These objects are imported from other packages. Follow the links below to see their documentation.
activeFeatType
, activeFeatType<-
, activeSpatUnit
, activeSpatUnit<-
, addCellMetadata
, addFeatMetadata
, addGiottoImage
, addGiottoImageMG
, addGiottoLargeImage
, addGiottoPoints
, addGiottoPoints3D
, addGiottoPolygons
, addNetworkLayout
, addSpatialCentroidLocations
, addSpatialCentroidLocationsLayer
, aggregateStacks
, aggregateStacksExpression
, aggregateStacksLocations
, aggregateStacksPolygonOverlaps
, aggregateStacksPolygons
, anndataToGiotto
, annotateGiotto
, annotateSpatialGrid
, annotateSpatialNetwork
, as.points
, as.polygons
, as.sf
, as.sp
, as.stars
, as.terra
, calculateMetaTable
, calculateMetaTableCells
, calculateOverlap
, calculateOverlapParallel
, calculateOverlapPolygonImages
, calculateOverlapRaster
, calculateOverlapSerial
, calculateSpatCellMetadataProportions
, centroids
, changeGiottoInstructions
, changeImageBg
, checkGiottoEnvironment
, circleVertices
, combineCellData
, combineFeatureData
, combineFeatureOverlapData
, combineMetadata
, combineSpatialCellMetadataInfo
, combineToMultiPolygon
, convertGiottoLargeImageToMG
, copy
, createBentoAdata
, createCellMetaObj
, createDimObj
, createExprObj
, createFeatMetaObj
, createGiottoImage
, createGiottoInstructions
, createGiottoLargeImage
, createGiottoLargeImageList
, createGiottoObject
, createGiottoObjectSubcellular
, createGiottoPoints
, createGiottoPolygon
, createGiottoPolygonsFromDfr
, createGiottoPolygonsFromGeoJSON
, createGiottoPolygonsFromMask
, createMetafeats
, createNearestNetObj
, createNearestNetwork
, createSpatEnrObj
, createSpatialDefaultGrid
, createSpatialDelaunayNetwork
, createSpatialFeaturesKNNnetwork
, createSpatialGrid
, createSpatialKNNnetwork
, createSpatialNetwork
, createSpatialWeightMatrix
, createSpatLocsObj
, createSpatNetObj
, crop
, cropGiottoLargeImage
, density
, distGiottoImage
, estimateImageBg
, ext
, ext<-
, fDataDT
, featIDs
, featType
, featType<-
, featureNetwork
, flip
, gefToGiotto
, getCellMetadata
, getDimReduction
, getExpression
, getFeatureInfo
, getFeatureMetadata
, getGiottoImage
, getMultiomics
, getNearestNetwork
, getPolygonInfo
, getSpatialEnrichment
, getSpatialEnrichment
, getSpatialGrid
, getSpatialGrid
, getSpatialLocations
, getSpatialLocations
, getSpatialNetwork
, getSpatialNetwork
, giotto
, giottoImage
, giottoLargeImage
, giottoMasterToSuite
, giottoPoints
, giottoPolygon
, giottoToAnnData
, giottoToSeurat
, giottoToSeuratV4
, giottoToSeuratV5
, giottoToSpatialExperiment
, hexVertices
, hist
, installGiottoEnvironment
, instructions
, instructions<-
, joinGiottoObjects
, loadGiotto
, makePseudoVisium
, objHistory
, objName
, objName<-
, orthoGrid
, overlapImagesToMatrix
, overlaps
, overlapToMatrix
, overlapToMatrixMultiPoly
, pDataDT
, plotGiottoImage
, polyStamp
, prov
, prov<-
, readCellMetadata
, readDimReducData
, readExprData
, readExprMatrix
, readFeatData
, readFeatMetadata
, readGiottoInstructions
, readNearestNetData
, readPolygonData
, readSpatEnrichData
, readSpatLocsData
, readSpatNetData
, reconnectGiottoImage
, rectVertices
, removeCellAnnotation
, removeFeatAnnotation
, removeGiottoEnvironment
, replaceGiottoInstructions
, rescale
, rescalePolygons
, saveGiotto
, setCellMetadata
, setDimReduction
, setExpression
, setFeatureInfo
, setFeatureMetadata
, setGiotto
, setGiottoImage
, setMultiomics
, setNearestNetwork
, setPolygonInfo
, setSpatialEnrichment
, setSpatialGrid
, setSpatialLocations
, setSpatialNetwork
, seuratToGiotto
, seuratToGiottoV4
, seuratToGiottoV5
, showGiottoCellMetadata
, showGiottoDimRed
, showGiottoExpression
, showGiottoFeatInfo
, showGiottoFeatMetadata
, showGiottoImageNames
, showGiottoInstructions
, showGiottoNearestNetworks
, showGiottoSpatEnrichments
, showGiottoSpatGrids
, showGiottoSpatialInfo
, showGiottoSpatLocs
, showGiottoSpatNetworks
, showProcessingSteps
, smoothGiottoPolygons
, spatialExperimentToGiotto
, spatIDs
, spatQueryGiottoPolygons
, spatShift
, spatUnit
, spatUnit<-
, spin
, stitchFieldCoordinates
, stitchFieldCoordinates
, stitchGiottoLargeImage
, subsetGiotto
, subsetGiottoLocs
, subsetGiottoLocsMulti
, subsetGiottoLocsSubcellular
, tessellate
, triGrid
, updateGiottoImage
, updateGiottoImageMG
, updateGiottoLargeImage
, updateGiottoObject
, updateGiottoPointsObject
, updateGiottoPolygonObject
, vect
, wrap
, writeGiottoLargeImage
addGiottoImageToSpatPlot
, dimCellPlot
, dimCellPlot2D
, dimFeatPlot2D
, dimFeatPlot3D
, dimGenePlot3D
, dimPlot
, dimPlot2D
, dimPlot3D
, dotPlot
, getColors
, giottoSankeyPlan
, plotHeatmap
, plotMetaDataCellsHeatmap
, plotMetaDataHeatmap
, plotPCA
, plotPCA_2D
, plotPCA_3D
, plotStatDelaunayNetwork
, plotTSNE
, plotTSNE_2D
, plotTSNE_3D
, plotUMAP
, plotUMAP_2D
, plotUMAP_3D
, sankeyLabel
, sankeyLabel<-
, sankeyPlot
, sankeyRelate
, sankeyRelate<-
, sankeySet
, sankeySetAddresses
, showClusterDendrogram
, showClusterHeatmap
, showColorInstructions
, showSaveParameters
, spatCellPlot
, spatCellPlot2D
, spatDeconvPlot
, spatDimCellPlot
, spatDimCellPlot2D
, spatDimFeatPlot2D
, spatDimFeatPlot3D
, spatDimGenePlot3D
, spatDimPlot
, spatDimPlot2D
, spatDimPlot3D
, spatFeatPlot2D
, spatFeatPlot2D_single
, spatFeatPlot3D
, spatGenePlot3D
, spatInSituPlotDensity
, spatInSituPlotHex
, spatInSituPlotPoints
, spatNetwDistributions
, spatNetwDistributionsDistance
, spatNetwDistributionsKneighbors
, spatPlot
, spatPlot2D
, spatPlot3D
, subsetSankeySet
, violinPlot
pipe operator
vector of colors
vector of colors