Brian Lee

icon company Icahn School of Medicine at Mt. Sinai icon location Computational Scientist at the Human Immune Monitoring Center (HIMC) at Mt. Sinai

Results 4 comments of Brian Lee

plot Regulon different in plot_AUC_given_ax and sc.pl.umap

Hi @SeppeDeWinter and @LILI-0000-0002-8173-7367 I am having the exact same error. I used the same code as Li Li's first post. When I compare the actual values for a specific...

plot Regulon different in plot_AUC_given_ax and sc.pl.umap

Hi @SeppeDeWinter and @LILI-0000-0002-8173-7367 I found out what's wrong! The scplus_obj.uns['eRegulon_AUC'] dictionary has the cell indices sorted in alphabetical order that doesn't match the scplus_obj.metadata_cell. ``` import pandas as pd...

Generating a Umap with eRegulon AUC does not produce proper clusters

You might want to see my response on [Issue#287](https://github.com/aertslab/scenicplus/issues/287) I had the same issue. In short try: ``` import pandas as pd import anndata import sklearn auc_key = 'eRegulon_AUC' signature_keys...

Calculate path matrices for differentiation arrows (branched tracjectory)

Hi @SeppeDeWinter and @Umaarasu I found out the issue. When you concat the adata and TF expression you make adata_all, but you never assign it back to adata. You can...