Convert CCC results to OmicVerse communication AnnData

Usage

ccc_to_adata(
  srt = NULL,
  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,
  liana_res = NULL,
  score_key = "score",
  pvalue_key = "pvalue",
  inverse_score = FALSE,
  inverse_pvalue = FALSE,
  sample_col = NULL,
  h5ad_path = NULL,
  verbose = TRUE
)

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.
liana_res: Optional precomputed LIANA-like data frame. If supplied, srt is not required.
score_key: Column in liana_res used for layers[["means"]].
pvalue_key: Column in liana_res used for layers[["pvalues"]].
inverse_score: Whether smaller score_key values should be converted to larger communication strengths. Useful for rank-like metrics.
inverse_pvalue: Whether smaller pvalue_key values should be inverted before writing to layers[["pvalues"]].
sample_col: Optional column used as sample/context/dataset key. If NULL, the first available column among "sample", "context", "condition", and "dataset" is used.
h5ad_path: Optional output path. If provided, the AnnData object is written to this file before being returned.
verbose: Whether to print progress messages.

Value

A Python anndata.AnnData communication object compatible with ov.pl.ccc_* plotting functions.