Skip to contents

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

Source: R/squidpy_pipe.R
call_squidpy.Rd

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

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.