From da8b4f407a8bbd1157dc0d80b4d7d6b58b971201 Mon Sep 17 00:00:00 2001 From: George Chen <72078254+jiajic@users.noreply.github.com> Date: Sat, 12 Oct 2024 14:33:46 -0400 Subject: [PATCH 1/2] chore: formatting --- R/normalize.R | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/R/normalize.R b/R/normalize.R index ff8c110dd..58d9cdafa 100644 --- a/R/normalize.R +++ b/R/normalize.R @@ -25,21 +25,21 @@ #' A. The standard method follows the standard protocol which can be adjusted #' using the provided parameters and follows the following order: \cr #' \itemize{ -#' \item{1. Data normalization for total library size and scaling by a custom +#' \item{1. Data normalization for total library size and scaling by a custom #' scale-factor.} #' \item{2. Log transformation of data.} #' \item{3. Z-scoring of data by genes and/or cells.} #' } -#' B. The normalization method as provided by the osmFISH paper is also +#' B. The normalization method as provided by the osmFISH paper is also #' implemented: \cr #' \itemize{ -#' \item{1. First normalize genes, for each gene divide the counts by the +#' \item{1. First normalize genes, for each gene divide the counts by the #' total gene count and multiply by the total number of genes.} -#' \item{2. Next normalize cells, for each cell divide the normalized gene -#' counts by the total counts per cell and multiply by the total number of +#' \item{2. Next normalize cells, for each cell divide the normalized gene +#' counts by the total counts per cell and multiply by the total number of #' cells.} #' } -#' C. The normalization method as provided by Lause/Kobak et al is also +#' C. The normalization method as provided by Lause/Kobak et al is also #' implemented: \cr #' \itemize{ #' \item{1. First calculate expected values based on Pearson correlations.} @@ -48,9 +48,9 @@ #' D. Quantile normalization across features #' \itemize{ #' \item{1. Rank feature expression} -#' \item{2. Define a common distribution by sorting expression values per +#' \item{2. Define a common distribution by sorting expression values per #' feature then finding the mean across all features per index} -#' \item{3. Apply common distribution to expression information by using +#' \item{3. Apply common distribution to expression information by using #' the ranks from step 1 as indices} #' } #' By default the latter two results will be saved in the Giotto slot for @@ -218,7 +218,7 @@ normalizeGiotto <- function( } else if (methods::is(mymatrix, "Matrix")) { mymatrix@x <- log(mymatrix@x + offset) / log(base) } else if (methods::is(mymatrix, "dbMatrix")) { - mymatrix[] <- dplyr::mutate(mymatrix[], x = x + offset) + mymatrix[] <- dplyr::mutate(mymatrix[], x = x + offset) # workaround for lack of @x slot mymatrix <- log(mymatrix) / log(base) } else { From 8046e593bf1719bff322340e563d21544c2f17b3 Mon Sep 17 00:00:00 2001 From: George Chen <72078254+jiajic@users.noreply.github.com> Date: Tue, 15 Oct 2024 09:41:33 -0400 Subject: [PATCH 2/2] !feat: remove re-export of `combineSpatialCellFeatureInfo()` --- NAMESPACE | 2 -- R/suite_reexports.R | 2 -- man/labelTransfer.Rd | 6 +++--- man/reexports.Rd | 3 +-- 4 files changed, 4 insertions(+), 9 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index 0a34513e7..8aca099c2 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -97,7 +97,6 @@ export(combineICG) export(combineInteractionChangedFeats) export(combineInteractionChangedGenes) export(combineMetadata) -export(combineSpatialCellFeatureInfo) export(combineSpatialCellMetadataInfo) export(combineToMultiPolygon) export(compareCellAbundance) @@ -575,7 +574,6 @@ importFrom(GiottoClass,combineCellData) importFrom(GiottoClass,combineFeatureData) importFrom(GiottoClass,combineFeatureOverlapData) importFrom(GiottoClass,combineMetadata) -importFrom(GiottoClass,combineSpatialCellFeatureInfo) importFrom(GiottoClass,combineSpatialCellMetadataInfo) importFrom(GiottoClass,combineToMultiPolygon) importFrom(GiottoClass,convertGiottoLargeImageToMG) diff --git a/R/suite_reexports.R b/R/suite_reexports.R index f3f51f5c5..905811ab7 100644 --- a/R/suite_reexports.R +++ b/R/suite_reexports.R @@ -167,8 +167,6 @@ GiottoClass::combineFeatureOverlapData #' @export GiottoClass::combineMetadata #' @export -GiottoClass::combineSpatialCellFeatureInfo -#' @export GiottoClass::combineSpatialCellMetadataInfo #' @export GiottoClass::combineToMultiPolygon diff --git a/man/labelTransfer.Rd b/man/labelTransfer.Rd index 8d4c6f55b..dbf876a0b 100644 --- a/man/labelTransfer.Rd +++ b/man/labelTransfer.Rd @@ -55,10 +55,12 @@ voting} \item{prob}{output knn probabilities together with label predictions} -\item{reduction_name}{name of shared reduction space (default name = "pca")} +\item{reduction}{reduction on cells or features (default = "cells")} \item{reduction_method}{shared reduction method (default = "pca" space)} +\item{reduction_name}{name of shared reduction space (default name = "pca")} + \item{dimensions_to_use}{dimensions to use in shared reduction space (default = 1:10)} @@ -72,8 +74,6 @@ voting} \item{target_cell_ids}{cell/spatial IDs to transfer the labels to. IDs from \code{source_cell_ids} are always included as well.} - -\item{reduction}{reduction on cells or features (default = "cells")} } \value{ object \code{x} with new transferred labels added to metadata diff --git a/man/reexports.Rd b/man/reexports.Rd index 6b000402a..f9575eb02 100644 --- a/man/reexports.Rd +++ b/man/reexports.Rd @@ -81,7 +81,6 @@ \alias{combineFeatureData} \alias{combineFeatureOverlapData} \alias{combineMetadata} -\alias{combineSpatialCellFeatureInfo} \alias{combineSpatialCellMetadataInfo} \alias{combineToMultiPolygon} \alias{convertGiottoLargeImageToMG} @@ -298,7 +297,7 @@ These objects are imported from other packages. Follow the links below to see their documentation. \describe{ - \item{GiottoClass}{\code{\link[GiottoClass:activeFeatType-generic]{activeFeatType}}, \code{\link[GiottoClass:activeFeatType-generic]{activeFeatType<-}}, \code{\link[GiottoClass:activeSpatUnit-generic]{activeSpatUnit}}, \code{\link[GiottoClass:activeSpatUnit-generic]{activeSpatUnit<-}}, \code{\link[GiottoClass]{addCellMetadata}}, \code{\link[GiottoClass]{addFeatMetadata}}, \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]{addNetworkLayout}}, \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]{anndataToGiotto}}, \code{\link[GiottoClass]{annotateGiotto}}, \code{\link[GiottoClass]{annotateSpatialGrid}}, \code{\link[GiottoClass]{annotateSpatialNetwork}}, \code{\link[GiottoClass]{as.points}}, \code{\link[GiottoClass]{as.polygons}}, \code{\link[GiottoClass:r_spatial_conversions]{as.sf}}, \code{\link[GiottoClass:r_spatial_conversions]{as.sp}}, \code{\link[GiottoClass:r_spatial_conversions]{as.stars}}, \code{\link[GiottoClass:r_spatial_conversions]{as.terra}}, \code{\link[GiottoClass]{calculateMetaTable}}, \code{\link[GiottoClass]{calculateMetaTableCells}}, \code{\link[GiottoClass]{calculateOverlap}}, \code{\link[GiottoClass]{calculateOverlapParallel}}, \code{\link[GiottoClass]{calculateOverlapPolygonImages}}, \code{\link[GiottoClass]{calculateOverlapRaster}}, \code{\link[GiottoClass]{calculateOverlapSerial}}, \code{\link[GiottoClass]{calculateSpatCellMetadataProportions}}, \code{\link[GiottoClass:centroids-generic]{centroids}}, \code{\link[GiottoClass]{changeGiottoInstructions}}, \code{\link[GiottoClass]{changeImageBg}}, \code{\link[GiottoClass:giotto_python]{checkGiottoEnvironment}}, \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]{combineToMultiPolygon}}, \code{\link[GiottoClass]{convertGiottoLargeImageToMG}}, \code{\link[GiottoClass]{copy}}, \code{\link[GiottoClass]{createBentoAdata}}, \code{\link[GiottoClass]{createCellMetaObj}}, \code{\link[GiottoClass]{createDimObj}}, \code{\link[GiottoClass]{createExprObj}}, \code{\link[GiottoClass]{createFeatMetaObj}}, \code{\link[GiottoClass]{createGiottoImage}}, \code{\link[GiottoClass:giotto_instructions]{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}}, \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]{createNearestNetwork}}, \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]{crop}}, \code{\link[GiottoClass]{cropGiottoLargeImage}}, \code{\link[GiottoClass]{density}}, \code{\link[GiottoClass]{distGiottoImage}}, \code{\link[GiottoClass]{estimateImageBg}}, \code{\link[GiottoClass]{ext}}, \code{\link[GiottoClass:ext]{ext<-}}, \code{\link[GiottoClass]{fDataDT}}, \code{\link[GiottoClass:spatIDs-generic]{featIDs}}, \code{\link[GiottoClass:featType-generic]{featType}}, \code{\link[GiottoClass:featType-generic]{featType<-}}, \code{\link[GiottoClass:featureNetwork-class]{featureNetwork}}, \code{\link[GiottoClass]{flip}}, \code{\link[GiottoClass]{gefToGiotto}}, \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]{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]{giottoToSeuratV4}}, \code{\link[GiottoClass]{giottoToSeuratV5}}, \code{\link[GiottoClass]{giottoToSpatialExperiment}}, \code{\link[GiottoClass]{hexVertices}}, \code{\link[GiottoClass]{hist}}, \code{\link[GiottoClass:giotto_python]{installGiottoEnvironment}}, \code{\link[GiottoClass:giotto_instructions]{instructions}}, \code{\link[GiottoClass:giotto_instructions]{instructions<-}}, \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:objName-generic]{objName<-}}, \code{\link[GiottoClass:generate_grid]{orthoGrid}}, \code{\link[GiottoClass]{overlapImagesToMatrix}}, \code{\link[GiottoClass:overlaps-generic]{overlaps}}, \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:prov-generic]{prov<-}}, \code{\link[GiottoClass]{readCellMetadata}}, \code{\link[GiottoClass]{readDimReducData}}, \code{\link[GiottoClass]{readExprData}}, \code{\link[GiottoClass]{readExprMatrix}}, \code{\link[GiottoClass]{readFeatData}}, \code{\link[GiottoClass]{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:giotto_python]{removeGiottoEnvironment}}, \code{\link[GiottoClass]{replaceGiottoInstructions}}, \code{\link[GiottoClass]{rescale}}, \code{\link[GiottoClass]{rescalePolygons}}, \code{\link[GiottoClass]{saveGiotto}}, \code{\link[GiottoClass]{setCellMetadata}}, \code{\link[GiottoClass]{setDimReduction}}, \code{\link[GiottoClass]{setExpression}}, \code{\link[GiottoClass]{setFeatureInfo}}, \code{\link[GiottoClass]{setFeatureMetadata}}, \code{\link[GiottoClass]{setGiotto}}, \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]{seuratToGiottoV4}}, \code{\link[GiottoClass]{seuratToGiottoV5}}, \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]{showProcessingSteps}}, \code{\link[GiottoClass]{smoothGiottoPolygons}}, \code{\link[GiottoClass]{spatialExperimentToGiotto}}, \code{\link[GiottoClass:spatIDs-generic]{spatIDs}}, \code{\link[GiottoClass]{spatQueryGiottoPolygons}}, \code{\link[GiottoClass]{spatShift}}, \code{\link[GiottoClass:spatUnit-generic]{spatUnit}}, \code{\link[GiottoClass:spatUnit-generic]{spatUnit<-}}, \code{\link[GiottoClass]{spin}}, \code{\link[GiottoClass]{stitchFieldCoordinates}}, \code{\link[GiottoClass]{stitchFieldCoordinates}}, \code{\link[GiottoClass]{stitchGiottoLargeImage}}, \code{\link[GiottoClass]{subsetGiotto}}, \code{\link[GiottoClass]{subsetGiottoLocs}}, \code{\link[GiottoClass]{subsetGiottoLocsMulti}}, \code{\link[GiottoClass]{subsetGiottoLocsSubcellular}}, \code{\link[GiottoClass]{tessellate}}, \code{\link[GiottoClass:generate_grid]{triGrid}}, \code{\link[GiottoClass]{updateGiottoImage}}, \code{\link[GiottoClass]{updateGiottoImageMG}}, \code{\link[GiottoClass]{updateGiottoLargeImage}}, \code{\link[GiottoClass]{updateGiottoObject}}, \code{\link[GiottoClass]{updateGiottoPointsObject}}, \code{\link[GiottoClass]{updateGiottoPolygonObject}}, \code{\link[GiottoClass:wrap]{vect}}, \code{\link[GiottoClass]{wrap}}, \code{\link[GiottoClass]{writeGiottoLargeImage}}} + \item{GiottoClass}{\code{\link[GiottoClass:activeFeatType-generic]{activeFeatType}}, \code{\link[GiottoClass:activeFeatType-generic]{activeFeatType<-}}, \code{\link[GiottoClass:activeSpatUnit-generic]{activeSpatUnit}}, \code{\link[GiottoClass:activeSpatUnit-generic]{activeSpatUnit<-}}, \code{\link[GiottoClass]{addCellMetadata}}, \code{\link[GiottoClass]{addFeatMetadata}}, \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]{addNetworkLayout}}, \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]{anndataToGiotto}}, \code{\link[GiottoClass]{annotateGiotto}}, \code{\link[GiottoClass]{annotateSpatialGrid}}, \code{\link[GiottoClass]{annotateSpatialNetwork}}, \code{\link[GiottoClass]{as.points}}, \code{\link[GiottoClass]{as.polygons}}, \code{\link[GiottoClass:r_spatial_conversions]{as.sf}}, \code{\link[GiottoClass:r_spatial_conversions]{as.sp}}, \code{\link[GiottoClass:r_spatial_conversions]{as.stars}}, \code{\link[GiottoClass:r_spatial_conversions]{as.terra}}, \code{\link[GiottoClass]{calculateMetaTable}}, \code{\link[GiottoClass]{calculateMetaTableCells}}, \code{\link[GiottoClass]{calculateOverlap}}, \code{\link[GiottoClass]{calculateOverlapParallel}}, \code{\link[GiottoClass]{calculateOverlapPolygonImages}}, \code{\link[GiottoClass]{calculateOverlapRaster}}, \code{\link[GiottoClass]{calculateOverlapSerial}}, \code{\link[GiottoClass]{calculateSpatCellMetadataProportions}}, \code{\link[GiottoClass:centroids-generic]{centroids}}, \code{\link[GiottoClass]{changeGiottoInstructions}}, \code{\link[GiottoClass]{changeImageBg}}, \code{\link[GiottoClass:giotto_python]{checkGiottoEnvironment}}, \code{\link[GiottoClass]{circleVertices}}, \code{\link[GiottoClass]{combineCellData}}, \code{\link[GiottoClass]{combineFeatureData}}, \code{\link[GiottoClass]{combineFeatureOverlapData}}, \code{\link[GiottoClass]{combineMetadata}}, \code{\link[GiottoClass]{combineSpatialCellMetadataInfo}}, \code{\link[GiottoClass]{combineToMultiPolygon}}, \code{\link[GiottoClass]{convertGiottoLargeImageToMG}}, \code{\link[GiottoClass]{copy}}, \code{\link[GiottoClass]{createBentoAdata}}, \code{\link[GiottoClass]{createCellMetaObj}}, \code{\link[GiottoClass]{createDimObj}}, \code{\link[GiottoClass]{createExprObj}}, \code{\link[GiottoClass]{createFeatMetaObj}}, \code{\link[GiottoClass]{createGiottoImage}}, \code{\link[GiottoClass:giotto_instructions]{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}}, \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]{createNearestNetwork}}, \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]{crop}}, \code{\link[GiottoClass]{cropGiottoLargeImage}}, \code{\link[GiottoClass]{density}}, \code{\link[GiottoClass]{distGiottoImage}}, \code{\link[GiottoClass]{estimateImageBg}}, \code{\link[GiottoClass]{ext}}, \code{\link[GiottoClass:ext]{ext<-}}, \code{\link[GiottoClass]{fDataDT}}, \code{\link[GiottoClass:spatIDs-generic]{featIDs}}, \code{\link[GiottoClass:featType-generic]{featType}}, \code{\link[GiottoClass:featType-generic]{featType<-}}, \code{\link[GiottoClass:featureNetwork-class]{featureNetwork}}, \code{\link[GiottoClass]{flip}}, \code{\link[GiottoClass]{gefToGiotto}}, \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]{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]{giottoToSeuratV4}}, \code{\link[GiottoClass]{giottoToSeuratV5}}, \code{\link[GiottoClass]{giottoToSpatialExperiment}}, \code{\link[GiottoClass]{hexVertices}}, \code{\link[GiottoClass]{hist}}, \code{\link[GiottoClass:giotto_python]{installGiottoEnvironment}}, \code{\link[GiottoClass:giotto_instructions]{instructions}}, \code{\link[GiottoClass:giotto_instructions]{instructions<-}}, \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:objName-generic]{objName<-}}, \code{\link[GiottoClass:generate_grid]{orthoGrid}}, \code{\link[GiottoClass]{overlapImagesToMatrix}}, \code{\link[GiottoClass:overlaps-generic]{overlaps}}, \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:prov-generic]{prov<-}}, \code{\link[GiottoClass]{readCellMetadata}}, \code{\link[GiottoClass]{readDimReducData}}, \code{\link[GiottoClass]{readExprData}}, \code{\link[GiottoClass]{readExprMatrix}}, \code{\link[GiottoClass]{readFeatData}}, \code{\link[GiottoClass]{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:giotto_python]{removeGiottoEnvironment}}, \code{\link[GiottoClass]{replaceGiottoInstructions}}, \code{\link[GiottoClass]{rescale}}, \code{\link[GiottoClass]{rescalePolygons}}, \code{\link[GiottoClass]{saveGiotto}}, \code{\link[GiottoClass]{setCellMetadata}}, \code{\link[GiottoClass]{setDimReduction}}, \code{\link[GiottoClass]{setExpression}}, \code{\link[GiottoClass]{setFeatureInfo}}, \code{\link[GiottoClass]{setFeatureMetadata}}, \code{\link[GiottoClass]{setGiotto}}, \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]{seuratToGiottoV4}}, \code{\link[GiottoClass]{seuratToGiottoV5}}, \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]{showProcessingSteps}}, \code{\link[GiottoClass]{smoothGiottoPolygons}}, \code{\link[GiottoClass]{spatialExperimentToGiotto}}, \code{\link[GiottoClass:spatIDs-generic]{spatIDs}}, \code{\link[GiottoClass]{spatQueryGiottoPolygons}}, \code{\link[GiottoClass]{spatShift}}, \code{\link[GiottoClass:spatUnit-generic]{spatUnit}}, \code{\link[GiottoClass:spatUnit-generic]{spatUnit<-}}, \code{\link[GiottoClass]{spin}}, \code{\link[GiottoClass]{stitchFieldCoordinates}}, \code{\link[GiottoClass]{stitchFieldCoordinates}}, \code{\link[GiottoClass]{stitchGiottoLargeImage}}, \code{\link[GiottoClass]{subsetGiotto}}, \code{\link[GiottoClass]{subsetGiottoLocs}}, \code{\link[GiottoClass]{subsetGiottoLocsMulti}}, \code{\link[GiottoClass]{subsetGiottoLocsSubcellular}}, \code{\link[GiottoClass]{tessellate}}, \code{\link[GiottoClass:generate_grid]{triGrid}}, \code{\link[GiottoClass]{updateGiottoImage}}, \code{\link[GiottoClass]{updateGiottoImageMG}}, \code{\link[GiottoClass]{updateGiottoLargeImage}}, \code{\link[GiottoClass]{updateGiottoObject}}, \code{\link[GiottoClass]{updateGiottoPointsObject}}, \code{\link[GiottoClass]{updateGiottoPolygonObject}}, \code{\link[GiottoClass:wrap]{vect}}, \code{\link[GiottoClass]{wrap}}, \code{\link[GiottoClass]{writeGiottoLargeImage}}} \item{GiottoUtils}{\code{\link[GiottoUtils:pipe]{\%>\%}}, \code{\link[GiottoUtils]{getDistinctColors}}, \code{\link[GiottoUtils]{getRainbowColors}}}