Scanpy: sc.pl.paga_path: TypeError: float() argument must be a string or a number, not 'csr_matrix'

[plrlhb12]

I was plotting the paga path, I got the error of TypeError: float() argument must be a string or a number, not 'csr_matrix'. I guess this might be related with the sparse format of adata.raw.X, because my codes works if I deleted adata.raw. What would be the solution? Thank you

_, axs = pl.subplots(ncols=3, figsize=(6, 2.5), gridspec_kw={'wspace': 0.05, 'left': 0.12})
pl.subplots_adjust(left=0.05, right=0.98, top=0.82, bottom=0.2)
for ipath, (descr, path) in enumerate(paths):
_, data = sc.pl.paga_path(
adata, path, gene_names,
show_node_names=False,
ax=axs[ipath],
ytick_fontsize=8,
left_margin=0.15,
n_avg=50,
annotations=['distance'],
show_yticks=True if ipath==0 else False,
show_colorbar=False,
color_map='Greys',
groups_key='clusters',
color_maps_annotations={'distance': 'viridis'},
title='{} path'.format(descr),
return_data=True,
show=False)
data.to_csv('./write/paga_path_{}.csv'.format(descr))
pl.savefig('./figures/paga_path_panglao.pdf')
pl.show()

TypeError Traceback (most recent call last)
TypeError: float() argument must be a string or a number, not 'csr_matrix'

The above exception was the direct cause of the following exception:

ValueError Traceback (most recent call last)
in ()
18 title='{} path'.format(descr),
19 return_data=True,
---> 20 show=False)
21 data.to_csv('./write/paga_path_{}.csv'.format(descr))
22 pl.savefig('./figures/paga_path_panglao.pdf')

5 frames
<__array_function__ internals> in cumsum(args, *kwargs)

/usr/local/lib/python3.6/dist-packages/numpy/core/fromnumeric.py in _wrapit(obj, method, args, *kwds)
45 except AttributeError:
46 wrap = None
---> 47 result = getattr(asarray(obj), method)(args, *kwds)
48 if wrap:
49 if not isinstance(result, mu.ndarray):

ValueError: setting an array element with a sequence.

Versions:

scanpy==1.5.1 anndata==0.7.3 umap==0.4.4 numpy==1.18.5 scipy==1.4.1 pandas==1.0.5 scikit-learn==0.22.2.post1 statsmodels==0.10.2 python-igraph==0.8.2 leidenalg==0.8.1

[Blohrer]

When using scanpy.pl.paga_path, I experience the same error as @plrlhb12 (TypeError: float() argument must be a string or a number, not 'csr_matrix') and I can also only generate a plot after deleting adata.raw. As a consequence, I can only plot genes that are filtered for high variability during preprocessing and still present in adata.var.gene_ids.
I would be glad if there was a way to make it work without deleting adata.raw and therefore being able to plot also non-highly variable genes! Thank you!

Versions:

anndata==0.7.4 matplotlib==3.3.0 numpy==1.19.1 pandas==1.1.0 scanpy==1.6.0 scipy==1.5.2 sklearn==0.23.1 igraph==0.8.2 leidenalg==0.8.1 umap==0.4.6

[alevax]

The same error happens to me, @Blohrer

Versions:

scanpy==1.6.0 anndata==0.7.4 umap==0.4.6 numpy==1.18.5 scipy==1.5.0 pandas==1.0.5 scikit-learn==0.23.1 statsmodels==0.11.1 python-igraph==0.7.1 louvain==0.6.1 leidenalg==0.7.0