I've been trying to run through this tutorial (https://bedapub.github.io/besca/tutorials/scRNAseq_tutorial.html) for the past day and constantly get an error after running this portion:
bc.pl.kp_genes(adata, min_genes=min_genes, ax = ax1)
The error is the following:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/opt/miniconda3/lib/python3.9/site-packages/besca/pl/_filter_threshold_plots.py", line 57, in kp_genes
ax.set_yscale("log", basey=10)
File "/opt/miniconda3/lib/python3.9/site-packages/matplotlib/axes/_base.py", line 4108, in set_yscale
ax.yaxis._set_scale(value, **kwargs)
File "/opt/miniconda3/lib/python3.9/site-packages/matplotlib/axis.py", line 761, in _set_scale
self._scale = mscale.scale_factory(value, self, **kwargs)
File "/opt/miniconda3/lib/python3.9/site-packages/matplotlib/scale.py", line 597, in scale_factory
return scale_cls(axis, **kwargs)
TypeError: __init__() got an unexpected keyword argument 'basey'
Anyone have any thoughts? I've uninstalled and installed matplotlib to make sure its updated but that doesn't seem to have done anything either.
Would appreciate any help! And thank you in advance I'm a beginner!
It seems that ax.set_yscale("log", basey=10) does not recognise keyword argument basey. This keyword was replaced in the most recent matplotlib releases if you would install an older version it should work:
pip install matplotlib==3.3.4
So why is this happening in the first place? The package you are using does not have specific dependencies pinned down so it installs the most recent versions of dependencies. If there are any API changes to the more recent versions of packages the code breaks - it's good practice to pin down dependency versions of the project.