiottoClass]{giottoToSeurat}}, \code{\link[GiottoClass]{giottoToSpatialExperiment}}, \code{\link[GiottoClass]{hexVertices}}, \code{\link[GiottoClass]{joinGiottoObjects}}, \code{\link[GiottoClass]{loadGiotto}}, \code{\link[GiottoClass]{makePseudoVisium}}, \code{\link[GiottoClass]{objHistory}}, \code{\link[GiottoClass:objName-generic]{objName}}, \code{\link[GiottoClass]{overlapImagesToMatrix}}, \code{\link[GiottoClass]{overlapToMatrix}}, \code{\link[GiottoClass]{overlapToMatrixMultiPoly}}, \code{\link[GiottoClass]{pDataDT}}, \code{\link[GiottoClass]{plotGiottoImage}}, \code{\link[GiottoClass]{polyStamp}}, \code{\link[GiottoClass:prov-generic]{prov}}, \code{\link[GiottoClass:read_cell_metadata]{readCellMetadata}}, \code{\link[GiottoClass]{readDimReducData}}, \code{\link[GiottoClass]{readExprData}}, \code{\link[GiottoClass]{readExprMatrix}}, \code{\link[GiottoClass]{readFeatData}}, \code{\link[GiottoClass:read_feature_metadata]{readFeatMetadata}}, \code{\link[GiottoClass]{readGiottoInstructions}}, \code{\link[GiottoClass]{readNearestNetData}}, \code{\link[GiottoClass]{readPolygonData}}, \code{\link[GiottoClass]{readSpatEnrichData}}, \code{\link[GiottoClass]{readSpatLocsData}}, \code{\link[GiottoClass]{readSpatNetData}}, \code{\link[GiottoClass]{reconnectGiottoImage}}, \code{\link[GiottoClass]{rectVertices}}, \code{\link[GiottoClass]{removeCellAnnotation}}, \code{\link[GiottoClass]{removeFeatAnnotation}}, \code{\link[GiottoClass]{replaceGiottoInstructions}}, \code{\link[GiottoClass]{rescalePolygons}}, \code{\link[GiottoClass]{saveGiotto}}, \code{\link[GiottoClass]{set_dimReduction}}, \code{\link[GiottoClass]{set_expression_values}}, \code{\link[GiottoClass]{set_feature_info}}, \code{\link[GiottoClass]{set_giottoImage}}, \code{\link[GiottoClass]{set_multiomics}}, \code{\link[GiottoClass]{set_NearestNetwork}}, \code{\link[GiottoClass]{set_polygon_info}}, \code{\link[GiottoClass]{set_spatial_enrichment}}, \code{\link[GiottoClass]{set_spatial_locations}}, \code{\link[GiottoClass]{set_spatialGrid}}, \code{\link[GiottoClass]{set_spatialNetwork}}, \code{\link[GiottoClass]{setDimReduction}}, \code{\link[GiottoClass]{setExpression}}, \code{\link[GiottoClass]{setFeatureInfo}}, \code{\link[GiottoClass]{setGiottoImage}}, \code{\link[GiottoClass]{setMultiomics}}, \code{\link[GiottoClass]{setNearestNetwork}}, \code{\link[GiottoClass]{setPolygonInfo}}, \code{\link[GiottoClass]{setSpatialEnrichment}}, \code{\link[GiottoClass]{setSpatialGrid}}, \code{\link[GiottoClass]{setSpatialLocations}}, \code{\link[GiottoClass]{setSpatialNetwork}}, \code{\link[GiottoClass]{seuratToGiotto}}, \code{\link[GiottoClass]{showGiottoCellMetadata}}, \code{\link[GiottoClass]{showGiottoDimRed}}, \code{\link[GiottoClass]{showGiottoExpression}}, \code{\link[GiottoClass]{showGiottoFeatInfo}}, \code{\link[GiottoClass]{showGiottoFeatMetadata}}, \code{\link[GiottoClass]{showGiottoImageNames}}, \code{\link[GiottoClass]{showGiottoInstructions}}, \code{\link[GiottoClass]{showGiottoNearestNetworks}}, \code{\link[GiottoClass]{showGiottoSpatEnrichments}}, \code{\link[GiottoClass]{showGiottoSpatGrids}}, \code{\link[GiottoClass]{showGiottoSpatialInfo}}, \code{\link[GiottoClass]{showGiottoSpatLocs}}, \code{\link[GiottoClass]{showGiottoSpatNetworks}}, \code{\link[GiottoClass]{showGrids}}, \code{\link[GiottoClass]{showNetworks}}, \code{\link[GiottoClass]{showProcessingSteps}}}
+  \item{GiottoClass}{\code{\link[GiottoClass]{addCellMetadata}}, \code{\link[GiottoClass]{addGiottoImage}}, \code{\link[GiottoClass]{addGiottoImageMG}}, \code{\link[GiottoClass]{addGiottoLargeImage}}, \code{\link[GiottoClass]{addGiottoPoints}}, \code{\link[GiottoClass]{addGiottoPoints3D}}, \code{\link[GiottoClass]{addGiottoPolygons}}, \code{\link[GiottoClass]{addSpatialCentroidLocations}}, \code{\link[GiottoClass]{addSpatialCentroidLocationsLayer}}, \code{\link[GiottoClass]{aggregateStacks}}, \code{\link[GiottoClass]{aggregateStacksExpression}}, \code{\link[GiottoClass]{aggregateStacksLocations}}, \code{\link[GiottoClass]{aggregateStacksPolygonOverlaps}}, \code{\link[GiottoClass]{aggregateStacksPolygons}}, \code{\link[GiottoClass]{aggregateStacksPolygonsOLD}}, \code{\link[GiottoClass]{anndataToGiotto}}, \code{\link[GiottoClass]{annotateGiotto}}, \code{\link[GiottoClass]{annotateSpatialGrid}}, \code{\link[GiottoClass]{annotateSpatialNetwork}}, \code{\link[GiottoClass]{calculateMetaTable}}, \code{\link[GiottoClass]{calculateMetaTableCells}}, \code{\link[GiottoClass]{calculateOverlapParallel}}, \code{\link[GiottoClass]{calculateOverlapPolygonImages}}, \code{\link[GiottoClass]{calculateOverlapRaster}}, \code{\link[GiottoClass]{calculateOverlapSerial}}, \code{\link[GiottoClass]{changeGiottoInstructions}}, \code{\link[GiottoClass]{changeImageBg}}, \code{\link[GiottoClass]{circleVertices}}, \code{\link[GiottoClass]{combineCellData}}, \code{\link[GiottoClass]{combineFeatureData}}, \code{\link[GiottoClass]{combineFeatureOverlapData}}, \code{\link[GiottoClass]{combineMetadata}}, \code{\link[GiottoClass]{combineSpatialCellFeatureInfo}}, \code{\link[GiottoClass]{combineSpatialCellMetadataInfo}}, \code{\link[GiottoClass]{convertGiottoLargeImageToMG}}, \code{\link[GiottoClass]{createCellMetaObj}}, \code{\link[GiottoClass]{createDimObj}}, \code{\link[GiottoClass]{createExprObj}}, \code{\link[GiottoClass]{createFeatMetaObj}}, \code{\link[GiottoClass]{createGiottoImage}}, \code{\link[GiottoClass]{createGiottoInstructions}}, \code{\link[GiottoClass]{createGiottoLargeImage}}, \code{\link[GiottoClass]{createGiottoLargeImageList}}, \code{\link[GiottoClass]{createGiottoObject}}, \code{\link[GiottoClass]{createGiottoObjectSubcellular}}, \code{\link[GiottoClass]{createGiottoPoints}}, \code{\link[GiottoClass:createGiottoPolygon]{createGiottoPolygonsFromDfr}}, \code{\link[GiottoClass:createGiottoPolygon]{createGiottoPolygonsFromGeoJSON}}, \code{\link[GiottoClass:createGiottoPolygon]{createGiottoPolygonsFromMask}}, \code{\link[GiottoClass]{createMetafeats}}, \code{\link[GiottoClass]{createNearestNetObj}}, \code{\link[GiottoClass]{createSpatEnrObj}}, \code{\link[GiottoClass]{createSpatialDefaultGrid}}, \code{\link[GiottoClass]{createSpatialDelaunayNetwork}}, \code{\link[GiottoClass]{createSpatialFeaturesKNNnetwork}}, \code{\link[GiottoClass]{createSpatialGrid}}, \code{\link[GiottoClass]{createSpatialKNNnetwork}}, \code{\link[GiottoClass]{createSpatialNetwork}}, \code{\link[GiottoClass]{createSpatialWeightMatrix}}, \code{\link[GiottoClass]{createSpatLocsObj}}, \code{\link[GiottoClass]{createSpatNetObj}}, \code{\link[GiottoClass]{cropGiottoLargeImage}}, \code{\link[GiottoClass]{distGiottoImage}}, \code{\link[GiottoClass]{estimateImageBg}}, \code{\link[GiottoClass]{fDataDT}}, \code{\link[GiottoClass:featType-generic]{featType}}, \code{\link[GiottoClass:featureNetwork-class]{featureNetwork}}, \code{\link[GiottoClass]{gefToGiotto}}, \code{\link[GiottoClass]{get_dimReduction}}, \code{\link[GiottoClass]{get_dimReduction}}, \code{\link[GiottoClass]{get_feature_info}}, \code{\link[GiottoClass]{get_feature_info}}, \code{\link[GiottoClass]{get_giottoImage}}, \code{\link[GiottoClass]{get_giottoImage}}, \code{\link[GiottoClass]{get_multiomics}}, \code{\link[GiottoClass]{get_multiomics}}, \code{\link[GiottoClass]{get_NearestNetwork}}, \code{\link[GiottoClass]{get_NearestNetwork}}, \code{\link[GiottoClass]{get_polygon_info}}, \code{\link[GiottoClass]{get_polygon_info}}, \code{\link[GiottoClass]{get_spatial_enrichment}}, \code{\link[GiottoClass]{get_spatial_enrichment}}, \code{\link[GiottoClass]{get_spatial_locations}}, \code{\link[GiottoClass]{get_spatial_locations}}, \code{\link[GiottoClass]{get_spatialGrid}}, \code{\link[GiottoClass]{get_spatialGrid}}, \code{\link[GiottoClass]{get_spatialNetwork}}, \code{\link[GiottoClass]{get_spatialNetwork}}, \code{\link[GiottoClass]{getCellMetadata}}, \code{\link[GiottoClass]{getDimReduction}}, \code{\link[GiottoClass]{getExpression}}, \code{\link[GiottoClass]{getFeatureInfo}}, \code{\link[GiottoClass]{getFeatureMetadata}}, \code{\link[GiottoClass]{getGiottoImage}}, \code{\link[GiottoClass]{getMultiomics}}, \code{\link[GiottoClass]{getNearestNetwork}}, \code{\link[GiottoClass]{getPolygonInfo}}, \code{\link[GiottoClass]{getRainbowColors}}, \code{\link[GiottoClass]{getSpatialEnrichment}}, \code{\link[GiottoClass]{getSpatialEnrichment}}, \code{\link[GiottoClass]{getSpatialGrid}}, \code{\link[GiottoClass]{getSpatialGrid}}, \code{\link[GiottoClass]{getSpatialLocations}}, \code{\link[GiottoClass]{getSpatialLocations}}, \code{\link[GiottoClass]{getSpatialNetwork}}, \code{\link[GiottoClass]{getSpatialNetwork}}, \code{\link[GiottoClass:giotto-class]{giotto}}, \code{\link[GiottoClass:giottoImage-class]{giottoImage}}, \code{\link[GiottoClass:giottoLargeImage-class]{giottoLargeImage}}, \code{\link[GiottoClass]{giottoMasterToSuite}}, \code{\link[GiottoClass:giottoPoints-class]{giottoPoints}}, \code{\link[GiottoClass:giottoPolygon-class]{giottoPolygon}}, \code{\link[GiottoClass]{giottoToAnnData}}, \code{\link[GiottoClass]{giottoToSeurat}}, \code{\link[GiottoClass]{giottoToSpatialExperiment}}, \code{\link[GiottoClass]{hexVertices}}, \code{\link[GiottoClass]{joinGiottoObjects}}, \code{\link[GiottoClass]{loadGiotto}}, \code{\link[GiottoClass]{makePseudoVisium}}, \code{\link[GiottoClass]{objHistory}}, \code{\link[GiottoClass:objName-generic]{objName}}, \code{\link[GiottoClass]{overlapImagesToMatrix}}, \code{\link[GiottoClass]{overlapToMatrix}}, \code{\link[GiottoClass]{overlapToMatrixMultiPoly}}, \code{\link[GiottoClass]{pDataDT}}, \code{\link[GiottoClass]{plotGiottoImage}}, \code{\link[GiottoClass]{polyStamp}}, \code{\link[GiottoClass:prov-generic]{prov}}, \code{\link[GiottoClass:read_cell_metadata]{readCellMetadata}}, \code{\link[GiottoClass]{readDimReducData}}, \code{\link[GiottoClass]{readExprData}}, \code{\link[GiottoClass]{readExprMatrix}}, \code{\link[GiottoClass]{readFeatData}}, \code{\link[GiottoClass:read_feature_metadata]{readFeatMetadata}}, \code{\link[GiottoClass]{readGiottoInstructions}}, \code{\link[GiottoClass]{readNearestNetData}}, \code{\link[GiottoClass]{readPolygonData}}, \code{\link[GiottoClass]{readSpatEnrichData}}, \code{\link[GiottoClass]{readSpatLocsData}}, \code{\link[GiottoClass]{readSpatNetData}}, \code{\link[GiottoClass]{reconnectGiottoImage}}, \code{\link[GiottoClass]{rectVertices}}, \code{\link[GiottoClass]{removeCellAnnotation}}, \code{\link[GiottoClass]{removeFeatAnnotation}}, \code{\link[GiottoClass]{replaceGiottoInstructions}}, \code{\link[GiottoClass]{rescalePolygons}}, \code{\link[GiottoClass]{saveGiotto}}, \code{\link[GiottoClass]{set_dimReduction}}, \code{\link[GiottoClass]{set_expression_values}}, \code{\link[GiottoClass]{set_feature_info}}, \code{\link[GiottoClass]{set_giottoImage}}, \code{\link[GiottoClass]{set_multiomics}}, \code{\link[GiottoClass]{set_NearestNetwork}}, \code{\link[GiottoClass]{set_polygon_info}}, \code{\link[GiottoClass]{set_spatial_enrichment}}, \code{\link[GiottoClass]{set_spatial_locations}}, \code{\link[GiottoClass]{set_spatialGrid}}, \code{\link[GiottoClass]{set_spatialNetwork}}, \code{\link[GiottoClass]{setDimReduction}}, \code{\link[GiottoClass]{setExpression}}, \code{\link[GiottoClass]{setFeatureInfo}}, \code{\link[GiottoClass]{setGiottoImage}}, \code{\link[GiottoClass]{setMultiomics}}, \code{\link[GiottoClass]{setNearestNetwork}}, \code{\link[GiottoClass]{setPolygonInfo}}, \code{\link[GiottoClass]{setSpatialEnrichment}}, \code{\link[GiottoClass]{setSpatialGrid}}, \code{\link[GiottoClass]{setSpatialLocations}}, \code{\link[GiottoClass]{setSpatialNetwork}}, \code{\link[GiottoClass]{seuratToGiotto}}, \code{\link[GiottoClass]{showGiottoCellMetadata}}, \code{\link[GiottoClass]{showGiottoDimRed}}, \code{\link[GiottoClass]{showGiottoExpression}}, \code{\link[GiottoClass]{showGiottoFeatInfo}}, \code{\link[GiottoClass]{showGiottoFeatMetadata}}, \code{\link[GiottoClass]{showGiottoImageNames}}, \code{\link[GiottoClass]{showGiottoInstructions}}, \code{\link[GiottoClass]{showGiottoNearestNetworks}}, \code{\link[GiottoClass]{showGiottoSpatEnrichments}}, \code{\link[GiottoClass]{showGiottoSpatGrids}}, \code{\link[GiottoClass]{showGiottoSpatialInfo}}, \code{\link[GiottoClass]{showGiottoSpatLocs}}, \code{\link[GiottoClass]{showGiottoSpatNetworks}}, \code{\link[GiottoClass]{showGrids}}, \code{\link[GiottoClass]{showNetworks}}, \code{\link[GiottoClass]{showProcessingSteps}}}
 
   \item{GiottoUtils}{\code{\link[GiottoUtils:pipe]{\%>\%}}}
 
diff --git a/man/runPCAprojection.Rd b/man/runPCAprojection.Rd
index ae2546d97..bdf95f934 100644
--- a/man/runPCAprojection.Rd
+++ b/man/runPCAprojection.Rd
@@ -37,7 +37,7 @@ runPCAprojection(
 
 \item{reduction}{cells or genes}
 
-\item{random_subset}{numeric. random subset to perform PCA on}
+\item{random_subset}{random subset to perform PCA on}
 
 \item{name}{arbitrary name for PCA run}
 
diff --git a/tests/testthat/test_mini_vizgen.R b/tests/testthat/test_mini_vizgen.R
deleted file mode 100644
index fa1a58f85..000000000
--- a/tests/testthat/test_mini_vizgen.R
+++ /dev/null
@@ -1,314 +0,0 @@
-# Continuing on from GiottoClass mini vizgen
-
-options('giotto.use_conda' = FALSE)
-g <- GiottoData::loadGiottoMini('vizgen')
-
-# reset portions of object to before aggregate spat_unit filtering and normalization
-
-
-
-# 5. normalize on aggregated layer #####
-# ----------------------------------- ##
-
-# rna data, default.
-# other feature modalities can be processed and filtered in an anologous manner
-vizsubc <- normalizeGiotto(gobject = vizsubc, spat_unit = 'aggregate',
-                           scalefactor = 5000, verbose = T)
-vizsubc <- addStatistics(gobject = vizsubc, spat_unit = 'aggregate')
-vizsubc <- normalizeGiotto(gobject = vizsubc, spat_unit = 'aggregate',
-                           norm_methods = 'pearson_resid', update_slot = 'pearson')
-
-
-# 6. highly variable genes ####
-# ----------------------------- #
-
-# typical way of calculating HVG
-vizsubc <- calculateHVF(gobject = vizsubc, spat_unit = 'aggregate', HVFname = 'hvg_orig')
-
-# new method based on variance of pearson residuals for each gene
-vizsubc <- calculateHVF(gobject = vizsubc,
-                        spat_unit = 'aggregate',
-                        method = 'var_p_resid',
-                        expression_values = 'pearson',
-                        show_plot = T)
-
-
-
-# 7. dimension reduction ####
-# --------------------------- #
-
-# ** 7.1 PCA ####
-
-# we will run pca on the pre-scaled matrix from the pearson residual normalization
-# if features are not specified it will automatically search for the hvf column in the feature metadata
-
-vizsubc <- runPCA(gobject = vizsubc,
-                  spat_unit = 'aggregate',
-                  expression_values = 'pearson',
-                  scale_unit = F, center = F)
-
-screePlot(vizsubc,
-          ncp = 20,
-          spat_unit = 'aggregate')
-
-showGiottoDimRed(vizsubc)
-
-plotPCA(vizsubc,
-        spat_unit = 'aggregate',
-        dim_reduction_name = 'pca',
-        dim1_to_use = 1,
-        dim2_to_use = 2)
-
-
-# ** 7.2 UMAP and TSN ####
-vizsubc <- runUMAP(vizsubc, dimensions_to_use = 1:8, n_threads = 4, spat_unit = 'aggregate')
-plotUMAP(gobject = vizsubc, spat_unit = 'aggregate')
-
-vizsubc <- runtSNE(vizsubc, dimensions_to_use = 1:8, spat_unit = 'aggregate')
-plotTSNE(gobject = vizsubc, spat_unit = 'aggregate')
-
-
-# 8. graph-based clustering ####
-# ---------------------------- #
-vizsubc <- createNearestNetwork(gobject = vizsubc, dimensions_to_use = 1:8, k = 10,
-                                spat_unit = 'aggregate')
-vizsubc <- doLeidenCluster(gobject = vizsubc, resolution = 0.05, n_iterations = 1000,
-                           spat_unit = 'aggregate')
-vizsubc <- doLouvainCluster(gobject = vizsubc, resolution = 5,
-                            spat_unit = 'aggregate')
-
-
-# visualize UMAP / TSNE cluster results
-plotUMAP(gobject = vizsubc,
-         spat_unit = 'aggregate',
-         cell_color = 'leiden_clus',
-         show_NN_network = T,
-         point_size = 2.5)
-
-spatInSituPlotPoints(vizsubc,
-                     show_polygon = TRUE,
-                     spat_unit = 'aggregate',
-                     polygon_feat_type = 'aggregate',
-                     polygon_color = 'white',
-                     polygon_line_size = 0.1,
-                     polygon_fill = 'leiden_clus',
-                     polygon_fill_as_factor = T,
-                     coord_fix_ratio = T)
-
-plotTSNE(gobject = vizsubc,
-         spat_unit = 'aggregate',
-         cell_color = 'louvain_clus',
-         show_NN_network = T,
-         point_size = 2.5)
-
-spatInSituPlotPoints(vizsubc,
-                     show_polygon = TRUE,
-                     spat_unit = 'aggregate',
-                     polygon_feat_type = 'aggregate',
-                     polygon_color = 'white',
-                     polygon_line_size = 0.1,
-                     polygon_fill = 'louvain_clus',
-                     polygon_fill_as_factor = T,
-                     coord_fix_ratio = T)
-
-spatInSituPlotPoints(vizsubc,
-                     spat_unit = 'aggregate',
-                     show_image = T,
-                     largeImage_name = 'dapi_z0',
-                     feats = list('rna' = c("Htr1b", "Ackr1", "Epha7")),
-                     feats_color_code = c("Htr1b" = 'green', 'Ackr1' = 'blue', 'Epha7' = 'red'),
-                     point_size = 0.35,
-                     show_polygon = TRUE,
-                     polygon_feat_type = 'aggregate',
-                     polygon_color = 'white',
-                     polygon_line_size = 0.1,
-                     polygon_fill = 'leiden_clus',
-                     polygon_fill_as_factor = T,
-                     coord_fix_ratio = TRUE)
-
-
-
-
-# 9. spatial network ####
-# --------------------- #
-# defaults to delaunay
-vizsubc = createSpatialNetwork(vizsubc, spat_unit = 'aggregate')
-# kNN with k of 8 nearest
-vizsubc = createSpatialNetwork(vizsubc, spat_unit = 'aggregate', method = 'kNN', k = 8)
-# create spatial weight matrix
-vizsubc = createSpatialWeightMatrix(vizsubc,
-                                    spat_unit = 'aggregate',
-                                    method = 'distance',
-                                    spatial_network_to_use = 'kNN_network',
-                                    return_gobject = TRUE)
-
-pDataDT(vizsubc, 'aggregate')
-spatPlot(gobject = vizsubc,
-         spat_unit = 'aggregate',
-         show_network = T,
-         network_color = 'lightgray',
-         spatial_network_name = 'Delaunay_network',
-         point_size = 2.5,
-         cell_color = 'leiden_clus')
-
-
-## 9.1 spatial genes ####
-km_spatialfeats = binSpect(vizsubc, spat_unit = 'aggregate')
-
-spatFeatPlot2D_single(vizsubc,
-                      spat_unit = 'aggregate',
-                      expression_values = 'scaled',
-                      feats = km_spatialfeats[1:4]$feats,
-                      point_shape = 'border',
-                      point_border_stroke = 0.1,
-                      show_network = F,
-                      network_color = 'lightgrey',
-                      point_size = 2.5,
-                      cow_n_col = 2)
-
-## 9.2 spatial co-expression ####
-# here we use existing detectSpatialCorGenes function to calculate pairwise distances between genes
-ext_spatial_genes = km_spatialfeats[1:200,]$feats
-spat_cor_netw_DT = detectSpatialCorFeats(vizsubc,
-                                         spat_unit = 'aggregate',
-                                         method = 'network',
-                                         spatial_network_name = 'Delaunay_network',
-                                         subset_feats = ext_spatial_genes)
-
-# cluster and visualize spatial co-expression genes
-spat_cor_netw_DT = clusterSpatialCorFeats(spat_cor_netw_DT,
-                                          name = 'spat_netw_clus',
-                                          k = 5)
-
-heatmSpatialCorFeats(vizsubc,
-                     spatCorObject = spat_cor_netw_DT,
-                     use_clus_name = 'spat_netw_clus',
-                     heatmap_legend_param = list(title = NULL),
-                     save_param = list(base_height = 6,
-                                       base_width = 8,
-                                       units = 'cm'))
-
-# create and visualize metafeatures
-testweight = getBalancedSpatCoexpressionFeats(spat_cor_netw_DT, rank = 'weighted', maximum = 30)
-
-vizsubc = createMetafeats(vizsubc,
-                          spat_unit = 'aggregate',
-                          feat_clusters = testweight,
-                          name = 'cluster_metagene')
-
-spatCellPlot(vizsubc,
-             spat_unit = 'aggregate',
-             spat_enr_names = 'cluster_metagene',
-             cell_annotation_values = as.character(c(1:6)),
-             gradient_style = 's',
-             point_size = 1.8,
-             save_param = list(base_width = 15))
-
-
-
-## 9.3 spatial structure ####
-cell_proximities = cellProximityEnrichment(gobject = vizsubc,
-                                           spat_unit = 'aggregate',
-                                           cluster_column = 'leiden_clus',
-                                           spatial_network_name = 'Delaunay_network',
-                                           adjust_method = 'fdr',
-                                           number_of_simulations = 2000)
-## barplot
-cellProximityBarplot(gobject = vizsubc,
-                     CPscore = cell_proximities,
-                     min_orig_ints = 5, min_sim_ints = 5)
-
-## heatmap
-cellProximityHeatmap(gobject = vizsubc,
-                     CPscore = cell_proximities,
-                     order_cell_types = T, scale = T,
-                     color_breaks = c(-1.5, 0, 1.5),
-                     color_names = c('blue', 'white', 'red'))
-
-spatInSituPlotPoints(
-  vizsubc,
-  spat_unit = 'aggregate',
-  show_image = T,
-  largeImage_name = 'dapi_z0',
-  feats = list('rna' = c("Htr1b", "Ackr1", "Epha7")),
-  feats_color_code = c("Htr1b" = 'green', 'Ackr1' = 'blue', 'Epha7' = 'red'),
-  point_size = 0.75,
-  show_polygon = TRUE,
-  polygon_feat_type = 'aggregate',
-  polygon_color = 'white',
-  polygon_line_size = 0.1,
-  polygon_fill = 'leiden_clus',
-  polygon_fill_as_factor = T,
-  coord_fix_ratio = 1
-)
-
-showGiottoSpatialInfo(vizsubc)
-
-
-spatInSituPlotDensity(vizsubc,
-                      polygon_feat_type = 'aggregate',
-                      feats = c("Htr1b", "Ackr1", "Epha7"),
-                      alpha = 0.5,
-                      polygon_color = 'white')
-
-spatInSituPlotHex(vizsubc,
-                  polygon_feat_type = 'aggregate',
-                  feats = c("Htr1b", "Ackr1", "Epha7"))
-
-
-
-# 10. save Giotto object ####
-# ------------------------- #
-format(object.size(vizsubc), units = 'Mb')
-
-# you need to use your local GiottoData repo
-# giottodata_repo = '/Users/rubendries/Packages/R_Packages/GiottoData/inst/Mini_datasets/'
-giottodata_repo = '/Users/rubendries/r_packages/GiottoData//inst/Mini_datasets/'
-
-saveGiotto(vizsubc,
-           foldername = 'VizgenObject',
-           #dir = paste0(system.file(package = 'GiottoData'),'/', 'Mini_datasets/Vizgen/'),
-           dir = paste0(giottodata_repo, '/', 'Vizgen/'),
-           overwrite = TRUE)
-
-pDataDT(vizsubc, spat_unit = 'aggregate')
-pDataDT(vizsubc, spat_unit = 'aggregate')
-
-
-
-## some quick tests ##
-gvizg = loadGiotto(path_to_folder = system.file('/Mini_datasets/Vizgen/VizgenObject/',
-                                                package = 'GiottoData'))
-
-
-# subsetting
-selected_ids = pDataDT(gvizg)$cell_ID[1:100]
-
-# important to specify which spatial_unit to use and which polygon information slots to update
-mySubset <- subsetGiotto(gobject = gvizg,
-                         cell_ids = selected_ids,
-                         spat_unit = 'aggregate',
-                         poly_info = c('aggregate'))
-
-pDataDT(mySubset, 'aggregate')
-fDataDT(mySubset)
-
-spatInSituPlotPoints(mySubset,
-                     spat_unit = 'aggregate',
-                     show_image = T,
-                     largeImage_name = 'dapi_z0',
-                     feats = list('rna' = c("Htr1b", "Ackr1", "Epha7")),
-                     feats_color_code = c("Htr1b" = 'green', 'Ackr1' = 'blue', 'Epha7' = 'red'),
-                     point_size = 0.35,
-                     show_polygon = TRUE,
-                     polygon_feat_type = 'aggregate',
-                     polygon_color = 'white',
-                     polygon_line_size = 0.1,
-                     polygon_fill = 'leiden_clus',
-                     polygon_fill_as_factor = T,
-                     coord_fix_ratio = TRUE)
-
-
-spatPlot(gobject = mySubset, spat_unit = 'aggregate', show_network = T,
-         network_color = 'lightgray', spatial_network_name = 'Delaunay_network',
-         point_size = 2.5, cell_color = 'leiden_clus')

From 8f5dd12a3ef1ffd4e8b6b4214e870f25db9afe10 Mon Sep 17 00:00:00 2001
From: jiajic <72078254+jiajic@users.noreply.github.com>
Date: Wed, 29 Nov 2023 12:08:40 -0500
Subject: [PATCH 6/6] run document

---
 man/findScranMarkers.Rd | 2 +-
 man/reexports.Rd        | 2 +-
 man/runPCAprojection.Rd | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/man/findScranMarkers.Rd b/man/findScranMarkers.Rd
index 84f39d7b7..b35d9b18c 100644
--- a/man/findScranMarkers.Rd
+++ b/man/findScranMarkers.Rd
@@ -15,7 +15,7 @@ findScranMarkers(
   group_1_name = NULL,
   group_2 = NULL,
   group_2_name = NULL,
-  verbose = FALSE,
+  verbose = TRUE,
   ...
 )
 }
diff --git a/man/reexports.Rd b/man/reexports.Rd
index 01e774cb3..6c9417f73 100644
--- a/man/reexports.Rd
+++ b/man/reexports.Rd
@@ -206,7 +206,7 @@ These objects are imported from other packages. Follow the links
 below to see their documentation.
 
 \describe{
-  \item{GiottoClass}{\code{\link[GiottoClass]{addCellMetadata}}, \code{\link[GiottoClass]{addGiottoImage}}, \code{\link[GiottoClass]{addGiottoImageMG}}, \code{\link[GiottoClass]{addGiottoLargeImage}}, \code{\link[GiottoClass]{addGiottoPoints}}, \code{\link[GiottoClass]{addGiottoPoints3D}}, \code{\link[GiottoClass]{addGiottoPolygons}}, \code{\link[GiottoClass]{addSpatialCentroidLocations}}, \code{\link[GiottoClass]{addSpatialCentroidLocationsLayer}}, \code{\link[GiottoClass]{aggregateStacks}}, \code{\link[GiottoClass]{aggregateStacksExpression}}, \code{\link[GiottoClass]{aggregateStacksLocations}}, \code{\link[GiottoClass]{aggregateStacksPolygonOverlaps}}, \code{\link[GiottoClass]{aggregateStacksPolygons}}, \code{\link[GiottoClass]{aggregateStacksPolygonsOLD}}, \code{\link[GiottoClass]{anndataToGiotto}}, \code{\link[GiottoClass]{annotateGiotto}}, \code{\link[GiottoClass]{annotateSpatialGrid}}, \code{\link[GiottoClass]{annotateSpatialNetwork}}, \code{\link[GiottoClass]{calculateMetaTable}}, \code{\link[GiottoClass]{calculateMetaTableCells}}, \code{\link[GiottoClass]{calculateOverlapParallel}}, \code{\link[GiottoClass]{calculateOverlapPolygonImages}}, \code{\link[GiottoClass]{calculateOverlapRaster}}, \code{\link[GiottoClass]{calculateOverlapSerial}}, \code{\link[GiottoClass]{changeGiottoInstructions}}, \code{\link[GiottoClass]{changeImageBg}}, \code{\link[GiottoClass]{circleVertices}}, \code{\link[GiottoClass]{combineCellData}}, \code{\link[GiottoClass]{combineFeatureData}}, \code{\link[GiottoClass]{combineFeatureOverlapData}}, \code{\link[GiottoClass]{combineMetadata}}, \code{\link[GiottoClass]{combineSpatialCellFeatureInfo}}, \code{\link[GiottoClass]{combineSpatialCellMetadataInfo}}, \code{\link[GiottoClass]{convertGiottoLargeImageToMG}}, \code{\link[GiottoClass]{createCellMetaObj}}, \code{\link[GiottoClass]{createDimObj}}, \code{\link[GiottoClass]{createExprObj}}, \code{\link[GiottoClass]{createFeatMetaObj}}, \code{\link[GiottoClass]{createGiottoImage}}, \code{\link[GiottoClass]{createGiottoInstructions}}, \code{\link[GiottoClass]{createGiottoLargeImage}}, \code{\link[GiottoClass]{createGiottoLargeImageList}}, \code{\link[GiottoClass]{createGiottoObject}}, \code{\link[GiottoClass]{createGiottoObjectSubcellular}}, \code{\link[GiottoClass]{createGiottoPoints}}, \code{\link[GiottoClass:createGiottoPolygon]{createGiottoPolygonsFromDfr}}, \code{\link[GiottoClass:createGiottoPolygon]{createGiottoPolygonsFromGeoJSON}}, \code{\link[GiottoClass:createGiottoPolygon]{createGiottoPolygonsFromMask}}, \code{\link[GiottoClass]{createMetafeats}}, \code{\link[GiottoClass]{createNearestNetObj}}, \code{\link[GiottoClass]{createSpatEnrObj}}, \code{\link[GiottoClass]{createSpatialDefaultGrid}}, \code{\link[GiottoClass]{createSpatialDelaunayNetwork}}, \code{\link[GiottoClass]{createSpatialFeaturesKNNnetwork}}, \code{\link[GiottoClass]{createSpatialGrid}}, \code{\link[GiottoClass]{createSpatialKNNnetwork}}, \code{\link[GiottoClass]{createSpatialNetwork}}, \code{\link[GiottoClass]{createSpatialWeightMatrix}}, \code{\link[GiottoClass]{createSpatLocsObj}}, \code{\link[GiottoClass]{createSpatNetObj}}, \code{\link[GiottoClass]{cropGiottoLargeImage}}, \code{\link[GiottoClass]{distGiottoImage}}, \code{\link[GiottoClass]{estimateImageBg}}, \code{\link[GiottoClass]{fDataDT}}, \code{\link[GiottoClass:featType-generic]{featType}}, \code{\link[GiottoClass:featureNetwork-class]{featureNetwork}}, \code{\link[GiottoClass]{gefToGiotto}}, \code{\link[GiottoClass]{get_dimReduction}}, \code{\link[GiottoClass]{get_dimReduction}}, \code{\link[GiottoClass]{get_feature_info}}, \code{\link[GiottoClass]{get_feature_info}}, \code{\link[GiottoClass]{get_giottoImage}}, \code{\link[GiottoClass]{get_giottoImage}}, \code{\link[GiottoClass]{get_multiomics}}, \code{\link[GiottoClass]{get_multiomics}}, \code{\link[GiottoClass]{get_NearestNetwork}}, \code{\link[GiottoClass]{get_NearestNetwork}}, \code{\link[GiottoClass]{get_polygon_info}}, \code{\link[GiottoClass]{get_polygon_info}}, \code{\link[GiottoClass]{get_spatial_enrichment}}, \code{\link[GiottoClass]{get_spatial_enrichment}}, \code{\link[GiottoClass]{get_spatial_locations}}, \code{\link[GiottoClass]{get_spatial_locations}}, \code{\link[GiottoClass]{get_spatialGrid}}, \code{\link[GiottoClass]{get_spatialGrid}}, \code{\link[GiottoClass]{get_spatialNetwork}}, \code{\link[GiottoClass]{get_spatialNetwork}}, \code{\link[GiottoClass]{getCellMetadata}}, \code{\link[GiottoClass]{getDimReduction}}, \code{\link[GiottoClass]{getExpression}}, \code{\link[GiottoClass]{getFeatureInfo}}, \code{\link[GiottoClass]{getFeatureMetadata}}, \code{\link[GiottoClass]{getGiottoImage}}, \code{\link[GiottoClass]{getMultiomics}}, \code{\link[GiottoClass]{getNearestNetwork}}, \code{\link[GiottoClass]{getPolygonInfo}}, \code{\link[GiottoClass]{getRainbowColors}}, \code{\link[GiottoClass]{getSpatialEnrichment}}, \code{\link[GiottoClass]{getSpatialEnrichment}}, \code{\link[GiottoClass]{getSpatialGrid}}, \code{\link[GiottoClass]{getSpatialGrid}}, \code{\link[GiottoClass]{getSpatialLocations}}, \code{\link[GiottoClass]{getSpatialLocations}}, \code{\link[GiottoClass]{getSpatialNetwork}}, \code{\link[GiottoClass]{getSpatialNetwork}}, \code{\link[GiottoClass:giotto-class]{giotto}}, \code{\link[GiottoClass:giottoImage-class]{giottoImage}}, \code{\link[GiottoClass:giottoLargeImage-class]{giottoLargeImage}}, \code{\link[GiottoClass]{giottoMasterToSuite}}, \code{\link[GiottoClass:giottoPoints-class]{giottoPoints}}, \code{\link[GiottoClass:giottoPolygon-class]{giottoPolygon}}, \code{\link[GiottoClass]{giottoToAnnData}}, \code{\link[GiottoClass]{giottoToSeurat}}, \code{\link[GiottoClass]{giottoToSpatialExperiment}}, \code{\link[GiottoClass]{hexVertices}}, \code{\link[GiottoClass]{joinGiottoObjects}}, \code{\link[GiottoClass]{loadGiotto}}, \code{\link[GiottoClass]{makePseudoVisium}}, \code{\link[GiottoClass]{objHistory}}, \code{\link[GiottoClass:objName-generic]{objName}}, \code{\link[GiottoClass]{overlapImagesToMatrix}}, \code{\link[GiottoClass]{overlapToMatrix}}, \code{\link[GiottoClass]{overlapToMatrixMultiPoly}}, \code{\link[GiottoClass]{pDataDT}}, \code{\link[GiottoClass]{plotGiottoImage}}, \code{\link[GiottoClass]{polyStamp}}, \code{\link[GiottoClass:prov-generic]{prov}}, \code{\link[GiottoClass:read_cell_metadata]{readCellMetadata}}, \code{\link[GiottoClass]{readDimReducData}}, \code{\link[GiottoClass]{readExprData}}, \code{\link[GiottoClass]{readExprMatrix}}, \code{\link[GiottoClass]{readFeatData}}, \code{\link[GiottoClass:read_feature_metadata]{readFeatMetadata}}, \code{\link[GiottoClass]{readGiottoInstructions}}, \code{\link[GiottoClass]{readNearestNetData}}, \code{\link[GiottoClass]{readPolygonData}}, \code{\link[GiottoClass]{readSpatEnrichData}}, \code{\link[GiottoClass]{readSpatLocsData}}, \code{\link[GiottoClass]{readSpatNetData}}, \code{\link[GiottoClass]{reconnectGiottoImage}}, \code{\link[GiottoClass]{rectVertices}}, \code{\link[GiottoClass]{removeCellAnnotation}}, \code{\link[GiottoClass]{removeFeatAnnotation}}, \code{\link[GiottoClass]{replaceGiottoInstructions}}, \code{\link[GiottoClass]{rescalePolygons}}, \code{\link[GiottoClass]{saveGiotto}}, \code{\link[GiottoClass]{set_dimReduction}}, \code{\link[GiottoClass]{set_expression_values}}, \code{\link[GiottoClass]{set_feature_info}}, \code{\link[GiottoClass]{set_giottoImage}}, \code{\link[GiottoClass]{set_multiomics}}, \code{\link[GiottoClass]{set_NearestNetwork}}, \code{\link[GiottoClass]{set_polygon_info}}, \code{\link[GiottoClass]{set_spatial_enrichment}}, \code{\link[GiottoClass]{set_spatial_locations}}, \code{\link[GiottoClass]{set_spatialGrid}}, \code{\link[GiottoClass]{set_spatialNetwork}}, \code{\link[GiottoClass]{setDimReduction}}, \code{\link[GiottoClass]{setExpression}}, \code{\link[GiottoClass]{setFeatureInfo}}, \code{\link[GiottoClass]{setGiottoImage}}, \code{\link[GiottoClass]{setMultiomics}}, \code{\link[GiottoClass]{setNearestNetwork}}, \code{\link[GiottoClass]{setPolygonInfo}}, \code{\link[GiottoClass]{setSpatialEnrichment}}, \code{\link[GiottoClass]{setSpatialGrid}}, \code{\link[GiottoClass]{setSpatialLocations}}, \code{\link[GiottoClass]{setSpatialNetwork}}, \code{\link[GiottoClass]{seuratToGiotto}}, \code{\link[GiottoClass]{showGiottoCellMetadata}}, \code{\link[GiottoClass]{showGiottoDimRed}}, \code{\link[GiottoClass]{showGiottoExpression}}, \code{\link[GiottoClass]{showGiottoFeatInfo}}, \code{\link[GiottoClass]{showGiottoFeatMetadata}}, \code{\link[GiottoClass]{showGiottoImageNames}}, \code{\link[GiottoClass]{showGiottoInstructions}}, \code{\link[GiottoClass]{showGiottoNearestNetworks}}, \code{\link[GiottoClass]{showGiottoSpatEnrichments}}, \code{\link[GiottoClass]{showGiottoSpatGrids}}, \code{\link[GiottoClass]{showGiottoSpatialInfo}}, \code{\link[GiottoClass]{showGiottoSpatLocs}}, \code{\link[GiottoClass]{showGiottoSpatNetworks}}, \code{\link[GiottoClass]{showGrids}}, \code{\link[GiottoClass]{showNetworks}}, \code{\link[GiottoClass]{showProcessingSteps}}}
+  \item{GiottoClass}{\code{\link[GiottoClass]{addCellMetadata}}, \code{\link[GiottoClass]{addGiottoImage}}, \code{\link[GiottoClass]{addGiottoImageMG}}, \code{\link[GiottoClass]{addGiottoLargeImage}}, \code{\link[GiottoClass]{addGiottoPoints}}, \code{\link[GiottoClass:addGiottoPoints]{addGiottoPoints3D}}, \code{\link[GiottoClass]{addGiottoPolygons}}, \code{\link[GiottoClass]{addSpatialCentroidLocations}}, \code{\link[GiottoClass]{addSpatialCentroidLocationsLayer}}, \code{\link[GiottoClass]{aggregateStacks}}, \code{\link[GiottoClass]{aggregateStacksExpression}}, \code{\link[GiottoClass]{aggregateStacksLocations}}, \code{\link[GiottoClass]{aggregateStacksPolygonOverlaps}}, \code{\link[GiottoClass]{aggregateStacksPolygons}}, \code{\link[GiottoClass]{aggregateStacksPolygonsOLD}}, \code{\link[GiottoClass]{anndataToGiotto}}, \code{\link[GiottoClass]{annotateGiotto}}, \code{\link[GiottoClass]{annotateSpatialGrid}}, \code{\link[GiottoClass]{annotateSpatialNetwork}}, \code{\link[GiottoClass]{calculateMetaTable}}, \code{\link[GiottoClass]{calculateMetaTableCells}}, \code{\link[GiottoClass]{calculateOverlapParallel}}, \code{\link[GiottoClass]{calculateOverlapPolygonImages}}, \code{\link[GiottoClass]{calculateOverlapRaster}}, \code{\link[GiottoClass]{calculateOverlapSerial}}, \code{\link[GiottoClass]{changeGiottoInstructions}}, \code{\link[GiottoClass]{changeImageBg}}, \code{\link[GiottoClass]{circleVertices}}, \code{\link[GiottoClass]{combineCellData}}, \code{\link[GiottoClass]{combineFeatureData}}, \code{\link[GiottoClass]{combineFeatureOverlapData}}, \code{\link[GiottoClass]{combineMetadata}}, \code{\link[GiottoClass]{combineSpatialCellFeatureInfo}}, \code{\link[GiottoClass]{combineSpatialCellMetadataInfo}}, \code{\link[GiottoClass]{convertGiottoLargeImageToMG}}, \code{\link[GiottoClass]{createCellMetaObj}}, \code{\link[GiottoClass]{createDimObj}}, \code{\link[GiottoClass]{createExprObj}}, \code{\link[GiottoClass]{createFeatMetaObj}}, \code{\link[GiottoClass]{createGiottoImage}}, \code{\link[GiottoClass]{createGiottoInstructions}}, \code{\link[GiottoClass]{createGiottoLargeImage}}, \code{\link[GiottoClass]{createGiottoLargeImageList}}, \code{\link[GiottoClass]{createGiottoObject}}, \code{\link[GiottoClass]{createGiottoObjectSubcellular}}, \code{\link[GiottoClass]{createGiottoPoints}}, \code{\link[GiottoClass:createGiottoPolygon]{createGiottoPolygonsFromDfr}}, \code{\link[GiottoClass:createGiottoPolygon]{createGiottoPolygonsFromGeoJSON}}, \code{\link[GiottoClass:createGiottoPolygon]{createGiottoPolygonsFromMask}}, \code{\link[GiottoClass]{createMetafeats}}, \code{\link[GiottoClass]{createNearestNetObj}}, \code{\link[GiottoClass]{createSpatEnrObj}}, \code{\link[GiottoClass]{createSpatialDefaultGrid}}, \code{\link[GiottoClass]{createSpatialDelaunayNetwork}}, \code{\link[GiottoClass]{createSpatialFeaturesKNNnetwork}}, \code{\link[GiottoClass]{createSpatialGrid}}, \code{\link[GiottoClass]{createSpatialKNNnetwork}}, \code{\link[GiottoClass]{createSpatialNetwork}}, \code{\link[GiottoClass]{createSpatialWeightMatrix}}, \code{\link[GiottoClass]{createSpatLocsObj}}, \code{\link[GiottoClass]{createSpatNetObj}}, \code{\link[GiottoClass]{cropGiottoLargeImage}}, \code{\link[GiottoClass]{distGiottoImage}}, \code{\link[GiottoClass]{estimateImageBg}}, \code{\link[GiottoClass]{fDataDT}}, \code{\link[GiottoClass:featType-generic]{featType}}, \code{\link[GiottoClass:featureNetwork-class]{featureNetwork}}, \code{\link[GiottoClass]{gefToGiotto}}, \code{\link[GiottoClass]{get_dimReduction}}, \code{\link[GiottoClass]{get_dimReduction}}, \code{\link[GiottoClass]{get_feature_info}}, \code{\link[GiottoClass]{get_feature_info}}, \code{\link[GiottoClass]{get_giottoImage}}, \code{\link[GiottoClass]{get_giottoImage}}, \code{\link[GiottoClass]{get_multiomics}}, \code{\link[GiottoClass]{get_multiomics}}, \code{\link[GiottoClass]{get_NearestNetwork}}, \code{\link[GiottoClass]{get_NearestNetwork}}, \code{\link[GiottoClass]{get_polygon_info}}, \code{\link[GiottoClass]{get_polygon_info}}, \code{\link[GiottoClass]{get_spatial_enrichment}}, \code{\link[GiottoClass]{get_spatial_enrichment}}, \code{\link[GiottoClass]{get_spatial_locations}}, \code{\link[GiottoClass]{get_spatial_locations}}, \code{\link[GiottoClass]{get_spatialGrid}}, \code{\link[GiottoClass]{get_spatialGrid}}, \code{\link[GiottoClass]{get_spatialNetwork}}, \code{\link[GiottoClass]{get_spatialNetwork}}, \code{\link[GiottoClass]{getCellMetadata}}, \code{\link[GiottoClass]{getDimReduction}}, \code{\link[GiottoClass]{getExpression}}, \code{\link[GiottoClass]{getFeatureInfo}}, \code{\link[GiottoClass]{getFeatureMetadata}}, \code{\link[GiottoClass]{getGiottoImage}}, \code{\link[GiottoClass]{getMultiomics}}, \code{\link[GiottoClass]{getNearestNetwork}}, \code{\link[GiottoClass]{getPolygonInfo}}, \code{\link[GiottoClass]{getRainbowColors}}, \code{\link[GiottoClass]{getSpatialEnrichment}}, \code{\link[GiottoClass]{getSpatialEnrichment}}, \code{\link[GiottoClass]{getSpatialGrid}}, \code{\link[GiottoClass]{getSpatialGrid}}, \code{\link[GiottoClass]{getSpatialLocations}}, \code{\link[GiottoClass]{getSpatialLocations}}, \code{\link[GiottoClass]{getSpatialNetwork}}, \code{\link[GiottoClass]{getSpatialNetwork}}, \code{\link[GiottoClass:giotto-class]{giotto}}, \code{\link[GiottoClass:giottoImage-class]{giottoImage}}, \code{\link[GiottoClass:giottoLargeImage-class]{giottoLargeImage}}, \code{\link[GiottoClass]{giottoMasterToSuite}}, \code{\link[GiottoClass:giottoPoints-class]{giottoPoints}}, \code{\link[GiottoClass:giottoPolygon-class]{giottoPolygon}}, \code{\link[GiottoClass]{giottoToAnnData}}, \code{\link[GiottoClass]{giottoToSeurat}}, \code{\link[GiottoClass]{giottoToSpatialExperiment}}, \code{\link[GiottoClass]{hexVertices}}, \code{\link[GiottoClass]{joinGiottoObjects}}, \code{\link[GiottoClass]{loadGiotto}}, \code{\link[GiottoClass]{makePseudoVisium}}, \code{\link[GiottoClass]{objHistory}}, \code{\link[GiottoClass:objName-generic]{objName}}, \code{\link[GiottoClass]{overlapImagesToMatrix}}, \code{\link[GiottoClass]{overlapToMatrix}}, \code{\link[GiottoClass]{overlapToMatrixMultiPoly}}, \code{\link[GiottoClass]{pDataDT}}, \code{\link[GiottoClass]{plotGiottoImage}}, \code{\link[GiottoClass]{polyStamp}}, \code{\link[GiottoClass:prov-generic]{prov}}, \code{\link[GiottoClass:read_cell_metadata]{readCellMetadata}}, \code{\link[GiottoClass]{readDimReducData}}, \code{\link[GiottoClass]{readExprData}}, \code{\link[GiottoClass]{readExprMatrix}}, \code{\link[GiottoClass]{readFeatData}}, \code{\link[GiottoClass:read_feature_metadata]{readFeatMetadata}}, \code{\link[GiottoClass]{readGiottoInstructions}}, \code{\link[GiottoClass]{readNearestNetData}}, \code{\link[GiottoClass]{readPolygonData}}, \code{\link[GiottoClass]{readSpatEnrichData}}, \code{\link[GiottoClass]{readSpatLocsData}}, \code{\link[GiottoClass]{readSpatNetData}}, \code{\link[GiottoClass]{reconnectGiottoImage}}, \code{\link[GiottoClass]{rectVertices}}, \code{\link[GiottoClass]{removeCellAnnotation}}, \code{\link[GiottoClass]{removeFeatAnnotation}}, \code{\link[GiottoClass]{replaceGiottoInstructions}}, \code{\link[GiottoClass]{rescalePolygons}}, \code{\link[GiottoClass]{saveGiotto}}, \code{\link[GiottoClass]{set_dimReduction}}, \code{\link[GiottoClass]{set_expression_values}}, \code{\link[GiottoClass]{set_feature_info}}, \code{\link[GiottoClass]{set_giottoImage}}, \code{\link[GiottoClass]{set_multiomics}}, \code{\link[GiottoClass]{set_NearestNetwork}}, \code{\link[GiottoClass]{set_polygon_info}}, \code{\link[GiottoClass]{set_spatial_enrichment}}, \code{\link[GiottoClass]{set_spatial_locations}}, \code{\link[GiottoClass]{set_spatialGrid}}, \code{\link[GiottoClass]{set_spatialNetwork}}, \code{\link[GiottoClass]{setDimReduction}}, \code{\link[GiottoClass]{setExpression}}, \code{\link[GiottoClass]{setFeatureInfo}}, \code{\link[GiottoClass]{setGiottoImage}}, \code{\link[GiottoClass]{setMultiomics}}, \code{\link[GiottoClass]{setNearestNetwork}}, \code{\link[GiottoClass]{setPolygonInfo}}, \code{\link[GiottoClass]{setSpatialEnrichment}}, \code{\link[GiottoClass]{setSpatialGrid}}, \code{\link[GiottoClass]{setSpatialLocations}}, \code{\link[GiottoClass]{setSpatialNetwork}}, \code{\link[GiottoClass]{seuratToGiotto}}, \code{\link[GiottoClass]{showGiottoCellMetadata}}, \code{\link[GiottoClass]{showGiottoDimRed}}, \code{\link[GiottoClass]{showGiottoExpression}}, \code{\link[GiottoClass]{showGiottoFeatInfo}}, \code{\link[GiottoClass]{showGiottoFeatMetadata}}, \code{\link[GiottoClass]{showGiottoImageNames}}, \code{\link[GiottoClass]{showGiottoInstructions}}, \code{\link[GiottoClass]{showGiottoNearestNetworks}}, \code{\link[GiottoClass]{showGiottoSpatEnrichments}}, \code{\link[GiottoClass]{showGiottoSpatGrids}}, \code{\link[GiottoClass]{showGiottoSpatialInfo}}, \code{\link[GiottoClass]{showGiottoSpatLocs}}, \code{\link[GiottoClass]{showGiottoSpatNetworks}}, \code{\link[GiottoClass]{showGrids}}, \code{\link[GiottoClass]{showNetworks}}, \code{\link[GiottoClass]{showProcessingSteps}}}
 
   \item{GiottoUtils}{\code{\link[GiottoUtils:pipe]{\%>\%}}}
 
diff --git a/man/runPCAprojection.Rd b/man/runPCAprojection.Rd
index bdf95f934..ae2546d97 100644
--- a/man/runPCAprojection.Rd
+++ b/man/runPCAprojection.Rd
@@ -37,7 +37,7 @@ runPCAprojection(
 
 \item{reduction}{cells or genes}
 
-\item{random_subset}{random subset to perform PCA on}
+\item{random_subset}{numeric. random subset to perform PCA on}
 
 \item{name}{arbitrary name for PCA run}