search

aertslab / scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
Other
163 stars 27 forks source link

Plotting the eRegulon enrichment score using the scanpy umap function [development branch] #351

Closed zfliu01 closed 2 months ago

zfliu01 commented 2 months ago

Hi Seppe,

It seems like when plotting the eRegulon enrichment score using the scanpy umap function will result in this error. It does look like it is a scanpy error instead of scenicplus itself.

sc.pl.umap(eRegulon_gene_AUC, color = "scRNA_counts:GROUP") /home/zfliu01/miniconda3/envs/scenicplus/lib/python3.11/site-packages/scanpy/plotting/_tools/scatterplots.py:378: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter( sc.pl.umap(eRegulon_gene_AUC, color = "scRNA_counts:sample") /home/zfliu01/miniconda3/envs/scenicplus/lib/python3.11/site-packages/scanpy/plotting/_tools/scatterplots.py:378: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter( sc.pl.umap(eRegulon_gene_AUC, color = "scRNA_counts:RNA_snn_res.0.5") /home/zfliu01/miniconda3/envs/scenicplus/lib/python3.11/site-packages/scanpy/plotting/_tools/scatterplots.py:378: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(

Version (please complete the following information):

Please let me know if anything else is needed.

Thank you! Jeff

SeppeDeWinter commented 2 months ago

Hi,

Yes this seems to be a scanpy issue, see https://github.com/scverse/scanpy/issues/2411.

All the best,

Seppe

zfliu01 commented 2 months ago

Just realized that since I'm using our cluster unless I specify save path I'm not getting graphical output... After setting that I'm seeing figures.

Sorry for the confusion, Jeff