Prepare a Seurat object for ShinyCellModular — prepShinyCellModular • ShinyCellModular

Takes a Seurat object from single cell experiments and prepares all files needed to run a ShinyCellModular interactive Shiny app. Writes HDF5 counts, ShinyCell config files, optional 3D UMAP, marker genes, and motif data to out_dir.

prepShinyCellModular(
  seurat_obj = NULL,
  seurat_rds = NULL,
  out_dir = "ShinyCellModular_app",
  shiny_title = "ShinyCellModular Intermediate",
  assays_selected = "RNA",
  ident_col = NULL,
  do_variable_features = TRUE,
  do_markers = FALSE,
  markers_file = NULL,
  markers_overwrite = FALSE,
  markers_res_pattern = "res\\.",
  do_umap3d = FALSE,
  umap3d_reductions = c("pca"),
  umap3d_dims = 1:30,
  umap3d_name_suffix = "_umap3d",
  do_counts_h5 = TRUE,
  counts_h5_file = NULL,
  counts_overwrite = TRUE,
  counts_layer = "counts",
  do_make_app = TRUE,
  gene_mapping = TRUE,
  install_missing = FALSE,
  verbose = TRUE,
  do_motifs = "auto",
  motifs_findmotifs = NULL,
  motifs_overwrite = TRUE,
  fragments_paths = NULL,
  custom_colors = NULL,
  default_genes = NULL,
  help = FALSE
)

Arguments

seurat_obj: Seurat object. Alternative to seurat_rds.
seurat_rds: Path to a .rds Seurat object. Alternative to seurat_obj.
out_dir: Output directory. Default: 'Files_ShinyCell'.
shiny_title: Title for the Shiny app.
assays_selected: Assay(s) to process. e.g. c('RNA', 'ATAC'). Default: 'RNA'.
ident_col: Column to set as Idents. Default: NULL (uses existing).
do_variable_features: Run FindVariableFeatures before creating the ShinyCell config. Default: TRUE.
do_markers: Compute marker genes with presto. Default: FALSE.
markers_file: Path for output markers parquet file. Default: auto.
markers_overwrite: Overwrite existing markers file. Default: FALSE.
markers_res_pattern: Regex pattern to find resolution columns. Default: 'res\\.'.
do_umap3d: Run 3D UMAP. Default: FALSE.
umap3d_reductions: Reductions to use as input for 3D UMAP. Default: c('pca').
umap3d_dims: Dims to pass to UMAP (auto-capped to available). Default: 1:30.
umap3d_name_suffix: Suffix appended to the 3D UMAP reduction name. Default: '_umap3d'.
do_counts_h5: Write raw counts to HDF5. Default: TRUE.
counts_h5_file: Path for output H5 file. Default: auto.
counts_overwrite: Overwrite existing H5 file. Default: TRUE.
counts_layer: Seurat layer to use for counts. Default: 'counts'.
do_make_app: Run makeShinyApp. Default: TRUE.
gene_mapping: Map gene names in ShinyCell. Default: TRUE.
install_missing: Auto-install missing packages. Default: FALSE.
verbose: Print progress messages. Default: TRUE.
do_motifs: Extract motifs from ATAC assay. Runs automatically when ATAC is in assays_selected and the motifs slot is populated. Set to FALSE to skip. Default: 'auto'.
motifs_findmotifs: Output of FindMotifs(), adds enrichment scores. Default: NULL.
motifs_overwrite: Overwrite existing motif files. Default: TRUE.
fragments_paths: Optional named list of fragment file path overrides by index. e.g. list('1' = '/path/to/sample1.tsv.gz'). If NULL, paths are copied from the original paths in the object. Default: NULL.
custom_colors: Named character vector of label -> hex color to override ShinyCell default colors. Extra names not in the data are ignored. Default: NULL.
default_genes: Character vector of gene names to set as defaults in the app (e.g. c('CD4', 'CD8A')). If NULL, ShinyCell picks its own defaults. Default: NULL.
help: Print the help message and return. Default: FALSE.

Value

Invisibly returns NULL. Writes output files to out_dir.

Examples

if (FALSE) { # \dontrun{
prepShinyCellModular(
  seurat_rds = "seurat_object.rds",
  out_dir    = "my_app_files",
  do_umap3d  = TRUE,
  do_markers = TRUE
)
} # }