Expand niche regions based on distance threshold

Expands existing niche regions by including neighboring spots within a specified distance threshold. Useful for defining broader influence zones around detected niches.

Usage

NicheExpand(
  STID_obj = NULL,
  meta_key = NULL,
  loop_id = "LoopAllSamp",
  pos_colnm = NULL,
  neg_value = "neg",
  center_colnm = NULL,
  expand_dist = 1,
  description = NULL,
  grp_nm = NULL,
  dir_nm = "M2_NicheExpand"
)

Arguments

STID_obj: An STID object containing niche detection results
meta_key: Character, metadata key containing niche information
loop_id: Character, sample grouping identifier (default: "LoopAllSamp")
pos_colnm: Character, column name containing positive spot labels
neg_value: Character, value indicating negative spots (default: "neg")
center_colnm: Character, column name indicating niche center spots (default: NULL)
expand_dist: Numeric, distance threshold for expansion (default: 1)
description: Character, description of the analysis
grp_nm: Character, group name for output organization (default: NULL, uses timestamp)
dir_nm: Character, directory name for output (default: "M2_NicheExpand")

Value

Returns the modified STID object with expanded ROI labels and updated distance calculations

Examples

if (FALSE) { # \dontrun{
# Expand niches by including spots within distance 5
STID_obj <- NicheExpand(
  STID_obj = ist_object,
  meta_key = "M2_NicheDetect_STS_20240101",
  pos_colnm = "ROI_label",
  expand_dist = 5
)
} # }