Convert anndata to Giotto

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,
  delaunay_spat_net = TRUE,
  spat_enrich_key_added = NULL,
  spat_unit = NULL,
  feat_type = NULL,
  h5_file = NULL,
  python_path = NULL,
  env_name = "giotto_env"
)

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, the keys are saved in .uns['NN_keys'] and all keys are used in conversion unless specified in the function call. 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, the keys are saved in .uns['SN_keys'] and all keys are used in conversion unless specified in the function call. Cannot be the same as n_key_added.

delaunay_spat_net

binary parameter for spatial network. If TRUE, the spatial network is a delaunay network.

spat_enrich_key_added

list of names of spatial enrichment annotations present in the anndata object. If converting an anndata object from giottoToAnnData and the original Giotto object had spatial enrichment annotations, the keys are saved in .uns['SE_keys'] and all keys are used in conversion unless specified in the function call.

spat_unit

desired spatial unit to use for conversion, default NULL

feat_type

desired feature type to use for conversion, default NULL

h5_file

name to create and on-disk HDF5 file

python_path

path to python executable within a conda/miniconda environment

env_name

name of environment containing python_path executable

Value

Giotto object

Details

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