Convert CCC results to a LIANA-like table

Usage

ccc_to_liana(
  srt,
  method = NULL,
  condition = NULL,
  dataset = 1,
  slot.name = "net",
  signaling = NULL,
  pairLR.use = NULL,
  sender.use = NULL,
  receiver.use = NULL,
  ligand.use = NULL,
  receptor.use = NULL,
  interaction.use = NULL,
  thresh = 0.05,
  aggregate = TRUE,
  sample_col = NULL,
  score_col = "score",
  pvalue_col = "pvalue"
)

Arguments

srt: A Seurat object.
method: Communication result type to use.
condition: Result name or comparison name.
dataset: Dataset index or name.
slot.name: CellChat slot name.
signaling: Signaling pathway to focus on.
pairLR.use: Specific ligand-receptor pair(s) to keep.
sender.use: Sender cell types to keep.
receiver.use: Receiver cell types to keep.
ligand.use: Ligands to keep.
receptor.use: Receptors to keep.
interaction.use: Interaction names to keep.
thresh: Significance threshold used when extracting communication results.
aggregate: Whether to aggregate duplicate source-target-ligand-receptor rows. This should usually stay TRUE for OmicVerse compatibility.
sample_col: Optional column used as sample/context/dataset key. If NULL, the first available column among "sample", "context", "condition", and "dataset" is used.
score_col: Column used as the exported communication score.
pvalue_col: Column used as the exported p-value/rank-like support.

Value

A data frame with LIANA/LIANA+ compatible columns: source, target, ligand_complex, receptor_complex, score, and pvalue, plus scop/OV-friendly metadata.