call_squidpy: Call Squidpy Pipeline via reticulate with OmniPath and format...

In saezlab/liana: LIANA: a LIgand-receptor ANalysis frAmework

Call Squidpy Pipeline via reticulate with OmniPath and format results [[DEPRECATED]]

Description

Call Squidpy Pipeline via reticulate with OmniPath and format results [[DEPRECATED]]

Usage

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

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; set to liana_env by default
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#squidpy.gr.ligrec

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.

Value

A list of Squidpy results for each resource

saezlab/liana documentation built on Nov. 8, 2023, 11:53 a.m.