If an obs column name is 0 or 1, they are not displayed by pl.render_shapes method

[sinanugur]

Hi,

I think this is a very specific issue. I cannot provide data to replicate. So obs has a column containing a continuous data and I want to visualize it. If the column name is "0" or "1", it shows a blank plot while other integers like "2", "3" or others work fine.

An example code to visualize a column.

sdata.pl.render_images("queried_cytassist").pl.render_shapes(
f"{sample_id}_square_00{bin_size}um", color="1",cmap=new_cmap,method="matplotlib",scale=0.8
).pl.show(coordinate_systems="global", title="cluster 1",legend_fontsize=8,figsize=(5,5),dpi=200)

My computer is Mac M1.

aiobotocore              2.5.4
aiohappyeyeballs         2.3.7
aiohttp                  3.10.4
aioitertools             0.11.0
aiosignal                1.3.1
anndata                  0.10.8
appnope                  0.1.4
array_api_compat         1.8
asciitree                0.3.3
asttokens                2.4.1
attrs                    24.2.0
botocore                 1.31.17
certifi                  2024.7.4
charset-normalizer       3.3.2
click                    8.1.7
cloudpickle              3.0.0
colorcet                 3.1.0
comm                     0.2.2
contourpy                1.2.1
csbdeep                  0.8.0
cycler                   0.12.1
dask                     2024.8.1
dask-expr                1.1.11
dask-image               2024.5.3
datashader               0.16.3
debugpy                  1.8.5
decorator                5.1.1
distributed              2024.8.1
docrep                   0.3.2
et-xmlfile               1.1.0
exceptiongroup           1.2.2
executing                2.0.1
fasteners                0.19
fcsparser                0.2.8
fonttools                4.53.1
frozenlist               1.4.1
fsspec                   2023.6.0
geopandas                1.0.1
h5py                     3.11.0
idna                     3.7
igraph                   0.11.6
imagecodecs              2024.6.1
imageio                  2.35.1
importlib_metadata       8.2.0
inflect                  7.3.1
iniconfig                2.0.0
ipykernel                6.29.5
ipython                  8.26.0
jedi                     0.19.1
Jinja2                   3.1.4
jmespath                 1.0.1
joblib                   1.4.2
jupyter_client           8.6.2
jupyter_core             5.7.2
kiwisolver               1.4.5
lamin_utils              0.13.2
lazy_loader              0.4
legacy-api-wrap          1.4
leidenalg                0.10.2
llvmlite                 0.43.0
locket                   1.0.0
markdown-it-py           3.0.0
MarkupSafe               2.1.5
matplotlib               3.9.2
matplotlib-inline        0.1.7
matplotlib-scalebar      0.8.1
mdurl                    0.1.2
more-itertools           10.4.0
msgpack                  1.0.8
multidict                6.0.5
multipledispatch         1.0.0
multiscale_spatial_image 1.0.1
natsort                  8.4.0
nest_asyncio             1.6.0
networkx                 3.3
numba                    0.60.0
numcodecs                0.13.0
numpy                    1.26.4
ome-zarr                 0.9.0
omnipath                 1.0.8
openpyxl                 3.1.5
packaging                24.1
pandas                   2.2.2
param                    2.1.1
parso                    0.8.4
partd                    1.4.2
patsy                    0.5.6
pexpect                  4.9.0
pickleshare              0.7.5
pillow                   10.4.0
PIMS                     0.7
pip                      24.2
platformdirs             4.2.2
pluggy                   1.5.0
pooch                    1.8.2
prompt_toolkit           3.0.47
psutil                   6.0.0
ptyprocess               0.7.0
pure_eval                0.2.3
pyarrow                  17.0.0
pyct                     0.5.0
Pygments                 2.18.0
pynndescent              0.5.13
pyogrio                  0.9.0
pyparsing                3.1.2
pyproj                   3.6.1
pytest                   8.3.2
python-dateutil          2.9.0
pytz                     2024.1
PyYAML                   6.0.2
pyzmq                    26.1.0
readfcs                  1.1.8
regex                    2024.7.24
requests                 2.32.3
rich                     13.7.1
s3fs                     2023.6.0
scanpy                   1.10.2
scikit-image             0.24.0
scikit-learn             1.5.1
scipy                    1.14.0
seaborn                  0.13.2
session_info             1.0.0
setuptools               72.1.0
shapely                  2.0.5
six                      1.16.0
slicerator               1.1.0
sortedcontainers         2.4.0
spatial_image            1.1.0
spatialdata              0.2.2
spatialdata-io           0.1.4
spatialdata-plot         0.2.4
squidpy                  1.6.0
stack-data               0.6.2
stardist                 0.9.1
statsmodels              0.14.2
stdlib-list              0.10.0
tblib                    3.0.0
texttable                1.7.0
threadpoolctl            3.5.0
tifffile                 2024.8.10
toolz                    0.12.1
tornado                  6.4.1
tqdm                     4.66.5
traitlets                5.14.3
typeguard                4.3.0
typing_extensions        4.12.2
tzdata                   2024.1
umap-learn               0.5.6
urllib3                  1.26.19
validators               0.33.0
wcwidth                  0.2.13
wheel                    0.44.0
wrapt                    1.16.0
xarray                   2024.7.0
xarray-dataclasses       1.8.0
xarray-datatree          0.0.14
xarray-schema            0.0.3
xarray-spatial           0.4.0
yarl                     1.9.4
zarr                     2.18.2
zict                     3.0.0
zipp                     3.20.0

[timtreis]

I assume this boils down to "0" and "1" sometimes being evaluated as booleans. I'll try to include a fix in my next PR, should be tiny. But in the meantime, you can probably avoid this by just not using 0/1.

[timtreis]

Hey @sinanugur,

I tried reproducing the bug by manually creating columns called "0" and "1" and they behave identical to let's say "2".

Buuuuut I'm on #323 locally right now, so it might be that this PR accidentally also fixes the underlying issue you reported. Could you try installing from this branch and report if the issue persists?

pip install git+https://github.com/scverse/spatialdata-plot.git@refs/pull/323/head

[sinanugur]

Hi @timtreis,

I got the same result.

spatialdata object table looks like this:

AnnData object with n_obs × n_vars = 56778 × 18058
    obs: 'in_tissue', 'array_row', 'array_col', 'location_id', 'region', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts', 'pct_counts_in_top_50_genes', 'pct_counts_in_top_100_genes', 'pct_counts_in_top_200_genes', 'pct_counts_in_top_500_genes', 'n_counts', 'x', '9', '5', '8', '6', '7', '0', '3', '1', '2', '4', '12', '11', '10'
    var: 'gene_ids', 'feature_types', 'genome', 'n_cells_by_counts', 'mean_counts', 'log1p_mean_counts', 'pct_dropout_by_counts', 'total_counts', 'log1p_total_counts', 'n_cells'
    uns: 'spatialdata_attrs', 'log1p'
    obsm: 'spatial'

My environment:

aiobotocore              2.5.4
aiohappyeyeballs         2.3.7
aiohttp                  3.10.4
aioitertools             0.11.0
aiosignal                1.3.1
anndata                  0.10.8
appnope                  0.1.4
array_api_compat         1.8
asciitree                0.3.3
asttokens                2.4.1
attrs                    24.2.0
botocore                 1.31.17
certifi                  2024.7.4
charset-normalizer       3.3.2
click                    8.1.7
cloudpickle              3.0.0
colorcet                 3.1.0
comm                     0.2.2
contourpy                1.2.1
csbdeep                  0.8.0
cycler                   0.12.1
dask                     2024.8.1
dask-expr                1.1.11
dask-image               2024.5.3
datashader               0.16.3
debugpy                  1.8.5
decorator                5.1.1
distributed              2024.8.1
docrep                   0.3.2
et-xmlfile               1.1.0
exceptiongroup           1.2.2
executing                2.0.1
fasteners                0.19
fcsparser                0.2.8
fonttools                4.53.1
frozenlist               1.4.1
fsspec                   2023.6.0
geopandas                1.0.1
h5py                     3.11.0
idna                     3.7
igraph                   0.11.6
imagecodecs              2024.6.1
imageio                  2.35.1
importlib_metadata       8.2.0
inflect                  7.3.1
iniconfig                2.0.0
ipykernel                6.29.5
ipython                  8.26.0
jedi                     0.19.1
Jinja2                   3.1.4
jmespath                 1.0.1
joblib                   1.4.2
jupyter_client           8.6.2
jupyter_core             5.7.2
kiwisolver               1.4.5
lamin_utils              0.13.2
lazy_loader              0.4
legacy-api-wrap          1.4
leidenalg                0.10.2
llvmlite                 0.43.0
locket                   1.0.0
markdown-it-py           3.0.0
MarkupSafe               2.1.5
matplotlib               3.9.2
matplotlib-inline        0.1.7
matplotlib-scalebar      0.8.1
mdurl                    0.1.2
more-itertools           10.4.0
msgpack                  1.0.8
multidict                6.0.5
multipledispatch         1.0.0
multiscale_spatial_image 1.0.1
natsort                  8.4.0
nest_asyncio             1.6.0
networkx                 3.3
numba                    0.60.0
numcodecs                0.13.0
numpy                    1.26.4
ome-zarr                 0.9.0
omnipath                 1.0.8
openpyxl                 3.1.5
packaging                24.1
pandas                   2.2.2
param                    2.1.1
parso                    0.8.4
partd                    1.4.2
patsy                    0.5.6
pexpect                  4.9.0
pickleshare              0.7.5
pillow                   10.4.0
PIMS                     0.7
pip                      24.2
platformdirs             4.2.2
pluggy                   1.5.0
pooch                    1.8.2
prompt_toolkit           3.0.47
psutil                   6.0.0
ptyprocess               0.7.0
pure_eval                0.2.3
pyarrow                  17.0.0
pyct                     0.5.0
Pygments                 2.18.0
pynndescent              0.5.13
pyogrio                  0.9.0
pyparsing                3.1.2
pyproj                   3.6.1
pytest                   8.3.2
python-dateutil          2.9.0
pytz                     2024.1
PyYAML                   6.0.2
pyzmq                    26.1.0
readfcs                  1.1.8
regex                    2024.7.24
requests                 2.32.3
rich                     13.7.1
s3fs                     2023.6.0
scanpy                   1.10.2
scikit-image             0.24.0
scikit-learn             1.5.1
scipy                    1.14.0
seaborn                  0.13.2
session_info             1.0.0
setuptools               72.1.0
shapely                  2.0.5
six                      1.16.0
slicerator               1.1.0
sortedcontainers         2.4.0
spatial_image            1.1.0
spatialdata              0.2.2
spatialdata-io           0.1.4
spatialdata-plot         0.2.5.dev35+g9ae69e9
squidpy                  1.6.0
stack-data               0.6.2
stardist                 0.9.1
statsmodels              0.14.2
stdlib-list              0.10.0
tblib                    3.0.0
texttable                1.7.0
threadpoolctl            3.5.0
tifffile                 2024.8.10
toolz                    0.12.1
tornado                  6.4.1
tqdm                     4.66.5
traitlets                5.14.3
typeguard                4.3.0
typing_extensions        4.12.2
tzdata                   2024.1
umap-learn               0.5.6
urllib3                  1.26.19
validators               0.33.0
wcwidth                  0.2.13
wheel                    0.44.0
wrapt                    1.16.0
xarray                   2024.7.0
xarray-dataclasses       1.8.0
xarray-datatree          0.0.14
xarray-schema            0.0.3
xarray-spatial           0.4.0
yarl                     1.9.4
zarr                     2.18.2
zict                     3.0.0
zipp                     3.20.0

[timtreis]

Which datatypes do your "0" or "1" columns have? And did you try to just rename the columns? Without a MRE I'll have to guess but it'd be good to pinpoint whether it's the column-name that's the issue or it's content. You could f.e. rename the columns to "xyz0" and "xyz1". If the issue is gone, it's the actual column name - if it persists, it's their content

[sinanugur]

Hi, It is continuous data.

Yes I tried renaming and created another column named x0 from "1" and it worked. That is why I am sure it must be related to column names. It is only for 0 and 1.

Cheers,
Sinan

[timtreis]

Was able to reproduce, will fix now. For some reason, matplotlib thinks "0" and "1" are colors:

This feels like unintended behaviour, so I opened an issue over at matplotlib: matplotlib/matplotlib#28759

[tacaswell]

https://matplotlib.org/stable/users/explain/colors/colors.html#color-formats

float values in [0, 1] as strings are short-hand for shades of gray.

[timtreis]

Thank you for your super quick clarification @tacaswell !