Run common cell-cell communication analyses

Usage

RunCCC(
  srt,
  group.by = NULL,
  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: Metadata column(s) used to color cells.
methods: Supported cell-cell communication methods to run. The default core methods are "CellChat", "CellphoneDB", and "LIANA". NicheNet, MultiNicheNet, SpatialCellChat, SpatialDM, and MDIC3 can be selected when their design-specific arguments are supplied through method_params. LIANA's default internal method set includes its CellPhoneDB scorer, so standalone CellphoneDB and LIANA consensus results are not statistically independent evidence.
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 only for result 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.