Violin plots - violins squished, points misaligned #3991
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'd appreciate any ideas about an issue with violins being squished and points not lining up. This started after a recent update of my mamba/conda environment but worked fine before. I tried searching for similar issues here and also on Seaborn's page but don't have any leads and can't say I'm well-versed with plotting in Python yet.
Thanks!
Minimal code sample
# /// script
# requires-python = ">=3.12"
# dependencies = [
# "scanpy@git+https://github.com/scverse/scanpy.git@main",
# "anndata==0.12.6"
# ]
# ///
#
# This script automatically imports the development branch of scanpy to check for issues
import scanpy as sc
import anndata as ad
adata = sc.datasets.pbmc68k_reduced()
sc.pl.violin(adata, ["n_genes", "n_counts", "percent_mito", "S_score"], groupby="bulk_labels", rotation=90)Error output
Versions
Details
scanpy 1.12
anndata 0.12.6
---- ----
ipykernel 6.29.5
cloudpickle 3.1.2
natsort 8.4.0
matplotlib 3.10.8
session-info2 0.4
colorama 0.4.6
PyQtWebEngine 5.15.7
psutil 7.2.2
ipywidgets 8.1.8
sphinxcontrib-applehelp 2.0.0
executing 2.2.1
pyzmq 27.1.0
beautifulsoup4 4.14.3
stack_data 0.6.3
scikit-learn 1.8.0
PyYAML 6.0.3
sphinxcontrib-serializinghtml 1.1.10
six 1.17.0
prompt_toolkit 3.0.52
joblib 1.5.3
platformdirs 4.9.2
numba 0.63.1
debugpy 1.8.20
seaborn 0.13.2
sphinxcontrib-qthelp 2.0.0
typing_extensions 4.15.0
packaging 26.0
pyxdg 0.28
spyder-kernels 3.1.3
jupyter_client 7.4.9
setuptools 82.0.0
donfig 0.8.1.post1
scipy 1.17.0
decorator 5.2.1
jedi 0.19.2
matplotlib-inline 0.2.1
numcodecs 0.16.5
legacy-api-wrap 1.5
PyQt5_sip 12.17.0
entrypoints 0.4
comm 0.2.3
asttokens 3.0.1
zarr 3.1.5
threadpoolctl 3.6.0
pillow 12.1.1
parso 0.8.6
statsmodels 0.14.6
ipython 9.10.0
google-crc32c 1.8.0
numpy 2.3.5
pytz 2025.2
defusedxml 0.7.1
pandas 3.0.1
sphinxcontrib-devhelp 2.0.0
kiwisolver 1.4.9
PyQt5 5.15.11
h5py 3.13.0
patsy 1.0.2
msgpack 1.1.2
traitlets 5.14.3
jupyter_core 5.9.1
tornado 6.5.4
charset-normalizer 3.4.4
sphinxcontrib-jsmath 1.0.1
astroid 4.0.4
pyparsing 3.3.2
python-dateutil 2.9.0.post0
lxml 6.0.2
Pygments 2.19.2
pure_eval 0.2.3
llvmlite 0.46.0
cycler 0.12.1
soupsieve 2.8.3
wcwidth 0.6.0
fast-array-utils 1.3.1
sphinxcontrib-htmlhelp 2.1.0
chardet 5.2.0
---- ----
Python 3.12.12 | packaged by conda-forge | (main, Jan 26 2026, 23:51:32) [GCC 14.3.0]
OS Linux-6.12.74-1-lts-x86_64-with-glibc2.43
CPU 32 logical CPU cores
GPU ID: 0, NVIDIA GeForce RTX 4070 Laptop GPU, Driver: 590.48.01, Memory: 8188 MiB
Updated 2026-02-26 19:08