sc.pl.stacked_violin overplotting of y-axis scale
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Description
Especially when using standard_scale = 'var', the scale values obscure each other if values are '0' and '1'. Is there a way to allow for off-center plotting of the scale values? Minimizing the font size helps somewhat but is far from ideal.
...
sc.settings.set_figure_params(dpi=150)
sc.pl.stacked_violin(adata, marker_genes, groupby='louvain', rotation = 90, standard_scale = 'var'
...
Output:
Versions:
<scanpy==1.4.4.post1 anndata==0.6.22.post1 umap==0.3.9 numpy==1.15.4 scipy==1.3.0 pandas==0.23.4 scikit-learn==0.20.2 statsmodels==0.10.2 python-igraph==0.7.1 louvain==0.6.1>
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Research direction
Start with the minimal reproducible example using sc.pl.stacked_violin and standard_scale='var'. Inspect how the y-axis scale values are positioned and reproduce the overlap shown in the attached output. Done means the scale values remain readable without relying only on a smaller font, while preserving the stacked violin plot.
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Assessment
- Tech stack
- python
- Domain
- data-visualization
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100