Missing plots data in the results folder
jiyuanj opened this issue · 1 comments
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.
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.