pl.violin will not take "hue" kwarg for seaborn?
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Description
Trying to make a violin plot adding the seaborn hue argument will result in ValueError.
In adata, 'timepoint' and 'replicate' are categorical adata.obs containing floats and ints, respectively. 'timepoint' is the age of the embryo from which cells were isolated (9.5, 10.5, etc) and 'replicate' the number of the replica (1, 2, 3).
sc.pl.violin(adata, 'n_genes', jitter=0.4, groupby = 'timepoint', stripplot=False, hue='replicate')
sc.pl.violin(adata, 'n_genes', jitter=0.4, groupby = 'timepoint', stripplot=False, hue='replicate')
Traceback (most recent call last):
File "<ipython-input-5-756b321177a2>", line 1, in <module>
sc.pl.violin(adata, 'n_genes', jitter=0.4, groupby = 'timepoint', stripplot=False, hue='replicate')
File "/home/auesro/anaconda3/envs/Scanpy/lib/python3.7/site-packages/scanpy/plotting/_anndata.py", line 759, in violin
**kwds,
File "/home/auesro/anaconda3/envs/Scanpy/lib/python3.7/site-packages/seaborn/categorical.py", line 2393, in violinplot
color, palette, saturation)
File "/home/auesro/anaconda3/envs/Scanpy/lib/python3.7/site-packages/seaborn/categorical.py", line 559, in __init__
self.establish_variables(x, y, hue, data, orient, order, hue_order)
File "/home/auesro/anaconda3/envs/Scanpy/lib/python3.7/site-packages/seaborn/categorical.py", line 152, in establish_variables
raise ValueError(err)
ValueError: Could not interpret input 'replicate'
Versions:
scanpy==1.4.6 anndata==0.7.1 umap==0.4.1 numpy==1.18.1 scipy==1.4.1 pandas==1.0.3 scikit-learn==0.22.2.post1 statsmodels==0.11.1 python-igraph==0.8.0
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start at the sc.pl.violin entry point and reproduce the reported call with the supplied categorical timepoint and replicate fields. Trace how the hue argument is passed to seaborn and verify the behavior against the reported versions. Done means the example accepts hue without raising the ValueError.
Written by the indexing model from the issue text.
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