332 lines (330 with data), 8.8 kB

# Generated by roxygen2: do not edit by hand

S3method("$",VoltRon)
S3method("$<-",VoltRon)
S3method(as.VoltRon,Seurat)
S3method(as.VoltRon,SpatialExperiment)
S3method(as.Zarr,"magick-image")
export("vrCoordinates<-")
export("vrEmbeddings<-")
export("vrFeatureData<-")
export("vrGraph<-")
export("vrImages<-")
export("vrMainAssay<-")
export("vrMainChannel<-")
export("vrMainFeatureType<-")
export("vrMainImage<-")
export("vrMainSpatial<-")
export("vrSegments<-")
export("vrSpatialPoints<-")
export(FromSegmentToCrop)
export(Metadata)
export(SampleMetadata)
export(addAssay)
export(addFeature)
export(addMetadata)
export(addSpatialLayer)
export(annotateSpatialData)
export(as.AnnData)
export(as.Giotto)
export(as.OmeTiff)
export(as.OmeZarr)
export(as.Seurat)
export(as.SpatialExperiment)
export(as.VoltRon)
export(as.Zarr)
export(combineChannels)
export(combineGraphs)
export(convertAnnDataToVoltRon)
export(flipCoordinates)
export(formAssay)
export(formImage)
export(formVoltRon)
export(generateCosMxImage)
export(generateGeoJSON)
export(generateSegments)
export(generateTileData)
export(generateXeniumImage)
export(getBasilisk)
export(getClusters)
export(getDeconvolution)
export(getDiffExp)
export(getFeatures)
export(getHotSpotAnalysis)
export(getNicheAssay)
export(getPCA)
export(getProfileNeighbors)
export(getRcppAutomatedRegistration)
export(getRcppManualRegistration)
export(getRcppWarpImage)
export(getSpatialNeighbors)
export(getUMAP)
export(getVariableFeatures)
export(import10Xh5)
export(importCosMx)
export(importDBITSeq)
export(importGenePS)
export(importGeoMx)
export(importImageData)
export(importOpenST)
export(importPhenoCycler)
export(importSTOmics)
export(importVisium)
export(importVisiumHD)
export(importXenium)
export(loadVoltRon)
export(modulateImage)
export(normalizeData)
export(registerSpatialData)
export(resizeImage)
export(saveVoltRon)
export(transferData)
export(updateAssay)
export(vrAssayNames)
export(vrAssayParams)
export(vrAssayTypes)
export(vrBarPlot)
export(vrCoordinates)
export(vrData)
export(vrEmbeddingFeaturePlot)
export(vrEmbeddingNames)
export(vrEmbeddingPlot)
export(vrEmbeddings)
export(vrFeatureData)
export(vrFeatureTypeNames)
export(vrFeatures)
export(vrGraph)
export(vrGraphNames)
export(vrHeatmapPlot)
export(vrImageChannelNames)
export(vrImageNames)
export(vrImages)
export(vrMainAssay)
export(vrMainChannel)
export(vrMainFeatureType)
export(vrMainImage)
export(vrMainSpatial)
export(vrNeighbourhoodEnrichment)
export(vrNeighbourhoodEnrichmentPlot)
export(vrProportionPlot)
export(vrSampleNames)
export(vrScatterPlot)
export(vrSegments)
export(vrSpatialFeaturePlot)
export(vrSpatialNames)
export(vrSpatialPlot)
export(vrSpatialPoints)
export(vrViolinPlot)
exportClasses(VoltRon)
exportClasses(vrAssay)
exportClasses(vrAssayV2)
exportClasses(vrBlock)
exportClasses(vrImage)
exportClasses(vrLayer)
exportClasses(vrMetadata)
exportClasses(vrSample)
exportClasses(vrSpatial)
exportMethods("Metadata<-")
exportMethods("[[")
exportMethods("[[<-")
exportMethods("vrCoordinates<-")
exportMethods("vrEmbeddings<-")
exportMethods("vrFeatureData<-")
exportMethods("vrImages<-")
exportMethods("vrMainAssay<-")
exportMethods("vrMainChannel<-")
exportMethods("vrMainFeatureType<-")
exportMethods("vrMainImage<-")
exportMethods("vrMainSpatial<-")
exportMethods("vrSegments<-")
exportMethods("vrSpatialPoints<-")
exportMethods(Metadata)
exportMethods(addAssay)
exportMethods(addFeature)
exportMethods(combineChannels)
exportMethods(flipCoordinates)
exportMethods(generateTileData)
exportMethods(getFeatures)
exportMethods(merge)
exportMethods(modulateImage)
exportMethods(normalizeData)
exportMethods(resizeImage)
exportMethods(subset)
exportMethods(updateAssay)
exportMethods(vrAssayNames)
exportMethods(vrAssayTypes)
exportMethods(vrCoordinates)
exportMethods(vrData)
exportMethods(vrEmbeddingNames)
exportMethods(vrEmbeddings)
exportMethods(vrFeatureData)
exportMethods(vrFeatureTypeNames)
exportMethods(vrFeatures)
exportMethods(vrImageChannelNames)
exportMethods(vrImageNames)
exportMethods(vrImages)
exportMethods(vrMainAssay)
exportMethods(vrMainChannel)
exportMethods(vrMainFeatureType)
exportMethods(vrMainImage)
exportMethods(vrMainSpatial)
exportMethods(vrSampleNames)
exportMethods(vrSegments)
exportMethods(vrSpatialNames)
exportMethods(vrSpatialPoints)
import(ggplot2)
import(shiny)
importClassesFrom(Matrix,dgCMatrix)
importClassesFrom(Matrix,dgRMatrix)
importClassesFrom(Matrix,dgeMatrix)
importClassesFrom(S4Arrays,Array)
importClassesFrom(data.table,data.table)
importFrom(EBImage,as.Image)
importFrom(EBImage,writeImage)
importFrom(Matrix,Matrix)
importFrom(Matrix,colSums)
importFrom(Matrix,rowMeans)
importFrom(Matrix,rowSums)
importFrom(Matrix,sparseMatrix)
importFrom(Matrix,t)
importFrom(RANN,nn2)
importFrom(RCDT,delaunay)
importFrom(RcppAnnoy,AnnoyEuclidean)
importFrom(data.table,alloc.col)
importFrom(data.table,as.data.table)
importFrom(data.table,chmatch)
importFrom(data.table,data.table)
importFrom(data.table,fread)
importFrom(data.table,is.data.table)
importFrom(data.table,melt)
importFrom(data.table,set)
importFrom(data.table,setkey)
importFrom(dplyr,"%>%")
importFrom(dplyr,add_row)
importFrom(dplyr,arrange)
importFrom(dplyr,as_tibble)
importFrom(dplyr,bind_cols)
importFrom(dplyr,bind_rows)
importFrom(dplyr,coalesce)
importFrom(dplyr,desc)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,full_join)
importFrom(dplyr,group_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,mutate_all)
importFrom(dplyr,n)
importFrom(dplyr,n_distinct)
importFrom(dplyr,right_join)
importFrom(dplyr,select)
importFrom(dplyr,summarize)
importFrom(dplyr,tibble)
importFrom(ggplot2,annotation_custom)
importFrom(ggplot2,annotation_raster)
importFrom(ggplot2,coord_fixed)
importFrom(ggplot2,geom_rect)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggproto)
importFrom(ggplot2,xlim)
importFrom(ggplot2,ylim)
importFrom(ggpubr,ggarrange)
importFrom(ggrepel,geom_label_repel)
importFrom(grDevices,as.raster)
importFrom(grDevices,col2rgb)
importFrom(grDevices,hcl)
importFrom(grDevices,rgb)
importFrom(grDevices,rgb2hsv)
importFrom(grid,gpar)
importFrom(grid,pointsGrob)
importFrom(grid,rasterGrob)
importFrom(grid,unit)
importFrom(ids,random_id)
importFrom(igraph,"E<-")
importFrom(igraph,"V<-")
importFrom(igraph,E)
importFrom(igraph,V)
importFrom(igraph,add_edges)
importFrom(igraph,as_adjacency_matrix)
importFrom(igraph,as_data_frame)
importFrom(igraph,cluster_leiden)
importFrom(igraph,components)
importFrom(igraph,disjoint_union)
importFrom(igraph,edge_attr_names)
importFrom(igraph,get.data.frame)
importFrom(igraph,graph_from_adjacency_matrix)
importFrom(igraph,induced_subgraph)
importFrom(igraph,make_empty_graph)
importFrom(igraph,neighborhood)
importFrom(igraph,simplify)
importFrom(igraph,subgraph)
importFrom(igraph,union)
importFrom(igraph,vcount)
importFrom(igraph,vertices)
importFrom(irlba,irlba)
importFrom(magick,geometry_size_percent)
importFrom(magick,image_composite)
importFrom(magick,image_contrast)
importFrom(magick,image_crop)
importFrom(magick,image_data)
importFrom(magick,image_flip)
importFrom(magick,image_flop)
importFrom(magick,image_ggplot)
importFrom(magick,image_info)
importFrom(magick,image_join)
importFrom(magick,image_modulate)
importFrom(magick,image_negate)
importFrom(magick,image_raster)
importFrom(magick,image_read)
importFrom(magick,image_resize)
importFrom(magick,image_rotate)
importFrom(magick,image_scale)
importFrom(magick,image_write)
importFrom(methods,"slot<-")
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,slot)
importFrom(methods,slotNames)
importFrom(rjson,fromJSON)
importFrom(rlang,"%||%")
importFrom(rlang,'!!')
importFrom(rlang,dots_list)
importFrom(rlang,enquo)
importFrom(rlang,eval_tidy)
importFrom(rlang,list2)
importFrom(rlang,quo_get_expr)
importFrom(rlang,quo_name)
importFrom(rlang,quo_text)
importFrom(rlang,sym)
importFrom(shiny,HTML)
importFrom(shiny,reactiveValuesToList)
importFrom(shiny,tags)
importFrom(shiny,validateCssUnit)
importFrom(shinyjs,hide)
importFrom(shinyjs,show)
importFrom(shinyjs,useShinyjs)
importFrom(sp,point.in.polygon)
importFrom(stats,aggregate)
importFrom(stats,as.formula)
importFrom(stats,dist)
importFrom(stats,kmeans)
importFrom(stats,loess)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,pnorm)
importFrom(stats,predict)
importFrom(stats,quantile)
importFrom(stats,setNames)
importFrom(stats,var)
importFrom(stringr,str_extract)
importFrom(stringr,str_order)
importFrom(stringr,str_remove)
importFrom(stringr,str_replace)
importFrom(stringr,str_sort)
importFrom(utils,.DollarNames)
importFrom(utils,capture.output)
importFrom(utils,head)
importFrom(utils,read.csv)
importFrom(utils,read.table)
importFrom(uwot,umap)
useDynLib(VoltRon)