Missing plots data in the results folder

bunnech / cellot

Learning Single-Cell Perturbation Responses using Neural Optimal Transport

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Missing plots data in the results folder #16

Closed jiyuanj closed 5 months ago

jiyuanj commented 5 months ago

After trained cellot, cae-4i, random, identity and scgen-4i models for 4i data, I tried running plot.py script by this command: python scripts/plot.py, I encountered error on file not found when plotting UMAP and KNN_MMD

This indicates umap.csv and knn_enrichment.csv are missing in evals_iid_data_space of results folder. Could you please tell me is there anything wrong? Is my command correct for running this plot script? Thanks.

bunnech commented 5 months ago

No, it cannot find the UMAP evaluation results from CellOT. You will need to run scripts/evaluate.py before scripts/plot.py. Might be that UMAP is not anymore included in scripts/evaluate.py as it is a method that in generally should not be used for quantitative evaluation. In that case, just remove those lines from scripts/plot.py.