scanpy.pl.spatial TypeError: can't multiply sequence by non-int of type 'float'

[cf98]

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---

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It is hard to show the error without my data, but here it is what I did. I read in my 10 visium data (output from SpaceRanger 2.0.0) and everything seems fine. All I had to do was to change a file name (tissue_positions.csv to tissue_positions_list.csv) in my outs/spatial folder.

healthy_A1 = sc.read_visium('../data/MGI3535_A1_010322NHK/outs/', count_file='raw_feature_bc_matrix.h5')

I calculated qc metrics with this command.

sc.pp.calculate_qc_metrics(healthy_A1, percent_top=None, log1p=False, inplace=True)

But then, the problem occurs when I try to use scanpy.pl.spatial

Minimal code sample (that we can copy&paste without having any data)

sc.pl.spatial(healthy_A1, img_key = "hires", color = "total_counts") 

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
/tmp/ipykernel_1314047/3602867448.py in <module>
----> 1 sc.pl.spatial(healthy_A1, img_key = "hires", color = "ACTA2")

~/.conda/envs/python_spatial/lib/python3.7/site-packages/scanpy/plotting/_tools/scatterplots.py in spatial(adata, basis, img, img_key, library_id, crop_coord, alpha_img, bw, size, scale_factor, spot_size, na_color, show, return_fig, save, **kwargs)
   1009         show=False,
   1010         save=False,
-> 1011         **kwargs,
   1012     )
   1013     if not isinstance(axs, list):

~/.conda/envs/python_spatial/lib/python3.7/site-packages/scanpy/plotting/_tools/scatterplots.py in embedding(adata, basis, color, gene_symbols, use_raw, sort_order, edges, edges_width, edges_color, neighbors_key, arrows, arrows_kwds, groups, components, dimensions, layer, projection, scale_factor, color_map, cmap, palette, na_color, na_in_legend, size, frameon, legend_fontsize, legend_fontweight, legend_loc, legend_fontoutline, colorbar_loc, vmax, vmin, vcenter, norm, add_outline, outline_width, outline_color, ncols, hspace, wspace, title, show, save, ax, return_fig, **kwargs)
    397                 rasterized=settings._vector_friendly,
    398                 norm=normalize,
--> 399                 **kwargs,
    400             )
    401 

~/.conda/envs/python_spatial/lib/python3.7/site-packages/scanpy/plotting/_utils.py in circles(x, y, s, ax, marker, c, vmin, vmax, scale_factor, **kwargs)
   1106     # while you can only set `facecolors` with a value for all.
   1107     if scale_factor != 1.0:
-> 1108         x = x * scale_factor
   1109         y = y * scale_factor
   1110     zipped = np.broadcast(x, y, s)

TypeError: can't multiply sequence by non-int of type 'float'

Bascially, the same type of error keeps showing up no matter what the color = parameter is. I put a gene name there, and the same message showed up.

Additional information about the error (the image that showed up together with the error message from the jupyter notebook cell):

Versions

---

anndata 0.8.0
scanpy 1.9.1

PIL 9.2.0
annoy NA
asciitree NA
backcall 0.2.0
beta_ufunc NA
binom_ufunc NA
cffi 1.15.1
cloudpickle 2.2.0
cycler 0.10.0
cython_runtime NA
dask 2022.02.0
dateutil 2.8.2
debugpy 1.6.3
decorator 5.1.1
defusedxml 0.7.1
entrypoints 0.4
fasteners 0.18
fbpca NA
fsspec 2022.11.0
google NA
h5py 3.7.0
igraph 0.10.2
intervaltree NA
ipykernel 6.16.2
ipython_genutils 0.2.0
ipywidgets 8.0.4
jedi 0.18.2
jinja2 3.1.2
joblib 1.2.0
jupyter_server 1.23.4
kiwisolver 1.4.4
leidenalg 0.9.1
llvmlite 0.39.1
markupsafe 2.1.1
matplotlib 3.5.3
matplotlib_inline 0.1.6
mpl_toolkits NA
msgpack 1.0.4
natsort 8.2.0
nbinom_ufunc NA
numba 0.56.4
numcodecs 0.10.2
numpy 1.21.6
packaging 22.0
pandas 1.3.5
parso 0.8.3
pexpect 4.8.0
pickleshare 0.7.5
pkg_resources NA
prompt_toolkit 3.0.36
psutil 5.9.3
ptyprocess 0.7.0
pydev_ipython NA
pydevconsole NA
pydevd 2.8.0
pydevd_file_utils NA
pydevd_plugins NA
pydevd_tracing NA
pygments 2.13.0
pyparsing 3.0.9
pytz 2022.7
scanorama 1.7.1
scipy 1.7.3
seaborn 0.12.1
session_info 1.0.0
setuptools 65.6.3
six 1.16.0
sklearn 1.0.2
sortedcontainers 2.4.0
statsmodels 0.13.5
storemagic NA
texttable 1.6.7
threadpoolctl 3.1.0
tlz 0.12.0
toolz 0.12.0
tornado 6.2
traitlets 5.8.0
typing_extensions NA
wcwidth 0.2.5
yaml 6.0
zarr 2.12.0
zipp NA
zmq 24.0.1

IPython 7.33.0
jupyter_client 7.4.8
jupyter_core 4.11.1
jupyterlab 3.5.2
notebook 6.5.2

Python 3.7.12 | packaged by conda-forge | (default, Oct 26 2021, 06:08:21) [GCC 9.4.0]
Linux-5.4.0-121-generic-x86_64-with-debian-bullseye-sid

Session information updated at 2022-12-28 21:40

[cf98]

This seems to be a compatibility issue with outputs from SpaceRanger 2.0.0.
Following this issue on Seurat, I was finally able to solve it.
Please consider an official fix for this. I am new to github and still trying to figure out how to do a pull request. Thanks! @falexwolf

[alexcwsmith]

Hi @cf98 what was the fix for this? Did you revert to SpaceRanger 1.0, or did you find a way to make scanPy compatible with SpaceRanger 2.0? I didn't see anything directly applicable to this in the Seurat thread.
Thanks!

[cf98]

Hi Alex,

I basically followed the discussion thread in Seurat: remove the header of the tissue_positions.csv, and change this file name to tissue_positions_list.csv.

Based on the discussion of another thread, the scanpy authors are maintaining squidpy for the spatial transcriptomics part. If you use the squidpy function to load the data, there's no such issue (they considered the versions in their code).

Best,
Changfeng

[swainasish]

@cf98 Thank you its work for me