Cannot find "clustering_result.csv" in the Example 1 mouse brain dataset

[cristalliao]

Dear Professor, I want to know where I can find this file "clustering_result.csv" in the mouse brain dataset when I try this great STitch3D in Example 1. plot3D_clusters(directory = "./results_6PCW", clusters = clusters, cluster_colors = cluster_colors, um = um, spot_radius = spot_radius, axis_rescale = axis_rescale ) in this part "Run STitch3D on the mouse heart dataset". The error said that

Warning: cannot open file '/albona/nobackup2/xiaoyinl/STitch3D_analysis_and_dataset/results_mouse_brain/clustering_result.csv': No such file or directoryError in file(file, "rt") : cannot open the connection

Because in the Example1 Tutorial, I cannot find the code to generate this "clustering_result.csv", is the same procedure like Example2? Could you provide more details about it?

Thanks in advance!

[gefeiwang]

Hi Cristal,

After running STitch3D, a clustering step is required to get domain labels from representation vectors. You can follow this tutorial for this and save the results by adata_all.obs["louvain"].to_csv(os.path.join(res_path, "clustering_result.csv")).

[cristalliao]

Dear Gefei, Got it! Thanks a lot! Very appreciated! Best regards, Cristal