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Calculate Niche Cell Communication using CellChat

Source: R/SingleSampAnalysis.R
CalSampCellComm.Rd

Analyzes cell-cell communication within niches using the CellChat framework. Supports both spatial and non-spatial modes with comprehensive visualization.

Usage

CalSampCellComm(
  STID_obj = NULL,
  loop_id = "LoopAllSamp",
  niche_key = NULL,
  meta_key = NULL,
  group_by = NULL,
  assay_id = "Spatial",
  layer_id = "data",
  is_Spatial = TRUE,
  spatial.factors = NULL,
  interaction.range = 250,
  remove_genes = NULL,
  col = NULL,
  return_data = TRUE,
  grp_nm = NULL,
  dir_nm = "M3_CalSampCellComm"
)

Arguments

STID_obj

An STID object containing niche analysis results

loop_id

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

niche_key

Character, niche key to analyze (default: NULL)

meta_key

Character, metadata key for cell annotations (default: NULL)

group_by

Character, column name for cell type grouping

assay_id

Character, assay name (default: "Spatial")

layer_id

Character, layer name (default: "data")

is_Spatial

Logical, whether to use spatial mode (default: TRUE)

spatial.factors

Data frame, spatial scaling factors (default: NULL)

interaction.range

Numeric, interaction range for spatial mode (default: 250)

remove_genes

Character vector, genes to exclude

col

Named vector, colors for cell types

return_data

Logical, whether to return results list (default: TRUE)

grp_nm

Character, group name for output organization (default: NULL)

dir_nm

Character, directory name for output (default: "M3_CalSampCellComm")

Value

If return_data = TRUE, returns a list of CellChat objects per sample

Examples

if (FALSE) { # \dontrun{
# Analyze cell communication in niches
results <- CalSampCellComm(
  STID_obj = STID_obj,
  niche_key = "niche_virulence",
  group_by = "cell_type",
  is_Spatial = TRUE,
  interaction.range = 200
)
} # }