Merge pull request drieslab#987 from drieslab/modular_readers

Modular readers

NAMESPACE

@@ -508,287 +508,6 @@ import(methods)
 import(stats, except = density)
 import(utils)
 importClassesFrom(data.table,data.table)
-importFrom(GiottoClass,"activeFeatType<-")
-importFrom(GiottoClass,"activeSpatUnit<-")
-importFrom(GiottoClass,"ext<-")
-importFrom(GiottoClass,"featType<-")
-importFrom(GiottoClass,"instructions<-")
-importFrom(GiottoClass,"objName<-")
-importFrom(GiottoClass,"prov<-")
-importFrom(GiottoClass,"spatUnit<-")
-importFrom(GiottoClass,activeFeatType)
-importFrom(GiottoClass,activeSpatUnit)
-importFrom(GiottoClass,addCellMetadata)
-importFrom(GiottoClass,addFeatMetadata)
-importFrom(GiottoClass,addGiottoImage)
-importFrom(GiottoClass,addGiottoImageMG)
-importFrom(GiottoClass,addGiottoLargeImage)
-importFrom(GiottoClass,addGiottoPoints)
-importFrom(GiottoClass,addGiottoPoints3D)
-importFrom(GiottoClass,addGiottoPolygons)
-importFrom(GiottoClass,addNetworkLayout)
-importFrom(GiottoClass,addSpatialCentroidLocations)
-importFrom(GiottoClass,addSpatialCentroidLocationsLayer)
-importFrom(GiottoClass,aggregateStacks)
-importFrom(GiottoClass,aggregateStacksExpression)
-importFrom(GiottoClass,aggregateStacksLocations)
-importFrom(GiottoClass,aggregateStacksPolygonOverlaps)
-importFrom(GiottoClass,aggregateStacksPolygons)
-importFrom(GiottoClass,anndataToGiotto)
-importFrom(GiottoClass,annotateGiotto)
-importFrom(GiottoClass,annotateSpatialGrid)
-importFrom(GiottoClass,annotateSpatialNetwork)
-importFrom(GiottoClass,as.points)
-importFrom(GiottoClass,as.polygons)
-importFrom(GiottoClass,as.sf)
-importFrom(GiottoClass,as.sp)
-importFrom(GiottoClass,as.stars)
-importFrom(GiottoClass,as.terra)
-importFrom(GiottoClass,calculateMetaTable)
-importFrom(GiottoClass,calculateMetaTableCells)
-importFrom(GiottoClass,calculateOverlap)
-importFrom(GiottoClass,calculateOverlapParallel)
-importFrom(GiottoClass,calculateOverlapPolygonImages)
-importFrom(GiottoClass,calculateOverlapRaster)
-importFrom(GiottoClass,calculateOverlapSerial)
-importFrom(GiottoClass,calculateSpatCellMetadataProportions)
-importFrom(GiottoClass,centroids)
-importFrom(GiottoClass,changeGiottoInstructions)
-importFrom(GiottoClass,changeImageBg)
-importFrom(GiottoClass,checkGiottoEnvironment)
-importFrom(GiottoClass,circleVertices)
-importFrom(GiottoClass,combineCellData)
-importFrom(GiottoClass,combineFeatureData)
-importFrom(GiottoClass,combineFeatureOverlapData)
-importFrom(GiottoClass,combineMetadata)
-importFrom(GiottoClass,combineSpatialCellFeatureInfo)
-importFrom(GiottoClass,combineSpatialCellMetadataInfo)
-importFrom(GiottoClass,combineToMultiPolygon)
-importFrom(GiottoClass,convertGiottoLargeImageToMG)
-importFrom(GiottoClass,copy)
-importFrom(GiottoClass,createBentoAdata)
-importFrom(GiottoClass,createCellMetaObj)
-importFrom(GiottoClass,createDimObj)
-importFrom(GiottoClass,createExprObj)
-importFrom(GiottoClass,createFeatMetaObj)
-importFrom(GiottoClass,createGiottoImage)
-importFrom(GiottoClass,createGiottoInstructions)
-importFrom(GiottoClass,createGiottoLargeImage)
-importFrom(GiottoClass,createGiottoLargeImageList)
-importFrom(GiottoClass,createGiottoObject)
-importFrom(GiottoClass,createGiottoObjectSubcellular)
-importFrom(GiottoClass,createGiottoPoints)
-importFrom(GiottoClass,createGiottoPolygon)
-importFrom(GiottoClass,createGiottoPolygonsFromDfr)
-importFrom(GiottoClass,createGiottoPolygonsFromGeoJSON)
-importFrom(GiottoClass,createGiottoPolygonsFromMask)
-importFrom(GiottoClass,createMetafeats)
-importFrom(GiottoClass,createNearestNetObj)
-importFrom(GiottoClass,createNearestNetwork)
-importFrom(GiottoClass,createSpatEnrObj)
-importFrom(GiottoClass,createSpatLocsObj)
-importFrom(GiottoClass,createSpatNetObj)
-importFrom(GiottoClass,createSpatialDefaultGrid)
-importFrom(GiottoClass,createSpatialDelaunayNetwork)
-importFrom(GiottoClass,createSpatialFeaturesKNNnetwork)
-importFrom(GiottoClass,createSpatialGrid)
-importFrom(GiottoClass,createSpatialKNNnetwork)
-importFrom(GiottoClass,createSpatialNetwork)
-importFrom(GiottoClass,createSpatialWeightMatrix)
-importFrom(GiottoClass,crop)
-importFrom(GiottoClass,cropGiottoLargeImage)
-importFrom(GiottoClass,density)
-importFrom(GiottoClass,distGiottoImage)
-importFrom(GiottoClass,estimateImageBg)
-importFrom(GiottoClass,ext)
-importFrom(GiottoClass,fDataDT)
-importFrom(GiottoClass,featIDs)
-importFrom(GiottoClass,featType)
-importFrom(GiottoClass,featureNetwork)
-importFrom(GiottoClass,flip)
-importFrom(GiottoClass,gefToGiotto)
-importFrom(GiottoClass,getCellMetadata)
-importFrom(GiottoClass,getDimReduction)
-importFrom(GiottoClass,getExpression)
-importFrom(GiottoClass,getFeatureInfo)
-importFrom(GiottoClass,getFeatureMetadata)
-importFrom(GiottoClass,getGiottoImage)
-importFrom(GiottoClass,getMultiomics)
-importFrom(GiottoClass,getNearestNetwork)
-importFrom(GiottoClass,getPolygonInfo)
-importFrom(GiottoClass,getSpatialEnrichment)
-importFrom(GiottoClass,getSpatialGrid)
-importFrom(GiottoClass,getSpatialLocations)
-importFrom(GiottoClass,getSpatialNetwork)
-importFrom(GiottoClass,giotto)
-importFrom(GiottoClass,giottoImage)
-importFrom(GiottoClass,giottoLargeImage)
-importFrom(GiottoClass,giottoMasterToSuite)
-importFrom(GiottoClass,giottoPoints)
-importFrom(GiottoClass,giottoPolygon)
-importFrom(GiottoClass,giottoToAnnData)
-importFrom(GiottoClass,giottoToSeurat)
-importFrom(GiottoClass,giottoToSeuratV4)
-importFrom(GiottoClass,giottoToSeuratV5)
-importFrom(GiottoClass,giottoToSpatialExperiment)
-importFrom(GiottoClass,hexVertices)
-importFrom(GiottoClass,hist)
-importFrom(GiottoClass,installGiottoEnvironment)
-importFrom(GiottoClass,instructions)
-importFrom(GiottoClass,joinGiottoObjects)
-importFrom(GiottoClass,loadGiotto)
-importFrom(GiottoClass,makePseudoVisium)
-importFrom(GiottoClass,objHistory)
-importFrom(GiottoClass,objName)
-importFrom(GiottoClass,orthoGrid)
-importFrom(GiottoClass,overlapImagesToMatrix)
-importFrom(GiottoClass,overlapToMatrix)
-importFrom(GiottoClass,overlapToMatrixMultiPoly)
-importFrom(GiottoClass,overlaps)
-importFrom(GiottoClass,pDataDT)
-importFrom(GiottoClass,plotGiottoImage)
-importFrom(GiottoClass,polyStamp)
-importFrom(GiottoClass,prov)
-importFrom(GiottoClass,readCellMetadata)
-importFrom(GiottoClass,readDimReducData)
-importFrom(GiottoClass,readExprData)
-importFrom(GiottoClass,readExprMatrix)
-importFrom(GiottoClass,readFeatData)
-importFrom(GiottoClass,readFeatMetadata)
-importFrom(GiottoClass,readGiottoInstructions)
-importFrom(GiottoClass,readNearestNetData)
-importFrom(GiottoClass,readPolygonData)
-importFrom(GiottoClass,readSpatEnrichData)
-importFrom(GiottoClass,readSpatLocsData)
-importFrom(GiottoClass,readSpatNetData)
-importFrom(GiottoClass,reconnectGiottoImage)
-importFrom(GiottoClass,rectVertices)
-importFrom(GiottoClass,removeCellAnnotation)
-importFrom(GiottoClass,removeFeatAnnotation)
-importFrom(GiottoClass,removeGiottoEnvironment)
-importFrom(GiottoClass,replaceGiottoInstructions)
-importFrom(GiottoClass,rescale)
-importFrom(GiottoClass,rescalePolygons)
-importFrom(GiottoClass,saveGiotto)
-importFrom(GiottoClass,setCellMetadata)
-importFrom(GiottoClass,setDimReduction)
-importFrom(GiottoClass,setExpression)
-importFrom(GiottoClass,setFeatureInfo)
-importFrom(GiottoClass,setFeatureMetadata)
-importFrom(GiottoClass,setGiotto)
-importFrom(GiottoClass,setGiottoImage)
-importFrom(GiottoClass,setMultiomics)
-importFrom(GiottoClass,setNearestNetwork)
-importFrom(GiottoClass,setPolygonInfo)
-importFrom(GiottoClass,setSpatialEnrichment)
-importFrom(GiottoClass,setSpatialGrid)
-importFrom(GiottoClass,setSpatialLocations)
-importFrom(GiottoClass,setSpatialNetwork)
-importFrom(GiottoClass,seuratToGiotto)
-importFrom(GiottoClass,seuratToGiottoV4)
-importFrom(GiottoClass,seuratToGiottoV5)
-importFrom(GiottoClass,showGiottoCellMetadata)
-importFrom(GiottoClass,showGiottoDimRed)
-importFrom(GiottoClass,showGiottoExpression)
-importFrom(GiottoClass,showGiottoFeatInfo)
-importFrom(GiottoClass,showGiottoFeatMetadata)
-importFrom(GiottoClass,showGiottoImageNames)
-importFrom(GiottoClass,showGiottoInstructions)
-importFrom(GiottoClass,showGiottoNearestNetworks)
-importFrom(GiottoClass,showGiottoSpatEnrichments)
-importFrom(GiottoClass,showGiottoSpatGrids)
-importFrom(GiottoClass,showGiottoSpatLocs)
-importFrom(GiottoClass,showGiottoSpatNetworks)
-importFrom(GiottoClass,showGiottoSpatialInfo)
-importFrom(GiottoClass,showProcessingSteps)
-importFrom(GiottoClass,smoothGiottoPolygons)
-importFrom(GiottoClass,spatIDs)
-importFrom(GiottoClass,spatQueryGiottoPolygons)
-importFrom(GiottoClass,spatShift)
-importFrom(GiottoClass,spatUnit)
-importFrom(GiottoClass,spatialExperimentToGiotto)
-importFrom(GiottoClass,spin)
-importFrom(GiottoClass,stitchFieldCoordinates)
-importFrom(GiottoClass,stitchGiottoLargeImage)
-importFrom(GiottoClass,subsetGiotto)
-importFrom(GiottoClass,subsetGiottoLocs)
-importFrom(GiottoClass,subsetGiottoLocsMulti)
-importFrom(GiottoClass,subsetGiottoLocsSubcellular)
-importFrom(GiottoClass,tessellate)
-importFrom(GiottoClass,triGrid)
-importFrom(GiottoClass,updateGiottoImage)
-importFrom(GiottoClass,updateGiottoImageMG)
-importFrom(GiottoClass,updateGiottoLargeImage)
-importFrom(GiottoClass,updateGiottoObject)
-importFrom(GiottoClass,updateGiottoPointsObject)
-importFrom(GiottoClass,updateGiottoPolygonObject)
-importFrom(GiottoClass,vect)
-importFrom(GiottoClass,wrap)
-importFrom(GiottoClass,writeGiottoLargeImage)
-importFrom(GiottoUtils,"%>%")
-importFrom(GiottoUtils,getDistinctColors)
-importFrom(GiottoUtils,getRainbowColors)
-importFrom(GiottoVisuals,"sankeyLabel<-")
-importFrom(GiottoVisuals,"sankeyRelate<-")
-importFrom(GiottoVisuals,addGiottoImageToSpatPlot)
-importFrom(GiottoVisuals,dimCellPlot)
-importFrom(GiottoVisuals,dimCellPlot2D)
-importFrom(GiottoVisuals,dimFeatPlot2D)
-importFrom(GiottoVisuals,dimFeatPlot3D)
-importFrom(GiottoVisuals,dimGenePlot3D)
-importFrom(GiottoVisuals,dimPlot)
-importFrom(GiottoVisuals,dimPlot2D)
-importFrom(GiottoVisuals,dimPlot3D)
-importFrom(GiottoVisuals,getColors)
-importFrom(GiottoVisuals,giottoSankeyPlan)
-importFrom(GiottoVisuals,plotHeatmap)
-importFrom(GiottoVisuals,plotMetaDataCellsHeatmap)
-importFrom(GiottoVisuals,plotMetaDataHeatmap)
-importFrom(GiottoVisuals,plotPCA)
-importFrom(GiottoVisuals,plotPCA_2D)
-importFrom(GiottoVisuals,plotPCA_3D)
-importFrom(GiottoVisuals,plotStatDelaunayNetwork)
-importFrom(GiottoVisuals,plotTSNE)
-importFrom(GiottoVisuals,plotTSNE_2D)
-importFrom(GiottoVisuals,plotTSNE_3D)
-importFrom(GiottoVisuals,plotUMAP)
-importFrom(GiottoVisuals,plotUMAP_2D)
-importFrom(GiottoVisuals,plotUMAP_3D)
-importFrom(GiottoVisuals,sankeyLabel)
-importFrom(GiottoVisuals,sankeyPlot)
-importFrom(GiottoVisuals,sankeyRelate)
-importFrom(GiottoVisuals,sankeySet)
-importFrom(GiottoVisuals,sankeySetAddresses)
-importFrom(GiottoVisuals,showClusterDendrogram)
-importFrom(GiottoVisuals,showClusterHeatmap)
-importFrom(GiottoVisuals,showColorInstructions)
-importFrom(GiottoVisuals,showSaveParameters)
-importFrom(GiottoVisuals,spatCellPlot)
-importFrom(GiottoVisuals,spatCellPlot2D)
-importFrom(GiottoVisuals,spatDeconvPlot)
-importFrom(GiottoVisuals,spatDimCellPlot)
-importFrom(GiottoVisuals,spatDimCellPlot2D)
-importFrom(GiottoVisuals,spatDimFeatPlot2D)
-importFrom(GiottoVisuals,spatDimFeatPlot3D)
-importFrom(GiottoVisuals,spatDimGenePlot3D)
-importFrom(GiottoVisuals,spatDimPlot)
-importFrom(GiottoVisuals,spatDimPlot2D)
-importFrom(GiottoVisuals,spatDimPlot3D)
-importFrom(GiottoVisuals,spatFeatPlot2D)
-importFrom(GiottoVisuals,spatFeatPlot2D_single)
-importFrom(GiottoVisuals,spatFeatPlot3D)
-importFrom(GiottoVisuals,spatGenePlot3D)
-importFrom(GiottoVisuals,spatInSituPlotDensity)
-importFrom(GiottoVisuals,spatInSituPlotHex)
-importFrom(GiottoVisuals,spatInSituPlotPoints)
-importFrom(GiottoVisuals,spatNetwDistributions)
-importFrom(GiottoVisuals,spatNetwDistributionsDistance)
-importFrom(GiottoVisuals,spatNetwDistributionsKneighbors)
-importFrom(GiottoVisuals,spatPlot)
-importFrom(GiottoVisuals,spatPlot2D)
-importFrom(GiottoVisuals,spatPlot3D)
-importFrom(GiottoVisuals,subsetSankeySet)
-importFrom(GiottoVisuals,violinPlot)
 importFrom(data.table,data.table)
 importFrom(data.table,frank)
 importFrom(data.table,fread)