Open stephwon opened 2 years ago
brykko
commented
2 years ago I just encountered the same issue, using scanpy 1.9.1 and matplotlib 3.5.3. I think it's a recent update to matbplotlib which broke something here. When I rolled back matplotlib to 3.5.2, it ran fine.
stephwon
commented
2 years ago I tried matplotlib 3.5.2 but didn't work but 3.1.3 does but doesn't put out multiple plot in one go
markddesimone
commented
1 year ago Hi Any suggestions on this? I am getting the same issue scanpy 1.9.2 (or 1.9.1):
Thanks
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
Input In [7], in <cell line: 1>()
----> 1 sc.pl.umap(adata,color=['EPCAM', 'CD79A', 'CD3D', 'NKG7', 'VFW', 'ACTB', 'ACTA2', 'TPSAB1', 'CD68'], size=12)
File ~/miniconda3/envs/scvi10j/lib/python3.8/site-packages/scanpy/plotting/_tools/scatterplots.py:669, in umap(adata, **kwargs)
610 @_wraps_plot_scatter
611 @_doc_params(
612 adata_color_etc=doc_adata_color_etc,
(...)
616 )
617 def umap(adata, **kwargs) -> Union[Axes, List[Axes], None]:
618 """\
619 Scatter plot in UMAP basis.
620
(...)
667 tl.umap
668 """
--> 669 return embedding(adata, 'umap', **kwargs)
File ~/miniconda3/envs/scvi10j/lib/python3.8/site-packages/scanpy/plotting/_tools/scatterplots.py:452, 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)
438 _add_categorical_legend(
439 ax,
440 color_source_vector,
(...)
449 multi_panel=bool(grid),
450 )
451 elif colorbar_loc is not None:
--> 452 pl.colorbar(
453 cax, ax=ax, pad=0.01, fraction=0.08, aspect=30, location=colorbar_loc
454 )
456 if return_fig is True:
457 return fig
File ~/miniconda3/envs/scvi10j/lib/python3.8/site-packages/matplotlib/pyplot.py:2194, in colorbar(mappable, cax, ax, **kw)
2192 if ax is None:
2193 ax = gca()
-> 2194 ret = gcf().colorbar(mappable, cax=cax, ax=ax, **kw)
2195 return ret
File ~/miniconda3/envs/scvi10j/lib/python3.8/site-packages/matplotlib/figure.py:2343, in Figure.colorbar(self, mappable, cax, ax, use_gridspec, **kw)
2340 NON_COLORBAR_KEYS = ['fraction', 'pad', 'shrink', 'aspect', 'anchor',
2341 'panchor']
2342 cb_kw = {k: v for k, v in kw.items() if k not in NON_COLORBAR_KEYS}
-> 2343 cb = cbar.colorbar_factory(cax, mappable, **cb_kw)
2345 self.sca(current_ax)
2346 self.stale = True
File ~/miniconda3/envs/scvi10j/lib/python3.8/site-packages/matplotlib/colorbar.py:1731, in colorbar_factory(cax, mappable, **kwargs)
1729 cb = ColorbarPatch(cax, mappable, **kwargs)
1730 else:
-> 1731 cb = Colorbar(cax, mappable, **kwargs)
1733 cid = mappable.callbacksSM.connect('changed', cb.update_normal)
1734 mappable.colorbar = cb
File ~/miniconda3/envs/scvi10j/lib/python3.8/site-packages/matplotlib/colorbar.py:1225, in Colorbar.__init__(self, ax, mappable, **kwargs)
1223 if isinstance(mappable, martist.Artist):
1224 _add_disjoint_kwargs(kwargs, alpha=mappable.get_alpha())
-> 1225 ColorbarBase.__init__(self, ax, **kwargs)
File ~/miniconda3/envs/scvi10j/lib/python3.8/site-packages/matplotlib/cbook/deprecation.py:451, in _make_keyword_only.<locals>.wrapper(*args, **kwargs)
445 if len(args) > idx:
446 warn_deprecated(
447 since, message="Passing the %(name)s %(obj_type)s "
448 "positionally is deprecated since Matplotlib %(since)s; the "
449 "parameter will become keyword-only %(removal)s.",
450 name=name, obj_type=f"parameter of {func.__name__}()")
--> 451 return func(*args, **kwargs)
TypeError: __init__() got an unexpected keyword argument 'location'I was having this problem with scanpy 1.9.1 and matplotlib 3.3.2 I just updated to 1.9.2 and confirm the issue is unchanged
scanpy==1.9.2 anndata==0.8.0 umap==0.5.2 numpy==1.21.5 scipy==1.8.0 pandas==1.4.1 scikit-learn==0.23.2 statsmodels==0.13.2 python-igraph==0.9.9 louvain==0.7.1 pynndescent==0.5.6
-----
anndata 0.8.0
scanpy 1.9.2
-----
PIL 9.0.1
absl NA
asttokens NA
attr 21.4.0
backcall 0.2.0
beta_ufunc NA
binom_ufunc NA
brotli NA
certifi 2022.06.15
cffi 1.14.5
charset_normalizer 2.0.12
chex 0.1.5
cloudpickle 2.2.0
colorama 0.4.4
contextlib2 NA
cycler 0.10.0
cython_runtime NA
cytoolz 0.12.0
dask 2022.11.1
dateutil 2.8.2
debugpy 1.5.1
decorator 5.1.1
defusedxml 0.7.1
deprecate 0.3.2
docrep 0.3.2
entrypoints 0.4
executing 0.8.3
flax 0.6.1
fsspec 2022.11.0
google NA
h5py 3.6.0
hypergeom_ufunc NA
idna 3.3
igraph 0.9.9
ipykernel 6.9.2
ipython_genutils 0.2.0
ipywidgets 7.6.5
jax 0.3.24
jaxlib 0.3.24
jedi 0.18.1
jinja2 3.0.3
joblib 1.1.0
kiwisolver 1.3.2
leidenalg 0.8.9
llvmlite 0.38.0
louvain 0.7.1
markupsafe 2.1.1
matplotlib 3.3.2
matplotlib_inline NA
ml_collections NA
mpl_toolkits NA
msgpack 1.0.4
mudata 0.2.1
multipledispatch 0.6.0
natsort 8.1.0
nbinom_ufunc NA
numba 0.55.1
numexpr 2.8.0
numpy 1.21.5
numpyro 0.10.1
opt_einsum v3.3.0
optax 0.1.3
packaging 21.3
pandas 1.4.1
parso 0.8.3
pexpect 4.8.0
pickleshare 0.7.5
pkg_resources NA
prompt_toolkit 3.0.27
psutil 5.9.0
ptyprocess 0.7.0
pure_eval 0.2.2
pycparser 2.21
pydev_ipython NA
pydevconsole NA
pydevd 2.6.0
pydevd_concurrency_analyser NA
pydevd_file_utils NA
pydevd_plugins NA
pydevd_tracing NA
pygments 2.11.2
pynndescent 0.5.6
pyparsing 3.0.7
pyro 1.8.2
pytorch_lightning 1.7.7
pytz 2021.3
requests 2.27.1
rich NA
scipy 1.8.0
scrublet NA
scvi 0.19.0
seaborn 0.11.2
session_info 1.0.0
setuptools 60.9.3
setuptools_scm NA
six 1.16.0
sklearn 0.23.2
socks 1.7.1
sphinxcontrib NA
stack_data 0.2.0
statsmodels 0.13.2
tensorboard 2.10.1
texttable 1.6.4
threadpoolctl 3.1.0
tlz 0.12.0
toolz 0.12.0
torch 1.11.0
torchmetrics 0.10.2
torchvision 0.12.0
tornado 6.1
tqdm 4.63.0
traitlets 5.1.1
tree 0.1.7
typing_extensions NA
umap 0.5.2
urllib3 1.26.8
wcwidth 0.2.5
yaml 6.0
zipp NA
zmq 22.3.0
-----
IPython 8.1.1
jupyter_client 7.1.2
jupyter_core 4.9.2
notebook 6.4.9
-----
Python 3.8.8 | packaged by conda-forge | (default, Feb 20 2021, 16:22:27) [GCC 9.3.0]
Linux-5.4.0-139-generic-x86_64-with-glibc2.10
-----
Session information updated at 2023-02-26 19:13The easiest workaround for this is to not plot the color bar. scanpy 1.9.0 added this option: e.g.:
sc.pl.umap(adata, color=['CD79A'], colorbar_loc=None)
I was running this code
sc.pl.umap(adata, color = ['KIR3DL1'], frameon = False, layer = 'scvi_normalized')to create umap but it gave me an error message with empty heatmap color bar legend.