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NAMESPACE
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# Generated by roxygen2: do not edit by hand
S3method("CellGraphs<-",MPXAssay)
S3method("CellGraphs<-",Seurat)
S3method("ColocalizationScores<-",MPXAssay)
S3method("ColocalizationScores<-",Seurat)
S3method("FSMap<-",MPXAssay)
S3method("FSMap<-",Seurat)
S3method("PolarizationScores<-",MPXAssay)
S3method("PolarizationScores<-",Seurat)
S3method(CellCountPlot,Seurat)
S3method(CellCountPlot,data.frame)
S3method(CellGraphs,MPXAssay)
S3method(CellGraphs,Seurat)
S3method(ColocalizationScores,MPXAssay)
S3method(ColocalizationScores,Seurat)
S3method(ColocalizationScoresToAssay,CellGraphAssay)
S3method(ColocalizationScoresToAssay,CellGraphAssay5)
S3method(ColocalizationScoresToAssay,MPXAssay)
S3method(ColocalizationScoresToAssay,Seurat)
S3method(ColocalizationScoresToAssay,data.frame)
S3method(ComputeLayout,CellGraph)
S3method(ComputeLayout,CellGraphAssay)
S3method(ComputeLayout,CellGraphAssay5)
S3method(ComputeLayout,MPXAssay)
S3method(ComputeLayout,Seurat)
S3method(ComputeLayout,tbl_graph)
S3method(FSMap,MPXAssay)
S3method(FSMap,Seurat)
S3method(JoinLayers,CellGraphAssay5)
S3method(KeepLargestComponent,CellGraph)
S3method(KeepLargestComponent,MPXAssay)
S3method(KeepLargestComponent,Seurat)
S3method(KeepLargestComponent,tbl_graph)
S3method(LoadCellGraphs,CellGraphAssay)
S3method(LoadCellGraphs,CellGraphAssay5)
S3method(LoadCellGraphs,FileSystemDataset)
S3method(LoadCellGraphs,MPXAssay)
S3method(LoadCellGraphs,Seurat)
S3method(LoadCellGraphs,tbl_df)
S3method(MoleculeRankPlot,Seurat)
S3method(MoleculeRankPlot,data.frame)
S3method(NormalizeMPX,Assay)
S3method(NormalizeMPX,Assay5)
S3method(NormalizeMPX,CellGraphAssay)
S3method(NormalizeMPX,CellGraphAssay5)
S3method(NormalizeMPX,MPXAssay)
S3method(NormalizeMPX,Matrix)
S3method(NormalizeMPX,Seurat)
S3method(PolarizationScores,MPXAssay)
S3method(PolarizationScores,Seurat)
S3method(PolarizationScoresToAssay,CellGraphAssay)
S3method(PolarizationScoresToAssay,CellGraphAssay5)
S3method(PolarizationScoresToAssay,MPXAssay)
S3method(PolarizationScoresToAssay,Seurat)
S3method(PolarizationScoresToAssay,data.frame)
S3method(RemoveCellGraphs,MPXAssay)
S3method(RemoveCellGraphs,Seurat)
S3method(RenameCells,CellGraphAssay)
S3method(RenameCells,CellGraphAssay5)
S3method(RenameCells,MPXAssay)
S3method(RestorePaths,CellGraphAssay)
S3method(RestorePaths,CellGraphAssay5)
S3method(RestorePaths,MPXAssay)
S3method(RestorePaths,Seurat)
S3method(RunDAA,Seurat)
S3method(RunDCA,Seurat)
S3method(RunDCA,data.frame)
S3method(RunDPA,Seurat)
S3method(RunDPA,data.frame)
S3method(TauPlot,Seurat)
S3method(TauPlot,data.frame)
S3method(as.CellGraphAssay,Assay)
S3method(as.CellGraphAssay5,Assay5)
S3method(edgelist_to_simple_Anode_graph,FileSystemDataset)
S3method(edgelist_to_simple_Anode_graph,data.frame)
S3method(merge,CellGraphAssay)
S3method(merge,CellGraphAssay5)
S3method(merge,MPXAssay)
S3method(print,pixelator_metadata)
S3method(subset,CellGraphAssay)
S3method(subset,CellGraphAssay5)
S3method(subset,MPXAssay)
export("CellGraphData<-")
export("CellGraphs<-")
export("ColocalizationScores<-")
export("FSMap<-")
export("PolarizationScores<-")
export(AbundanceColocalizationPlot)
export(CellCountPlot)
export(CellGraphData)
export(CellGraphs)
export(ColocalizationHeatmap)
export(ColocalizationScores)
export(ColocalizationScoresToAssay)
export(ComputeLayout)
export(CreateCellGraphAssay)
export(CreateCellGraphAssay5)
export(CreateCellGraphObject)
export(DensityScatterPlot)
export(EdgeRankPlot)
export(FSMap)
export(KeepLargestComponent)
export(LoadCellGraphs)
export(MoleculeRankPlot)
export(NormalizeMPX)
export(Plot2DGraph)
export(Plot2DGraphM)
export(Plot3DGraph)
export(PolarizationScores)
export(PolarizationScoresToAssay)
export(ReadMPX_Seurat)
export(ReadMPX_arrow_edgelist)
export(ReadMPX_colocalization)
export(ReadMPX_counts)
export(ReadMPX_edgelist)
export(ReadMPX_item)
export(ReadMPX_layouts)
export(ReadMPX_metadata)
export(ReadMPX_polarization)
export(RemoveCellGraphs)
export(RestorePaths)
export(RunDAA)
export(RunDCA)
export(RunDPA)
export(TauPlot)
export(WriteMPX_pxl_file)
export(as.CellGraphAssay)
export(as.CellGraphAssay5)
export(center_layout_coordinates)
export(color_by_marker)
export(compute_transition_probabilities)
export(cos_distance_weights)
export(edgelist_to_simple_Anode_graph)
export(edgelist_to_simple_bipart_graph)
export(inspect_pxl_file)
export(layout_with_weighted_pmds)
export(local_G)
export(node_markers_counts)
export(normalize_layout_coordinates)
export(pixelatorR_style)
export(prob_distance_weights)
export(project_layout_coordinates_on_unit_sphere)
exportClasses(CellGraph)
exportClasses(CellGraphAssay)
exportClasses(CellGraphAssay5)
exportClasses(MPXAssay)
exportMethods(show)
import(rlang)
importClassesFrom(Matrix,dgCMatrix)
importClassesFrom(SeuratObject,Assay)
importClassesFrom(SeuratObject,Assay5)
importFrom(Matrix,colSums)
importFrom(Matrix,rowSums)
importFrom(SeuratObject,"Key<-")
importFrom(SeuratObject,"LayerData<-")
importFrom(SeuratObject,"VariableFeatures<-")
importFrom(SeuratObject,Cells)
importFrom(SeuratObject,CreateAssay5Object)
importFrom(SeuratObject,CreateAssayObject)
importFrom(SeuratObject,CreateSeuratObject)
importFrom(SeuratObject,DefaultAssay)
importFrom(SeuratObject,FetchData)
importFrom(SeuratObject,JoinLayers)
importFrom(SeuratObject,Key)
importFrom(SeuratObject,LayerData)
importFrom(SeuratObject,Layers)
importFrom(SeuratObject,RenameCells)
importFrom(arrow,arrow_table)
importFrom(arrow,open_dataset)
importFrom(arrow,read_parquet)
importFrom(arrow,schema)
importFrom(arrow,to_duckdb)
importFrom(arrow,write_dataset)
importFrom(cli,cli_alert)
importFrom(cli,cli_alert_danger)
importFrom(cli,cli_alert_info)
importFrom(cli,cli_alert_success)
importFrom(cli,cli_alert_warning)
importFrom(cli,cli_h2)
importFrom(cli,cli_rule)
importFrom(cli,cli_status)
importFrom(cli,cli_status_clear)
importFrom(cli,cli_status_update)
importFrom(cli,cli_text)
importFrom(cli,col_blue)
importFrom(cli,col_br_blue)
importFrom(cli,col_br_magenta)
importFrom(cli,col_br_red)
importFrom(cli,col_green)
importFrom(cli,col_red)
importFrom(cli,symbol)
importFrom(dplyr,"%>%")
importFrom(dplyr,across)
importFrom(dplyr,all_of)
importFrom(dplyr,any_of)
importFrom(dplyr,arrange)
importFrom(dplyr,between)
importFrom(dplyr,bind_cols)
importFrom(dplyr,bind_rows)
importFrom(dplyr,case_when)
importFrom(dplyr,collect)
importFrom(dplyr,compute)
importFrom(dplyr,contains)
importFrom(dplyr,count)
importFrom(dplyr,cross_join)
importFrom(dplyr,distinct)
importFrom(dplyr,everything)
importFrom(dplyr,filter)
importFrom(dplyr,full_join)
importFrom(dplyr,group_by)
importFrom(dplyr,group_by_at)
importFrom(dplyr,group_data)
importFrom(dplyr,group_keys)
importFrom(dplyr,group_modify)
importFrom(dplyr,group_split)
importFrom(dplyr,inner_join)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,mutate_if)
importFrom(dplyr,n)
importFrom(dplyr,pick)
importFrom(dplyr,pull)
importFrom(dplyr,relocate)
importFrom(dplyr,rename)
importFrom(dplyr,row_number)
importFrom(dplyr,rowwise)
importFrom(dplyr,select)
importFrom(dplyr,summarise)
importFrom(dplyr,summarize)
importFrom(dplyr,ungroup)
importFrom(dplyr,vars)
importFrom(dplyr,where)
importFrom(ggplot2,aes)
importFrom(ggplot2,coord_fixed)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,expansion)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_col)
importFrom(ggplot2,geom_density)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_rect)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggplot_build)
importFrom(ggplot2,ggplot_gtable)
importFrom(ggplot2,labs)
importFrom(ggplot2,layer_scales)
importFrom(ggplot2,position_dodge)
importFrom(ggplot2,position_stack)
importFrom(ggplot2,scale_color_gradientn)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_color_viridis_c)
importFrom(ggplot2,scale_fill_gradientn)
importFrom(ggplot2,scale_size)
importFrom(ggplot2,scale_size_continuous)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_x_discrete)
importFrom(ggplot2,scale_x_log10)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,scale_y_discrete)
importFrom(ggplot2,scale_y_log10)
importFrom(ggplot2,sym)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_light)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,theme_void)
importFrom(ggplot2,unit)
importFrom(ggraph,geom_edge_link)
importFrom(ggraph,geom_node_point)
importFrom(ggraph,ggraph)
importFrom(glue,glue)
importFrom(grDevices,colorRampPalette)
importFrom(grid,gpar)
importFrom(grid,textGrob)
importFrom(igraph,as_adjacency_matrix)
importFrom(igraph,connect)
importFrom(igraph,edge_attr_names)
importFrom(igraph,gsize)
importFrom(igraph,layout_with_drl)
importFrom(igraph,layout_with_fr)
importFrom(igraph,layout_with_kk)
importFrom(igraph,vertex_attr_names)
importFrom(lifecycle,deprecated)
importFrom(methods,"slot<-")
importFrom(methods,as)
importFrom(methods,getMethod)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,setClass)
importFrom(methods,setClassUnion)
importFrom(methods,setMethod)
importFrom(methods,show)
importFrom(methods,slot)
importFrom(methods,slotNames)
importFrom(parallel,clusterEvalQ)
importFrom(parallel,clusterExport)
importFrom(patchwork,plot_annotation)
importFrom(patchwork,plot_layout)
importFrom(patchwork,plot_spacer)
importFrom(patchwork,wrap_elements)
importFrom(patchwork,wrap_plots)
importFrom(pbapply,pblapply)
importFrom(rlang,global_env)
importFrom(stats,as.formula)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,pnorm)
importFrom(stats,prcomp)
importFrom(stats,quantile)
importFrom(stats,rnorm)
importFrom(stats,wilcox.test)
importFrom(stringr,str_c)
importFrom(stringr,str_detect)
importFrom(stringr,str_sub)
importFrom(tibble,as_tibble)
importFrom(tibble,column_to_rownames)
importFrom(tibble,rownames_to_column)
importFrom(tibble,tibble)
importFrom(tidygraph,"%E>%")
importFrom(tidygraph,"%N>%")
importFrom(tidygraph,as_tbl_graph)
importFrom(tidygraph,bind_edges)
importFrom(tidygraph,to_components)
importFrom(tidyr,crossing)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,pivot_wider)
importFrom(tidyr,unite)
importFrom(utils,capture.output)
importFrom(utils,menu)
importFrom(utils,read.csv)
importFrom(utils,unzip)