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,
env_name = "giotto_env",
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
- env_name
name of environment containing python_path executable
- 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.