Calculate Niche Cell Type Composition

Analyzes and visualizes the cell type composition within and outside niches. Generates stacked barplots and faceted barplots showing cell type proportions for niche vs. bystander regions.

Usage

CalSampComp(
  STID_obj = NULL,
  samp_mode = "SS",
  loop_id = "LoopAllSamp",
  samp_grp_index = FALSE,
  meta_key = NULL,
  niche_key = NULL,
  group_by = NULL,
  col = COLOR_LIST[["PALETTE_WHITE_BG"]],
  return_data = FALSE
)

Arguments

STID_obj: An STID object containing niche analysis results
samp_mode: Character, sample type - "SS" (single sample) or "MS" (multi-sample) (default: "SS")
loop_id: Character, sample grouping identifier (default: "LoopAllSamp")
samp_grp_index: Logical, whether to group by sample groups in MS mode (default: FALSE)
meta_key: Character, metadata key for MS mode when niche_key is NULL
niche_key: Character, niche key to analyze (only one value supported)
group_by: Character, column name for cell type grouping
col: Color palette for visualization (default: COLOR_LIST$PALETTE_WHITE_BG)
return_data: Logical, whether to return the plot data (default: FALSE)

Value

If return_data = TRUE, returns a list of plots per sample; otherwise NULL

Examples

if (FALSE) { # \dontrun{
# Single-sample niche composition
CalSampComp(
  STID_obj = STID_obj,
  samp_mode  = "SS",
  niche_key = "niche_virulence",
  group_by = "cell_type"
)

# Multi-sample niche composition with sample grouping
CalSampComp(
  STID_obj = STID_obj,
  samp_mode  = "MS",
  loop_id = "LoopAllMulti",
  niche_key = "niche_virulence",
  samp_grp_index = TRUE,
  group_by = "cell_type"
)
} # }