NAMESPACE

# Generated by roxygen2: do not edit by hand

S3method(AlignImages,Seurat)
S3method(AlignImages,Staffli)
S3method(CropImages,Seurat)
S3method(CropImages,Staffli)
S3method(LoadImages,Seurat)
S3method(LoadImages,Staffli)
S3method(ManualAlignImages,Seurat)
S3method(ManualAlignImages,Staffli)
S3method(MaskImages,Seurat)
S3method(MaskImages,Staffli)
S3method(WarpImages,Seurat)
S3method(WarpImages,Staffli)
export(AlignImages)
export(ConvertGeneNames)
export(CorSpatialGenes)
export(Create3DStack)
export(CreateStaffliObject)
export(CropImages)
export(DimOverlay)
export(DimPlot3D)
export(EdgeMask)
export(FactorGeneLoadingPlot)
export(FeatureOverlay)
export(FeaturePlot3D)
export(GetCoords)
export(GetCropWindows)
export(GetSpatNet)
export(GetStaffli)
export(HSVOverlay)
export(HSVPlot)
export(HSVPlot3D)
export(ImagePlot)
export(InputFromTable)
export(LoadImages)
export(ManualAlignImages)
export(ManualAnnotation)
export(MaskImages)
export(MergeSTData)
export(RegionNeighbours)
export(RunNMF)
export(ST.DimPlot)
export(ST.FeaturePlot)
export(ST.ImagePlot)
export(ST.rgbDimPlot)
export(STPlot)
export(SubsetSTData)
export(SummarizeAssocFeatures)
export(SwitchResolution)
export(WarpImages)
export(combine.tr)
export(iminfo)
export(labelRGB)
export(palette.select)
export(rasterlists)
export(samplenames)
export(scaled.imdims)
exportClasses(Staffli)
exportMethods("[")
exportMethods("[<-")
exportMethods("[[")
exportMethods("[[<-")
exportMethods(iminfo)
exportMethods(names)
exportMethods(plot)
exportMethods(rasterlists)
exportMethods(samplenames)
exportMethods(scaled.imdims)
exportMethods(show)
import(Matrix)
importFrom(Matrix,bdiag)
importFrom(Matrix,colSums)
importFrom(Seurat,"DefaultAssay<-")
importFrom(Seurat,"Idents<-")
importFrom(Seurat,CreateDimReducObject)
importFrom(Seurat,CreateSeuratObject)
importFrom(Seurat,DarkTheme)
importFrom(Seurat,DefaultAssay)
importFrom(Seurat,Embeddings)
importFrom(Seurat,FetchData)
importFrom(Seurat,GetAssayData)
importFrom(Seurat,Idents)
importFrom(Seurat,Key)
importFrom(Seurat,Reductions)
importFrom(Seurat,RenameCells)
importFrom(Seurat,VariableFeatures)
importFrom(Seurat,WhichCells)
importFrom(cowplot,plot_grid)
importFrom(data.table,as.data.table)
importFrom(data.table,fread)
importFrom(dplyr,group_by)
importFrom(dplyr,mutate)
importFrom(dplyr,select)
importFrom(dplyr,summarize)
importFrom(dplyr,ungroup)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,annotate)
importFrom(ggplot2,annotation_custom)
importFrom(ggplot2,as_labeller)
importFrom(ggplot2,coord_fixed)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggplot_build)
importFrom(ggplot2,ggplot_gtable)
importFrom(ggplot2,ggproto)
importFrom(ggplot2,ggproto_parent)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_color_gradient2)
importFrom(ggplot2,scale_color_gradientn)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_gradient2)
importFrom(ggplot2,scale_fill_gradientn)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_size)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,sym)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,theme_void)
importFrom(ggplot2,vars)
importFrom(grDevices,as.raster)
importFrom(grDevices,col2rgb)
importFrom(grDevices,colorRamp)
importFrom(grDevices,densCols)
importFrom(grDevices,dev.off)
importFrom(grDevices,hcl)
importFrom(grDevices,hsv)
importFrom(grDevices,png)
importFrom(grDevices,rgb)
importFrom(grid,rasterGrob)
importFrom(grid,unit)
importFrom(igraph,graph_from_data_frame)
importFrom(imager,HSVtoRGB)
importFrom(imager,LabtosRGB)
importFrom(imager,RGBtoHSV)
importFrom(imager,add)
importFrom(imager,as.cimg)
importFrom(imager,as.pixset)
importFrom(imager,blur_anisotropic)
importFrom(imager,enorm)
importFrom(imager,grayscale)
importFrom(imager,imappend)
importFrom(imager,imgradient)
importFrom(imager,imlist)
importFrom(imager,imsplit)
importFrom(imager,imsub)
importFrom(imager,imwarp)
importFrom(imager,isoblur)
importFrom(imager,magick2cimg)
importFrom(imager,map_il)
importFrom(imager,medianblur)
importFrom(imager,nPix)
importFrom(imager,sRGBtoLab)
importFrom(imager,spectrum)
importFrom(imager,split_connected)
importFrom(imager,threshold)
importFrom(jsonlite,read_json)
importFrom(magick,geometry_area)
importFrom(magick,geometry_size_pixels)
importFrom(magick,image_annotate)
importFrom(magick,image_append)
importFrom(magick,image_border)
importFrom(magick,image_composite)
importFrom(magick,image_crop)
importFrom(magick,image_info)
importFrom(magick,image_read)
importFrom(magick,image_scale)
importFrom(magrittr,"%>%")
importFrom(parallel,detectCores)
importFrom(plotly,add_markers)
importFrom(plotly,ggplotly)
importFrom(plotly,layout)
importFrom(plotly,plot_ly)
importFrom(purrr,map)
importFrom(purrr,map_dbl)
importFrom(purrr,modify_at)
importFrom(raster,coordinates)
importFrom(raster,raster)
importFrom(scales,rescale)
importFrom(shiny,HTML)
importFrom(shiny,actionButton)
importFrom(shiny,checkboxInput)
importFrom(shiny,column)
importFrom(shiny,debounce)
importFrom(shiny,eventReactive)
importFrom(shiny,fluidPage)
importFrom(shiny,fluidRow)
importFrom(shiny,h4)
importFrom(shiny,headerPanel)
importFrom(shiny,hr)
importFrom(shiny,mainPanel)
importFrom(shiny,modalDialog)
importFrom(shiny,numericInput)
importFrom(shiny,observe)
importFrom(shiny,observeEvent)
importFrom(shiny,pageWithSidebar)
importFrom(shiny,plotOutput)
importFrom(shiny,radioButtons)
importFrom(shiny,reactive)
importFrom(shiny,reactiveValues)
importFrom(shiny,renderPlot)
importFrom(shiny,runApp)
importFrom(shiny,selectInput)
importFrom(shiny,showModal)
importFrom(shiny,sidebarPanel)
importFrom(shiny,sliderInput)
importFrom(shiny,stopApp)
importFrom(shiny,strong)
importFrom(shiny,submitButton)
importFrom(shiny,textInput)
importFrom(shiny,withProgress)
importFrom(shinyjs,reset)
importFrom(shinyjs,useShinyjs)
importFrom(stats,cor)
importFrom(stats,dist)
importFrom(stats,kmeans)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,quantile)
importFrom(stats,reorder)
importFrom(stats,runif)
importFrom(stats,setNames)
importFrom(utils,packageVersion)
importFrom(zeallot,"%<-%")