- Install by pip (recommend):
pip install Spanve- no install usage:
# install required packages
cd Evaluate/Softs
pip install spanve_requirements.txt
cp Spanve.py $your_pathspanve --helpUsage: Spanve [OPTIONS]
Options:
-i, --input_file PATH input anndata file(h5ad file.)
-r, --running_mode TEXT running mode, default is f(c:cluster;
i:imputation; f:fitting)
-s, --save_path PATH save path
-v, --verbose BOOLEAN verbose
-n, --njobs INTEGER
-p, --preprocessed BOOLEAN int preprocessed or not.
--help Show this message and exit.****
command line usage can only run in a standard h5ad file, where there is a anndata.AnnData.obsm key named 'spatial'.
from Spanve import Spanve
adata = sc.read_h5ad('data.h5ad')
spanve = Spanve(adata)
# -- fitting for spatial genes
spanve.fit()
spanve.save('result.csv')
# -- spatial imputation
X = adata_preprocess(adata)
X_ = spanve.impute_from_graph(X[:,spanve.rejects])see tutorial notebook or html page.
