giottoToAnnData: Convert Giotto to anndata

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Convert Giotto to anndata

Description

Converts a Giotto object to a spatial anndata (e.g. scanpy) .h5ad file

Usage

giottoToAnnData(
  gobject = NULL,
  spat_unit = NULL,
  feat_type = NULL,
  python_path = NULL,
  save_directory = NULL
)

Arguments

gobject	giotto object to be converted
spat_unit	spatial unit which will be used in conversion.
feat_type	feature type which will be used in conversion.
python_path	path to python executable within a conda/miniconda environment
save_directory	directory in which the file will be saved.

Details

Function in beta. Converts a Giotto object into .h5ad file(s).

If there are multiple spatial units and/or feature types, but only one spatial unit and/or feature type is specified, then only the specified spatial unit and/or feature type will be used. If NULL, by default, all spatial units will be used in conversion.

If multiple spatial units or feature types are specified, multiple AnnData object will be created and returned.

This function will create .txt files which will record any 'key_added' parameters for networks. They are named after the corresponding spatial unit and feature type pair.

The save_directory will be created if it does not already exist. The default save_directory is the working directory.

Value

vector containing .h5ad file path(s)

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.