From 83b8ca904114b62b3dd64adf8b3814c50b09bdf8 Mon Sep 17 00:00:00 2001 From: josschavezf Date: Fri, 16 Aug 2024 14:44:12 -0400 Subject: [PATCH] update R version --- DESCRIPTION | 6 +++--- man/reexports.Rd | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 2274bef4f..2b3959c6f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -27,9 +27,9 @@ URL: https://drieslab.github.io/Giotto/, https://github.com/drieslab/Giotto BugReports: https://github.com/drieslab/Giotto/issues RoxygenNote: 7.3.2 Depends: - base (>= 4.1.0), - utils (>= 4.1.0), - R (>= 4.1.0), + base (>= 4.4.0), + utils (>= 4.4.0), + R (>= 4.4.0), methods, GiottoClass (>= 0.3.3) Imports: diff --git a/man/reexports.Rd b/man/reexports.Rd index f5533929f..6b000402a 100644 --- a/man/reexports.Rd +++ b/man/reexports.Rd @@ -298,7 +298,7 @@ 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]{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]{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]{installGiottoEnvironment}}, \code{\link[GiottoClass:instructions-generic]{instructions}}, \code{\link[GiottoClass:instructions-generic]{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]{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]{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{GiottoUtils}{\code{\link[GiottoUtils:pipe]{\%>\%}}, \code{\link[GiottoUtils]{getDistinctColors}}, \code{\link[GiottoUtils]{getRainbowColors}}}