Calculate Niche Aggregation Index — CalSampCAI • STID

Computes spatial aggregation metrics for cell types within niches using k-nearest neighbors and graph-based clustering. Calculates aggregation index and aggregation region ratios.

Usage

CalSampCAI(
  STID_obj = NULL,
  samp_mode = "SS",
  loop_id = "LoopAllSamp",
  samp_grp_index = FALSE,
  meta_key = NULL,
  niche_key = NULL,
  group_by = NULL,
  dist_thres = NULL,
  k_neighbors = 8,
  min_agg_size = 2,
  col = COLOR_LIST[["PALETTE_WHITE_BG"]][-1],
  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
group_by: Character, column name for cell type grouping
dist_thres: Numeric, distance threshold for graph construction (default: NULL, uses median of 1st neighbor distances)
k_neighbors: Integer, number of nearest neighbors to consider (default: 8)
min_agg_size: Integer, minimum aggregation cluster size (default: 2)
col: Color palette for visualization (default: COLOR_LIST$PALETTE_WHITE_BG[-1])
return_data: Logical, whether to return the results list (default: FALSE)

Value

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

Examples

if (FALSE) { # \dontrun{
# Calculate aggregation index for niche cells
CalSampCAI(
  STID_obj = STID_obj,
  samp_mode  = "SS",
  niche_key = "niche_virulence",
  group_by = "cell_type",
  k_neighbors = 8,
  min_agg_size = 3
)
} # }