convert_to_anndata.md

If you have data in non-Visium format, the easiest way is to convert the data format to anndata. We will use LUAD sample for explaining it. Let us assume we have downloaded the LUAD sample into a directory "CellNEST/data/LUAD_GSM5702473_TD1/". It comes as a *.mtx format, so following script can be run to convert it to anndata format (assuming that your current working directory is CellNEST):

python to_anndata.py --data_from=data/LUAD_GSM5702473_TD1/ --data_to_path=data/LUAD_GSM5702473_TD1/ \
--file_name=LUAD_GSM5702473_TD1 --tissue_position_file=data/LUAD_GSM5702473_TD1/GSM5702473_TD1_tissue_positions_list.csv

This is just a sample script and you are welcome to modify to_anndata.py according to your input format. Just make sure that the anndata has following rows and columns, as well as, spatial coordinates:

    # now create anndata object
    adata = anndata.AnnData(count_matrix)
    adata.obs_names = cell_barcode
    adata.var_names = gene_ids
    adata.obsm['spatial'] = coordinates

Please note that the count matrix (.X field of AnnData) should have raw counts, without any normalization or transformation. After that, we will run preprocessing step with --data_type=anndata parameter as follows:

./cellnest preprocess --data_name=LUAD_TD1 --data_type=anndata --data_from=data/LUAD/LUAD_GSM5702473_TD1/LUAD_GSM5702473_TD1.h5ad