nichecompass.data.load_spatial_adata_from_csv
- nichecompass.data.load_spatial_adata_from_csv(counts_file_path, adj_file_path, cell_type_file_path=None, adj_key='spatial_connectivities', cell_type_col='cell_type', cell_type_key='cell_type')
Create AnnData object from two csv files containing gene expression feature matrix and adjacency matrix respectively. Optionally, a third csv file with cell types can be provided.
- Parameters:
counts_file_path (
str) – File path of the csv file which contains gene expression feature matrix data.adj_file_path (
str) – File path of the csv file which contains adjacency matrix data.cell_type_file_path (
Optional[str] (default:None)) – File path of the csv file which contains cell type data.adj_key (
str(default:'spatial_connectivities')) – Key under which the sparse adjacency matrix will be stored in ´adata.obsp´.cell_type_col (
str(default:'cell_type')) – Column under wich the cell type is stored in the ´cell_type_file´.cell_type_key (
str(default:'cell_type')) – Key under which the cell types will be stored in ´adata.obs´.
- Return type:
- Returns:
adata: AnnData object with gene expression data stored in ´adata.X´ and sparse adjacency matrix (coo format) stored in ´adata.obps[adj_key]´.