Call Squidpy Pipeline via reticulate with OmniPath and format results

Usage

call_squidpy(
  sce,
  op_resource,
  seed = 1004,
  conda_env = NULL,
  use_active_env = TRUE,
  assay = "RNA",
  assay.type = "logcounts",
  layer = NULL,
  ...
)

Arguments

sce: SingleCellExperiment or Seurat Object as input
op_resource: Tibble or list of OmniPath resources, typically obtained via select_resource
seed: seed passed to squidpy's ligrec function
conda_env: python conda environment to run Squidpy. If NULL, will try: 1. Currently active reticulate environment 2. Environment from RETICULATE_PYTHON_ENV environment variable 3. Fall back to "liana_env" for backward compatibility
use_active_env: logical. If TRUE and a Python environment is already active, use it instead of switching. Default: TRUE
assay: assay name
assay.type: count slot (logcounts by default)
...: kwargs passed to Squidpy; For more information see: https://squidpy.readthedocs.io/en/latest/api/squidpy.gr.ligrec.html

Value

A list of Squidpy results for each resource

Details

CellPhoneDBv2 algorithm re-implementation in Python.

Note that `cluster_key` is a parameter passed to the Squidpy function, by default this will be set to the default Ident of the Seurat object.