sc.pl.umap does not show legend when show=False and saving figure manually #3926
Description
Please make sure these conditions are met
- I have checked that this issue has not already been reported.
- I have confirmed this bug exists on the latest version of scanpy.
- (optional) I have confirmed this bug exists on the main branch of scanpy.
What happened?
Hi! I encountered an issue when using sc.pl.umap with show=False and then saving the figure manually. The resulting PDF does not include the legend, even though a legend is shown when show=True.
T_NK_leiden_res_3.00_cluster_3_umap.pdf
Minimal code sample
sc.pl.umap(mdata['gex'], color='cluster_3',show=False).figure.savefig('/mnt/UMAP/T_NK/T_NK_leiden_res_3.00_cluster_3_umap.pdf')Error output
Versions
Python | 3.10.18 | packaged by conda-forge | (main, Jun 4 2025, 14:45:41) [GCC 13.3.0]
OS | Linux-5.4.0-216-generic-x86_64-with-glibc2.31
| Dependency | Version |
|---|---|
| scanpy | 1.11.4 |
| joblib | 1.5.2 |
| numba | 0.62.1 |
| umap-learn | 0.5.9.post2 |
| patsy | 1.0.1 |
| pure_eval | 0.2.3 |
| jedi | 0.19.2 |
| importlib_metadata | 8.7.0 |
| adjustText | 1.3.0 |
| six | 1.17.0 |
| PyYAML | 6.0.3 |
| igraph | 0.11.9 |
| future | 1.0.0 |
| h5py | 3.14.0 |
| ipywidgets | 8.1.8 |
| statsmodels | 0.14.5 |
| debugpy | 1.8.17 |
| pytz | 2025.2 |
| url-normalize | 2.2.1 |
| wcwidth | 0.2.14 |
| python-dateutil | 2.9.0.post0 |
| pynndescent | 0.5.13 |
| stack-data | 0.6.3 |
| tqdm | 4.67.1 |
| pyarrow | 22.0.0 |
| zipp | 3.23.0 |
| asttokens | 3.0.0 |
| pooch | 1.8.2 (v1.8.2) |
| kiwisolver | 1.4.9 |
| Cython | 3.1.4 |
| tornado | 6.5.2 |
| setuptools | 80.9.0 |
| charset-normalizer | 3.4.3 |
| requests | 2.32.5 |
| leidenalg | 0.10.2 |
| natsort | 8.4.0 |
| prompt_toolkit | 3.0.52 |
| executing | 2.2.1 |
| plotly | 6.5.0 |
| certifi | 2025.8.3 (2025.08.03) |
| ipython | 8.37.0 |
| pillow | 11.3.0 |
| llvmlite | 0.45.1 |
| psutil | 7.1.0 |
| parso | 0.8.5 |
| texttable | 1.7.0 |
| networkx | 3.4.2 |
| decorator | 5.2.1 |