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