TypeError: scatter() got an unexpected keyword argument 'colorbar_loc' #3893
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?
Virtual env managed by micromamba
Python version: 3.11
Scanpy version: 1.11.5 (conda-forge installed or pip installed)
I am using sc.pl.scatter to plot a scatter of two genes coloured by a continuous variable (time) but do not want the colorbar shown beside.
sc.pl.scatter(ad, x=g1, y=g2, color='t', colorbar_loc=None)
# or plot on a existing ax
sc.pl.scatter(ad, x=g1, y=g2 color='t', show=False, colorbar_loc=None, ax=axes[i, j])The same error arises
File ~/Garage/micromamba/envs/pl/lib/python3.11/site-packages/legacy_api_wrap/__init__.py:82, in legacy_api.<locals>.wrapper.<locals>.fn_compatible(*args_all, **kw)
79 @wraps(fn)
80 def fn_compatible(*args_all: P.args, **kw: P.kwargs) -> R:
81 if len(args_all) <= n_positional:
---> 82 return fn(*args_all, **kw)
84 args_pos: P.args
85 args_pos, args_rest = args_all[:n_positional], args_all[n_positional:]
TypeError: scatter() got an unexpected keyword argument 'colorbar_loc'I have checked and followed the newest document of scanpy: https://scanpy.readthedocs.io/en/stable/generated/scanpy.pl.scatter.html, and I found there is indeed no colorbar_loc in the function's usage but it appears in explanation of Parameters.
Minimal code sample
# /// script
# requires-python = "==3.11"
# dependencies = [
# "scanpy@git+https://github.com/scverse/scanpy.git@main",
# ]
# ///
#
# This script automatically imports the development branch of scanpy to check for issues
import scanpy as sc
adata = sc.datasets.pbmc3k()
adata.obs['t'] = adata.X.toarray().sum(axis=1)
sc.pl.scatter(adata, x='MIR1302-10', y='FAM138A', color='t', colorbar_loc=None)Error output
File ~/Garage/micromamba/envs/pl/lib/python3.11/site-packages/legacy_api_wrap/__init__.py:82, in legacy_api.<locals>.wrapper.<locals>.fn_compatible(*args_all, **kw)
79 @wraps(fn)
80 def fn_compatible(*args_all: P.args, **kw: P.kwargs) -> R:
81 if len(args_all) <= n_positional:
---> 82 return fn(*args_all, **kw)
84 args_pos: P.args
85 args_pos, args_rest = args_all[:n_positional], args_all[n_positional:]
TypeError: scatter() got an unexpected keyword argument 'colorbar_loc'Versions
pandas 2.3.0 (2.3.2)
numpy 2.2.6
matplotlib 3.10.3 (3.10.6)
seaborn 0.13.2
scanpy 1.11.5
anndata 0.12.1
scipy 1.15.2
joblib 1.5.1 (1.5.2)
---- ----
pyparsing 3.2.3 (3.2.5)
pure_eval 0.2.3
pynndescent 0.5.13
texttable 1.7.0
zarr 3.1.3
decorator 5.2.1
kiwisolver 1.4.8 (1.4.9)
charset-normalizer 3.4.2
argcomplete 3.6.3
pyarrow 20.0.0
parso 0.8.4
cycler 0.12.1
executing 2.2.0
prompt_toolkit 3.0.51
stack_data 0.6.3
python-dateutil 2.9.0.post0
psutil 7.0.0
ipython 9.3.0
h5py 3.12.1
typing_extensions 4.14.0
cffi 1.17.1
legacy-api-wrap 1.4.1
natsort 8.4.0
igraph 1.0.0
Pygments 2.19.2
patsy 1.0.1
colorama 0.4.6
asttokens 3.0.0
session-info2 0.1.2
numba 0.61.2
jupyter_core 5.8.1
scikit-learn 1.7.2
tqdm 4.67.1
numcodecs 0.16.1
appnope 0.1.4
traitlets 5.14.3
umap-learn 0.5.7
pycparser 2.22
fsspec 2025.5.1
pytz 2025.2
plotly 6.1.2
debugpy 1.8.14
wcwidth 0.2.13
jedi 0.19.2
matplotlib-inline 0.1.7
ipykernel 6.29.5
tornado 6.5.1
threadpoolctl 3.6.0
statsmodels 0.14.5
defusedxml 0.7.1
leidenalg 0.11.0
packaging 25.0
comm 0.2.2
crc32c 2.7.1
donfig 0.8.1.post1
pyzmq 27.0.0
llvmlite 0.44.0
setuptools 80.9.0
pillow 11.2.1 (11.3.0)
ipywidgets 8.1.8
zstandard 0.23.0
msgpack 1.1.1
PyYAML 6.0.2
six 1.17.0
platformdirs 4.3.8
jupyter_client 8.6.3
---- ----
Python 3.11.13 | packaged by conda-forge | (main, Jun 4 2025, 14:52:34) [Clang 18.1.8 ]
OS macOS-15.5-arm64-arm-64bit
CPU 8 logical CPU cores, arm
GPU No GPU found
Updated 2025-11-13 05:06