Pass any of these tab IDs to enabled_tabs in
useShinyCellModular().
Tab ID (enabled_tabs) |
Tab title | What it shows | Extra prep needed | Multi-dataset variant (_multi) |
|---|---|---|---|---|
cellinfo_cellinfo |
CellInfo vs CellInfo | 2D embedding coloured by metadata | n/a | n/a |
cellinfo_geneexpr |
CellInfo vs GeneExpr | 2D embedding with gene expression overlay | n/a | cellinfo_geneexpr_multi |
cellinfo3D_cellinfo3D |
CellInfo3D | Interactive 3D embedding coloured by metadata |
do_umap3d = TRUE in prep |
n/a |
cellinfo3D_geneexpr3D |
CellInfo3D vs GeneExpr | Interactive 3D embedding with gene expression overlay |
do_umap3d = TRUE in prep |
cellinfo3D_geneexpr3D_multi |
genecoex |
Gene Coexpression | Coexpression of selected genes across cells or groups | n/a | genecoex_multi |
violin_boxplot |
Violin / BoxPlot | Violin and boxplots for gene expression or metadata | n/a | n/a |
proportions |
Cell Proportions | Cell composition across groups | n/a | n/a |
bubble_heatmap |
Bubble Plot / Heatmap | Bubble plot and heatmap for gene sets across groups | n/a | n/a |
pseudobulk |
Pseudobulk DE | Pseudobulk aggregation and differential expression |
do_counts_h5 = TRUE in prep |
n/a |
genexpr_waffle |
Gene Expression Waffle Plot | Waffle plot alternative to bubble plot / heatmap for a small gene list | n/a | n/a |
split_violin |
Split Violin Plot | Two groups compared side by side within one violin shape | n/a | n/a |
All ATAC tabs require "ATAC" in
assays_selected when running
prepShinyCellModular(), since that is what creates
dir_inputs/ATAC/ (assumed, based on the
active_assay == "ATAC" branch in prep).
Tab ID (enabled_tabs) |
Tab title | What it shows | Extra prep needed |
|---|---|---|---|
cellinfo_cellinfo_atac |
CellInfo vs CellInfo (ATAC) | 2D embedding coloured by metadata, ATAC assay version |
"ATAC" in assays_selected
|
cellinfo_peakaccess |
CellInfo vs PeakAccess | 2D embedding with peak accessibility overlay |
"ATAC" in assays_selected
|
cellinfo3D_cellinfo3D_atac |
CellInfo3D vs CellInfo3D (ATAC) | Interactive 3D embedding coloured by metadata, ATAC assay version |
"ATAC" in assays_selected,
do_umap3d = TRUE in prep |
cellinfo3D_peakaccess3D |
CellInfo3D vs PeakAccess3D | Interactive 3D embedding with peak accessibility overlay |
"ATAC" in assays_selected,
do_umap3d = TRUE in prep |
peakcoex |
Peak Coaccessibility | Coaccessibility of selected peaks across cells or groups |
"ATAC" in assays_selected
|
violin_boxplot_atac |
Violin / BoxPlot (ATAC) | Violin and boxplots for peak accessibility or metadata |
"ATAC" in assays_selected
|
proportions_atac |
Cell Proportions (ATAC) | Cell composition across groups, ATAC assay version |
"ATAC" in assays_selected
|
bubble_heatmap_atac |
Bubble Plot / Heatmap (ATAC) | Bubble plot and heatmap for peak sets across groups |
"ATAC" in assays_selected
|
pseudobulk_atac |
Pseudobulk DE (ATAC) | Pseudobulk aggregation and differential accessibility analysis |
"ATAC" in assays_selected
|
track_plot |
Coverage Plot (ATAC) | Genome browser coverage tracks for a single ATAC dataset, with optional peaks, links, and annotation tracks |
"ATAC" in assays_selected
|
Tabs in this folder are not all _multi dataset-list
variants, some are single-dataset ATAC-derived tabs that happen to live
here (assumed, since motif_plot and
coverage_plot don’t have _multi in their id
and aren’t listed as _multi variants above).
Tab ID (enabled_tabs) |
Tab title | What it shows | Extra prep needed |
|---|---|---|---|
motif_plot |
Motif Plot | Transcription factor motif sequence logos, with optional enrichment scores |
sc1motifs.rds and sc1motifs_meta.parquet
in dir_inputs/ATAC/ (written by prep when
do_motifs finds a populated @motifs slot) |
coverage_plot |
Coverage Plot | Genome browser style coverage tracks from ATAC fragments | Fragment files copied to dir_inputs/ATAC/fragments/
(sc1fragmentpaths.rds), supply fragments_paths
in prep if auto-detection fails (assumed, based on
.extract_atac_static()) |
cellinfo_geneexpr_multi |
CellInfo vs GeneExpr Multi | Multi-dataset 2D embedding with gene expression overlay | n/a |
cellinfo3D_geneexpr3D_multi |
CellInfo3D vs GeneExpr3D Multi | Multi-dataset interactive 3D embedding with gene expression overlay |
do_umap3d = TRUE in prep, per dataset |
genecoex_multi |
Gene Coexpression | Multi-dataset coexpression of selected genes across cells or groups | n/a |