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Create a SingleSampNiche object from analysis results

Source: R/STID-class.R
CreateSingleSampNiche.Rd

Creates and stores a SingleSampNiche object within an STID object, organizing niche detection results for a single sample. This function extracts relevant cell and gene information based on specified niche parameters.

Usage

CreateSingleSampNiche(
  STID_obj = NULL,
  loop_id = "LoopAllSamp",
  niche_key = NULL,
  meta_key = NULL,
  ROI_type = NULL,
  pos_colnm = NULL,
  neg_value = "neg",
  center_colnm = NULL,
  edge_colnm = NULL,
  all_label_colnm = NULL,
  all_dist_colnm = NULL,
  other_colnm = NULL,
  description = NULL
)

# S3 method for class 'STID'
CreateSingleSampNiche(
  STID_obj = NULL,
  loop_id = "LoopAllSamp",
  niche_key = NULL,
  meta_key = NULL,
  ROI_type = NULL,
  pos_colnm = NULL,
  neg_value = "neg",
  center_colnm = NULL,
  edge_colnm = NULL,
  all_label_colnm = NULL,
  all_dist_colnm = NULL,
  other_colnm = NULL,
  description = NULL
)

CreateSSNiche(...)

Arguments

STID_obj

An STID object containing analysis results

loop_id

Character, sample grouping identifier (default: "LoopAllSamp")

niche_key

Character, unique identifier for the niche analysis

meta_key

Character, metadata key containing the source data

ROI_type

Character, type of ROI - "ROI", "Spot", or "Unknown"

pos_colnm

Character, column name containing positive spot labels

neg_value

Character, value indicating negative spots (default: "neg")

center_colnm

Character, column name indicating center spots (optional)

edge_colnm

Character, column name indicating edge spots (optional)

all_label_colnm

Character, column name for all spot labels (optional)

all_dist_colnm

Character, column name for distance to center (optional)

other_colnm

Character vector, additional columns to include (optional)

description

Character, description of the niche analysis (optional)

...

Additional arguments passed to methods

Value

Modified STID object with added SingleSampNiche information

Examples

if (FALSE) { # \dontrun{
# Create SingleSampNiche object
STID_obj <- CreateSingleSampNiche(
  STID_obj = ist_obj,
  niche_key = "niche_virulence",
  meta_key = "M2_NicheDetect_STS_20240101",
  ROI_type = "ROI",
  pos_colnm = "ROI_label",
  center_colnm = "ROI_center",
  edge_colnm = "ROI_edge",
  all_label_colnm = "All_ROI_label",
  all_dist_colnm = "All_Dist2ROIcenter"
)
} # }