scanpy_usage
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Export to SPRING error
I'm using this tutorial for exporting adata object to SPRING input.
First suggestion to update this tutorial, I had to modify this slightly per the updates in the command:
sc.external.exporting.spring_project(adata, './spring_adata',embedding_method='umap',overwrite=True)
However, my main issue is even this command does not completely output the files required for SPRING plot. Specifically, the directory with files as follows are not created- gene_colors/color_data_all_genes-*.csv This is a required input for SPRING. Can you please update the code to reflect this output.