Run common cell-cell communication analyses

Run common cell-cell communication analyses

Usage

RunCCC(
  srt,
  group.by,
  methods = c("CellChat", "CellphoneDB", "LIANA"),
  method_params = list(),
  backend = c("cpp", "r"),
  skip_failed = FALSE,
  rebuild_unified = TRUE,
  thresh = 0.05,
  verbose = TRUE
)

Arguments

srt

A Seurat object.

group.by

Name of one or more meta.data columns to group (color) cells by.

methods

Cell-cell communication methods to run. Currently supports "CellChat", "CellphoneDB", and "LIANA" in the unified scheduler. NicheNet and MultiNicheNet require explicit receiver/sender/contrast design arguments and should be called through RunNichenetr() or RunMultiNichenetr().

method_params

Named list of method-specific arguments passed to the corresponding wrapper. For example, use method_params$CellphoneDB$pvalue for CellphoneDB-specific parameters.

backend

Backend used for scop post-processing and unified CCC table aggregation. The upstream CellChat, CellphoneDB, and LIANA inference logic is unchanged.

skip_failed

Whether to keep running remaining methods if one method fails.

rebuild_unified

Whether to rebuild srt@tools[["CCC"]] from the completed methods after all requested methods finish.

thresh

Significance threshold used when rebuilding unified CCC tables and passed to RunCellChat() unless overridden in method_params$CellChat.

verbose

Whether to print the message. Default is TRUE.

Value

A Seurat object with method-specific results and a unified srt@tools[["CCC"]] bundle.