NAMESPACE

# Generated by roxygen2: do not edit by hand

export(.extract_legend)
export(add_pct_of_pool_to_samplesheet)
export(beaut_label)
export(cell_palette)
export(close_tabset)
export(cluster_palette)
export(compact_num)
export(complete_proximity_scores)
export(component_abundance_per_marker)
export(component_annotation)
export(component_cell_recovery)
export(component_clustering_summary)
export(component_control_markers)
export(component_coreness)
export(component_crossing_edges)
export(component_denoising)
export(component_dimred_plots)
export(component_hashing)
export(component_molecule_plot)
export(component_node_degree)
export(component_node_edge_count)
export(component_proximity_heatmap_celltype)
export(component_proximity_heatmap_sample)
export(component_proximity_per_marker)
export(component_proximity_selected)
export(component_sequencing_reads_and_molecules)
export(component_sequencing_reads_per_cell)
export(component_sequencing_saturation)
export(component_sequencing_saturation_curve)
export(convert_png_to_webp)
export(create_sample_palette)
export(default_params)
export(displayed_cell_types)
export(downsample_data)
export(extract_sample_qc_metrics)
export(filter_proximity_scores)
export(find_stage)
export(format_with_info_bootstrap)
export(get_coreness_data)
export(get_crossing_edges)
export(get_degree_distribution)
export(get_denoising_data)
export(get_denoising_detail_data)
export(get_file_paths)
export(get_hash_stats)
export(get_qc_metrics)
export(get_read_stats)
export(get_seq_saturation)
export(get_test_data)
export(get_top_markers)
export(key_metric_table)
export(load_pxl_data_list)
export(merge_cell_types)
export(merge_data)
export(merged_cell_types)
export(order_cd_markers)
export(order_sample_alias_factors)
export(plot_embedding)
export(plot_embeddings_samplewise)
export(plot_violin)
export(plot_void)
export(preferred_dimred_order)
export(print_metadata_table)
export(print_params)
export(print_pixelator_version)
export(print_session_info)
export(process_data)
export(read_qc_files)
export(read_samplesheet)
export(run_abundance_anova)
export(run_proximity_anova)
export(section_intro)
export(section_table)
export(set_sample_levels)
export(style_table)
export(summarize_colocalization_scores_per_celltype)
export(summarize_colocalization_scores_per_sample)
export(tabset_figure_table)
export(tabset_nested_plotlist)
export(tabset_plotlist)
export(test_data_folder)
export(test_samplesheet)
export(theme_violin)
export(title_plotlist)
export(yes_no_palette)
importFrom(ComplexHeatmap,pheatmap)
importFrom(RcppSimdJson,fload)
importFrom(Seurat,FindClusters)
importFrom(Seurat,FindNeighbors)
importFrom(Seurat,NormalizeData)
importFrom(Seurat,RunPCA)
importFrom(Seurat,RunUMAP)
importFrom(Seurat,ScaleData)
importFrom(SeuratObject,AddMetaData)
importFrom(SeuratObject,CreateSeuratObject)
importFrom(SeuratObject,Embeddings)
importFrom(SeuratObject,FetchData)
importFrom(SeuratObject,JoinLayers)
importFrom(SeuratObject,LayerData)
importFrom(SeuratObject,Reductions)
importFrom(broom,tidy)
importFrom(cli,cli_abort)
importFrom(dplyr,"%>%")
importFrom(dplyr,across)
importFrom(dplyr,arrange)
importFrom(dplyr,bind_rows)
importFrom(dplyr,case_when)
importFrom(dplyr,collect)
importFrom(dplyr,count)
importFrom(dplyr,desc)
importFrom(dplyr,distinct)
importFrom(dplyr,everything)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,group_by_all)
importFrom(dplyr,group_keys)
importFrom(dplyr,group_split)
importFrom(dplyr,inner_join)
importFrom(dplyr,join_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,mutate_all)
importFrom(dplyr,n)
importFrom(dplyr,n_distinct)
importFrom(dplyr,pull)
importFrom(dplyr,recode)
importFrom(dplyr,reframe)
importFrom(dplyr,relocate)
importFrom(dplyr,rename)
importFrom(dplyr,row_number)
importFrom(dplyr,rowwise)
importFrom(dplyr,select)
importFrom(dplyr,slice_head)
importFrom(dplyr,slice_sample)
importFrom(dplyr,summarise)
importFrom(dplyr,summarize)
importFrom(dplyr,top_n)
importFrom(dplyr,tribble)
importFrom(dplyr,ungroup)
importFrom(ggbeeswarm,geom_quasirandom)
importFrom(ggbeeswarm,position_quasirandom)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotation_custom)
importFrom(ggplot2,coord_fixed)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,expansion)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_blank)
importFrom(ggplot2,geom_col)
importFrom(ggplot2,geom_errorbar)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_jitter)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_rect)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggplotGrob)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,margin)
importFrom(ggplot2,position_dodge)
importFrom(ggplot2,position_jitter)
importFrom(ggplot2,position_stack)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_gradientn)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_size_continuous)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_x_log10)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,scale_y_log10)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_void)
importFrom(ggplot2,waiver)
importFrom(ggplotify,as.ggplot)
importFrom(grid,unit)
importFrom(htmlwidgets,JS)
importFrom(knitr,hook_plot_md)
importFrom(magick,image_read)
importFrom(magick,image_write)
importFrom(methods,as)
importFrom(parallel,mclapply)
importFrom(patchwork,plot_layout)
importFrom(patchwork,plot_spacer)
importFrom(pixelatorR,AnnotateCells)
importFrom(pixelatorR,ColocalizationHeatmap)
importFrom(pixelatorR,Edgelists)
importFrom(pixelatorR,FilterProximityScores)
importFrom(pixelatorR,PixelDB)
importFrom(pixelatorR,PixelgenAccentColors)
importFrom(pixelatorR,Pixelgen_accent_colors)
importFrom(pixelatorR,ProximityScores)
importFrom(pixelatorR,ProximityScoresToAssay)
importFrom(pixelatorR,ReadPNA_Seurat)
importFrom(pixelatorR,SequenceSaturationCurve)
importFrom(pixelatorR,SummarizeProximityScores)
importFrom(pixelatorR,approximate_saturation_curve)
importFrom(pixelatorR,minimal_pna_pxl_file)
importFrom(pixelatorR,sequencing_saturation)
importFrom(purrr,keep)
importFrom(purrr,map)
importFrom(purrr,reduce)
importFrom(readr,col_character)
importFrom(readr,col_integer)
importFrom(readr,cols)
importFrom(readr,read_csv)
importFrom(rlang,":=")
importFrom(rlang,set_names)
importFrom(rlang,sym)
importFrom(rlang,syms)
importFrom(scales,percent)
importFrom(sessioninfo,package_info)
importFrom(stats,aov)
importFrom(stats,as.formula)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,median)
importFrom(stats,p.adjust)
importFrom(stats,p.adjust.methods)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,weighted.mean)
importFrom(stringr,str_detect)
importFrom(stringr,str_extract)
importFrom(stringr,str_remove)
importFrom(stringr,str_remove_all)
importFrom(stringr,str_replace)
importFrom(stringr,str_replace_all)
importFrom(stringr,str_to_sentence)
importFrom(tibble,as_tibble)
importFrom(tibble,column_to_rownames)
importFrom(tibble,deframe)
importFrom(tibble,enframe)
importFrom(tibble,rownames_to_column)
importFrom(tibble,tibble)
importFrom(tibble,tribble)
importFrom(tidyr,complete)
importFrom(tidyr,nesting)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,pivot_wider)
importFrom(tidyr,separate)
importFrom(tidyr,unite)
importFrom(tidyr,unnest)
importFrom(tidyselect,all_of)
importFrom(tidyselect,any_of)
importFrom(tidyselect,matches)
importFrom(tidyselect,where)
importFrom(utils,head)