Visualisation Issue 4

[giuliaelgarcia]

Scatter color function is not working and it can't recognize any inputs (even a hex colour code). Tried changing the pair_scatters_markers.csv colour indication to rna:douplet_scores, douplet_scores and a hex code and all of them errored The first two features are read fine but not the third one. Tested in python environment with mu.pl.scatter function and same error appeared. Also tested following error suggestion of doubling the rna:rna:doublet_scores and same issue appeared again. Additionally tested with the sc.pl.scatter function in a python environment using simple gene markers and color as doublet_scoresand it worked so it must be a muon issue. Additionally no instruction on how to accurately create the input file for scatter plots on the visualisation workflow or the gene format list.

[SarahOuologuem]

Hi! yes, you're right, it's a Muon issue.

When i run sc.pl.scatter() it throws an error when specifying the color as a list, e.g. color=["total_counts"]. Are you also getting this error? Therefore, for me, the errors were solved when i deleted the line color = [color] in line 75 in plot.py

I then ran the vis workflow of panpipes with the changed source code and the following paired_scatters_markers.csv and paired_scatters.csv (on the test data provided in the tutorial with the provided yaml of the tutorial)

I then get the following three plots

@giuliaelgarcia, please let me know whether it also works for you when changing the source code of muon in plot.py. Or are you getting any different errors? Thanks!