Spot-level niche detection — NicheDetect

Performs niche detection at the individual spot level, treating each positive spot as its own ROI. Calculates distances from all spots to the nearest positive spot.

Usage

NicheDetect_Spot(
  STID_obj = NULL,
  loop_id = "LoopAllSamp",
  pos_colnm = NULL,
  neg_value = "neg",
  meta_key = NULL,
  description = NULL,
  grp_nm = NULL,
  dir_nm = "M2_NicheDetect_Spot"
)

Arguments

STID_obj: An STID object containing spatial transcriptomics data
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")
meta_key: Character, metadata key containing positive spot information
description: Character, description of the analysis (default: NULL)
grp_nm: Character, group name for output organization (default: NULL, uses timestamp)
dir_nm: Character, directory name for output (default: "M2_NicheDetect_Spot")

Value

Returns the modified STID object with added metadata containing ROI labels and distances to nearest positive spots

Examples

if (FALSE) { # \dontrun{
# Perform spot-level niche detection
STID_obj <- NicheDetect_Spot(
  STID_obj = ist_object,
  meta_key = "M1_SpotDetect_Gene_20240101",
  pos_colnm = "Label_geneA"
)
} # }