anndataToGiotto: Convert anndata to Giotto
In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

anndataToGiotto

R Documentation

Convert anndata to Giotto

Description

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

Usage

anndataToGiotto(
  anndata_path = NULL,
  n_key_added = NULL,
  spatial_n_key_added = NULL,
  deluanay_spat_net = TRUE,
  spat_unit = NULL,
  feat_type = NULL,
  python_path = NULL
)

Arguments

`anndata_path`	path to the .h5ad file
`n_key_added`	equivalent of "key_added" argument from scanpy.pp.neighbors(). If multiple spatial networks are in the anndata object, a list of key_added terms may be provided. If converting an anndata object from giottoToAnnData, a .txt file may be provided, which was generated in that function, i.e. spat_unit_feat_type_nn_network_keys_added.txt Cannot be "spatial". This becomes the name of the nearest network in the gobject.
`spatial_n_key_added`	equivalent of "key_added" argument from squidpy.gr.spatial_neighbors. If multiple spatial networks are in the anndata object, a list of key_added terms may be provided. If converting an anndata object from giottoToAnnData, a .txt file may be provided, which was generated in that function, i.e. spat_unit_feat_type_spatial_network_keys_added.txt Cannot be the same as n_key_added.
`deluanay_spat_net`	binary parameter for spatial network. If TRUE, the spatial network is a deluanay network.
`spat_unit`	desired spatial unit for conversion, default NULL
`feat_type`	desired feature type for conversion, default NULL
`python_path`	path to python executable within a conda/miniconda environment

Details

Function in beta. Converts a .h5ad file into a Giotto object. The returned Giotto Object will take default insructions with the exception of the python path, which may be customized. See changeGiottoInstructions to modify instructions after creation.