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)
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
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)
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}