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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?
I pass a adata.var column header with my gene name that I want displayed, sc.pl.heatmap runs into a key error where my index values are being searched in the genename column
Minimal code sample
sc.pl.heatmap(
adata=adata,
var_names=top_25,
gene_symbols=adata.var.columns.tolist()[2],
groupby='slide_number',
swap_axes=True,
standard_scale='var',
)Error output
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
Cell In[86], line 1
----> 1 sc.pl.heatmap(
2 adata=adata,
3 var_names=top_25,
4 gene_symbols=adata.var.columns.tolist()[2],
5 groupby='slide_number',
6 swap_axes=True,
7 standard_scale='var',
8 )
File /opt/homebrew/Caskroom/mambaforge/base/envs/proteomics/lib/python3.12/site-packages/legacy_api_wrap/__init__.py:80, in legacy_api.<locals>.wrapper.<locals>.fn_compatible(*args_all, **kw)
77 @wraps(fn)
78 def fn_compatible(*args_all: P.args, **kw: P.kwargs) -> R:
79 if len(args_all) <= n_positional:
---> 80 return fn(*args_all, **kw)
82 args_pos: P.args
83 args_pos, args_rest = args_all[:n_positional], args_all[n_positional:]
File /opt/homebrew/Caskroom/mambaforge/base/envs/proteomics/lib/python3.12/site-packages/scanpy/plotting/_anndata.py:1120, in heatmap(adata, var_names, groupby, use_raw, log, num_categories, dendrogram, gene_symbols, var_group_positions, var_group_labels, var_group_rotation, layer, standard_scale, swap_axes, show_gene_labels, show, save, figsize, vmin, vmax, vcenter, norm, **kwds)
1070 """\
1071 Heatmap of the expression values of genes.
1072
(...)
1114 tl.rank_genes_groups
1115 """
1116 var_names, var_group_labels, var_group_positions = _check_var_names_type(
1117 var_names, var_group_labels, var_group_positions
1118 )
-> 1120 categories, obs_tidy = _prepare_dataframe(
1121 adata,
1122 var_names,
1123 groupby,
1124 use_raw=use_raw,
1125 log=log,
1126 num_categories=num_categories,
1127 gene_symbols=gene_symbols,
1128 layer=layer,
1129 )
1131 # check if var_group_labels are a subset of categories:
1132 if var_group_labels is not None:
File /opt/homebrew/Caskroom/mambaforge/base/envs/proteomics/lib/python3.12/site-packages/scanpy/plotting/_anndata.py:2057, in _prepare_dataframe(adata, var_names, groupby, use_raw, log, num_categories, layer, gene_symbols)
2055 groupby.remove(groupby_index)
2056 keys = list(groupby) + list(np.unique(var_names))
-> 2057 obs_tidy = get.obs_df(
2058 adata, keys=keys, layer=layer, use_raw=use_raw, gene_symbols=gene_symbols
2059 )
2060 assert np.all(np.array(keys) == np.array(obs_tidy.columns))
2062 if groupby_index is not None:
2063 # reset index to treat all columns the same way.
File /opt/homebrew/Caskroom/mambaforge/base/envs/proteomics/lib/python3.12/site-packages/scanpy/get/get.py:296, in obs_df(adata, keys, obsm_keys, layer, gene_symbols, use_raw)
293 else:
294 alias_index = None
--> 296 obs_cols, var_idx_keys, var_symbols = _check_indices(
297 adata.obs,
298 var.index,
299 dim="obs",
300 keys=keys,
301 alias_index=alias_index,
302 use_raw=use_raw,
303 )
305 # Make df
306 df = pd.DataFrame(index=adata.obs_names)
File /opt/homebrew/Caskroom/mambaforge/base/envs/proteomics/lib/python3.12/site-packages/scanpy/get/get.py:186, in _check_indices(dim_df, alt_index, dim, keys, alias_index, use_raw)
184 not_found.append(key)
185 if len(not_found) > 0:
--> 186 raise KeyError(
187 f"Could not find keys '{not_found}' in columns of `adata.{dim}` or in"
188 f" {alt_repr}.{alt_search_repr}."
189 )
191 return col_keys, index_keys, index_aliases
KeyError: "Could not find keys '[np.str_('O00154'), np.str_('O00515'), np.str_('O94886'), np.str_('P09493'), np.str_('P20338'), np.str_('P23141'), np.str_('P49419'), np.str_('P55268'), np.str_('P98095'), np.str_('P98160'), np.str_('Q01995'), np.str_('Q05682'), np.str_('Q09666'), np.str_('Q13751'), np.str_('Q14195'), np.str_('Q16795'), np.str_('Q8IUX7'), np.str_('Q8WX93'), np.str_('Q96AC1'), np.str_('Q96FZ7'), np.str_('Q96G03'), np.str_('Q9NSE4'), np.str_('Q9NZM1'), np.str_('Q9UN36'), np.str_('Q9Y4K1')]' in columns of `adata.obs` or in adata.var['Genes']."Versions
# packages in environment at /opt/homebrew/Caskroom/mambaforge/base/envs/proteomics:
#
# Name Version Build Channel
adjusttext 1.2.0 pyhd8ed1ab_0 conda-forge
anndata 0.10.9 pyhd8ed1ab_0 conda-forge
anyio 4.6.2.post1 pyhd8ed1ab_0 conda-forge
appnope 0.1.4 pyhd8ed1ab_0 conda-forge
argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py312h024a12e_5 conda-forge
array-api-compat 1.9 pyhd8ed1ab_0 conda-forge
arrow 1.3.0 pyhd8ed1ab_0 conda-forge
asttokens 2.4.1 pyhd8ed1ab_0 conda-forge
async-lru 2.0.4 pyhd8ed1ab_0 conda-forge
attrs 24.2.0 pyh71513ae_0 conda-forge
babel 2.14.0 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.12.3 pyha770c72_0 conda-forge
bleach 6.1.0 pyhd8ed1ab_0 conda-forge
brotli 1.1.0 hd74edd7_2 conda-forge
brotli-bin 1.1.0 hd74edd7_2 conda-forge
brotli-python 1.1.0 py312hde4cb15_2 conda-forge
bzip2 1.0.8 h99b78c6_7 conda-forge
c-ares 1.34.2 h7ab814d_0 conda-forge
ca-certificates 2024.8.30 hf0a4a13_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
certifi 2024.8.30 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py312h0fad829_0 conda-forge
charset-normalizer 3.4.0 pyhd8ed1ab_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
comm 0.2.2 pyhd8ed1ab_0 conda-forge
contourpy 1.3.0 py312h6142ec9_2 conda-forge
cycler 0.12.1 pyhd8ed1ab_0 conda-forge
debugpy 1.8.7 py312hde4cb15_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
exceptiongroup 1.2.2 pyhd8ed1ab_0 conda-forge
executing 2.1.0 pyhd8ed1ab_0 conda-forge
fonttools 4.54.1 py312h024a12e_0 conda-forge
fqdn 1.5.1 pyhd8ed1ab_0 conda-forge
freetype 2.12.1 hadb7bae_2 conda-forge
get-annotations 0.1.2 pyhd8ed1ab_0 conda-forge
h11 0.14.0 pyhd8ed1ab_0 conda-forge
h2 4.1.0 pyhd8ed1ab_0 conda-forge
h5py 3.11.0 nompi_py312h3cd0824_103 conda-forge
hdf5 1.14.3 nompi_hec07895_105 conda-forge
hpack 4.0.0 pyh9f0ad1d_0 conda-forge
httpcore 1.0.6 pyhd8ed1ab_0 conda-forge
httpx 0.27.2 pyhd8ed1ab_0 conda-forge
hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge
icu 75.1 hfee45f7_0 conda-forge
idna 3.10 pyhd8ed1ab_0 conda-forge
importlib-metadata 8.5.0 pyha770c72_0 conda-forge
importlib_metadata 8.5.0 hd8ed1ab_0 conda-forge
importlib_resources 6.4.5 pyhd8ed1ab_0 conda-forge
ipykernel 6.29.5 pyh57ce528_0 conda-forge
ipython 8.28.0 pyh707e725_0 conda-forge
ipywidgets 8.1.5 pyhd8ed1ab_0 conda-forge
isoduration 20.11.0 pyhd8ed1ab_0 conda-forge
jedi 0.19.1 pyhd8ed1ab_0 conda-forge
jinja2 3.1.4 pyhd8ed1ab_0 conda-forge
joblib 1.4.2 pyhd8ed1ab_0 conda-forge
json5 0.9.25 pyhd8ed1ab_0 conda-forge
jsonpointer 3.0.0 py312h81bd7bf_1 conda-forge
jsonschema 4.23.0 pyhd8ed1ab_0 conda-forge
jsonschema-specifications 2024.10.1 pyhd8ed1ab_0 conda-forge
jsonschema-with-format-nongpl 4.23.0 hd8ed1ab_0 conda-forge
jupyter 1.1.1 pyhd8ed1ab_0 conda-forge
jupyter-lsp 2.2.5 pyhd8ed1ab_0 conda-forge
jupyter_client 8.6.3 pyhd8ed1ab_0 conda-forge
jupyter_console 6.6.3 pyhd8ed1ab_0 conda-forge
jupyter_core 5.7.2 pyh31011fe_1 conda-forge
jupyter_events 0.10.0 pyhd8ed1ab_0 conda-forge
jupyter_server 2.14.2 pyhd8ed1ab_0 conda-forge
jupyter_server_terminals 0.5.3 pyhd8ed1ab_0 conda-forge
jupyterlab 4.2.5 pyhd8ed1ab_0 conda-forge
jupyterlab_pygments 0.3.0 pyhd8ed1ab_1 conda-forge
jupyterlab_server 2.27.3 pyhd8ed1ab_0 conda-forge
jupyterlab_widgets 3.0.13 pyhd8ed1ab_0 conda-forge
kaleido 0.2.1 pypi_0 pypi
kiwisolver 1.4.7 py312h6142ec9_0 conda-forge
krb5 1.21.3 h237132a_0 conda-forge
lcms2 2.16 ha0e7c42_0 conda-forge
legacy-api-wrap 1.4 pyhd8ed1ab_1 conda-forge
lerc 4.0.0 h9a09cb3_0 conda-forge
libaec 1.1.3 hebf3989_0 conda-forge
libblas 3.9.0 24_osxarm64_openblas conda-forge
libbrotlicommon 1.1.0 hd74edd7_2 conda-forge
libbrotlidec 1.1.0 hd74edd7_2 conda-forge
libbrotlienc 1.1.0 hd74edd7_2 conda-forge
libcblas 3.9.0 24_osxarm64_openblas conda-forge
libcurl 8.10.1 h13a7ad3_0 conda-forge
libcxx 19.1.2 ha82da77_0 conda-forge
libdeflate 1.22 hd74edd7_0 conda-forge
libedit 3.1.20191231 hc8eb9b7_2 conda-forge
libev 4.33 h93a5062_2 conda-forge
libexpat 2.6.3 hf9b8971_0 conda-forge
libffi 3.4.2 h3422bc3_5 conda-forge
libgfortran 5.0.0 13_2_0_hd922786_3 conda-forge
libgfortran5 13.2.0 hf226fd6_3 conda-forge
libhwloc 2.11.1 default_h7685b71_1000 conda-forge
libiconv 1.17 h0d3ecfb_2 conda-forge
libjpeg-turbo 3.0.0 hb547adb_1 conda-forge
liblapack 3.9.0 24_osxarm64_openblas conda-forge
libllvm14 14.0.6 hd1a9a77_4 conda-forge
libnghttp2 1.58.0 ha4dd798_1 conda-forge
libopenblas 0.3.27 openmp_h517c56d_1 conda-forge
libpng 1.6.44 hc14010f_0 conda-forge
libsodium 1.0.20 h99b78c6_0 conda-forge
libsqlite 3.46.1 hc14010f_0 conda-forge
libssh2 1.11.0 h7a5bd25_0 conda-forge
libtiff 4.7.0 hfce79cd_1 conda-forge
libwebp-base 1.4.0 h93a5062_0 conda-forge
libxcb 1.17.0 hdb1d25a_0 conda-forge
libxml2 2.12.7 h01dff8b_4 conda-forge
libzlib 1.3.1 h8359307_2 conda-forge
littleutils 0.2.4 pyhd8ed1ab_0 conda-forge
llvm-openmp 19.1.1 hb52a8e5_1 conda-forge
llvmlite 0.43.0 py312ha9ca408_1 conda-forge
loguru 0.7.2 py312h81bd7bf_2 conda-forge
markupsafe 3.0.1 py312h906988d_1 conda-forge
matplotlib 3.9.2 py312h1f38498_1 conda-forge
matplotlib-base 3.9.2 py312h9bd0bc6_1 conda-forge
matplotlib-inline 0.1.7 pyhd8ed1ab_0 conda-forge
mistune 3.0.2 pyhd8ed1ab_0 conda-forge
mpmath 1.3.0 pyhd8ed1ab_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
natsort 8.4.0 pyhd8ed1ab_0 conda-forge
nbclient 0.10.0 pyhd8ed1ab_0 conda-forge
nbconvert-core 7.16.4 pyhd8ed1ab_1 conda-forge
nbformat 5.10.4 pyhd8ed1ab_0 conda-forge
ncurses 6.5 h7bae524_1 conda-forge
nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge
networkx 3.4.1 pyhd8ed1ab_0 conda-forge
notebook 7.2.2 pyhd8ed1ab_0 conda-forge
notebook-shim 0.2.4 pyhd8ed1ab_0 conda-forge
numba 0.60.0 py312h41cea2d_0 conda-forge
numpy 2.0.2 py312h801f5e3_0 conda-forge
openjpeg 2.5.2 h9f1df11_0 conda-forge
openssl 3.3.2 h8359307_0 conda-forge
outdated 0.2.2 pyhd8ed1ab_1 conda-forge
overrides 7.7.0 pyhd8ed1ab_0 conda-forge
packaging 24.1 pyhd8ed1ab_0 conda-forge
pandas 2.2.3 py312hcd31e36_1 conda-forge
pandas-flavor 0.6.0 pyhd8ed1ab_2 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
parso 0.8.4 pyhd8ed1ab_0 conda-forge
patsy 0.5.6 pyhd8ed1ab_0 conda-forge
pexpect 4.9.0 pyhd8ed1ab_0 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 11.0.0 py312haf37ca6_0 conda-forge
pingouin 0.5.5 pyhd8ed1ab_0 conda-forge
pip 24.2 pyh8b19718_1 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge
platformdirs 4.3.6 pyhd8ed1ab_0 conda-forge
plotly 5.24.1 pyhd8ed1ab_0 conda-forge
prometheus_client 0.21.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.48 pyha770c72_0 conda-forge
prompt_toolkit 3.0.48 hd8ed1ab_0 conda-forge
psutil 6.0.0 py312h0bf5046_2 conda-forge
pthread-stubs 0.4 hd74edd7_1002 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pure_eval 0.2.3 pyhd8ed1ab_0 conda-forge
pycparser 2.22 pyhd8ed1ab_0 conda-forge
pygments 2.18.0 pyhd8ed1ab_0 conda-forge
pynndescent 0.5.13 pyhff2d567_0 conda-forge
pyobjc-core 10.3.1 py312hd24fc31_1 conda-forge
pyobjc-framework-cocoa 10.3.1 py312hd24fc31_1 conda-forge
pyparsing 3.2.0 pyhd8ed1ab_1 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.12.7 h739c21a_0_cpython conda-forge
python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
python-fastjsonschema 2.20.0 pyhd8ed1ab_0 conda-forge
python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge
python-tzdata 2024.2 pyhd8ed1ab_0 conda-forge
python_abi 3.12 5_cp312 conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.2 py312h024a12e_1 conda-forge
pyzmq 26.2.0 py312hf8a1cbd_3 conda-forge
qhull 2020.2 h420ef59_5 conda-forge
readline 8.2 h92ec313_1 conda-forge
referencing 0.35.1 pyhd8ed1ab_0 conda-forge
requests 2.32.3 pyhd8ed1ab_0 conda-forge
rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge
rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge
rpds-py 0.20.0 py312he431725_1 conda-forge
scanpy 1.10.3 pyhd8ed1ab_0 conda-forge
scikit-learn 1.5.2 py312h387f99c_1 conda-forge
scipy 1.14.1 py312heb3a901_0 conda-forge
seaborn 0.13.2 hd8ed1ab_2 conda-forge
seaborn-base 0.13.2 pyhd8ed1ab_2 conda-forge
send2trash 1.8.3 pyh31c8845_0 conda-forge
session-info 1.0.0 pyhd8ed1ab_0 conda-forge
setuptools 75.1.0 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sniffio 1.3.1 pyhd8ed1ab_0 conda-forge
soupsieve 2.5 pyhd8ed1ab_1 conda-forge
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
statsmodels 0.14.4 py312h755e627_0 conda-forge
stdlib-list 0.11.0 pyhd8ed1ab_0 conda-forge
tabulate 0.9.0 pyhd8ed1ab_1 conda-forge
tbb 2021.13.0 h7b3277c_0 conda-forge
tenacity 9.0.0 pyhd8ed1ab_0 conda-forge
terminado 0.18.1 pyh31c8845_0 conda-forge
threadpoolctl 3.5.0 pyhc1e730c_0 conda-forge
tinycss2 1.3.0 pyhd8ed1ab_0 conda-forge
tk 8.6.13 h5083fa2_1 conda-forge
tomli 2.0.2 pyhd8ed1ab_0 conda-forge
tornado 6.4.1 py312h024a12e_1 conda-forge
tqdm 4.66.5 pyhd8ed1ab_0 conda-forge
traitlets 5.14.3 pyhd8ed1ab_0 conda-forge
types-python-dateutil 2.9.0.20241003 pyhff2d567_0 conda-forge
typing-extensions 4.12.2 hd8ed1ab_0 conda-forge
typing_extensions 4.12.2 pyha770c72_0 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge
tzdata 2024b hc8b5060_0 conda-forge
umap-learn 0.5.6 py312h81bd7bf_1 conda-forge
uri-template 1.3.0 pyhd8ed1ab_0 conda-forge
urllib3 2.2.3 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge
webcolors 24.8.0 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pyhd8ed1ab_2 conda-forge
websocket-client 1.8.0 pyhd8ed1ab_0 conda-forge
wheel 0.44.0 pyhd8ed1ab_0 conda-forge
widgetsnbextension 4.0.13 pyhd8ed1ab_0 conda-forge
xarray 2024.9.0 pyhd8ed1ab_1 conda-forge
xorg-libxau 1.0.11 hd74edd7_1 conda-forge
xorg-libxdmcp 1.1.5 hd74edd7_0 conda-forge
xz 5.2.6 h57fd34a_0 conda-forge
yaml 0.2.5 h3422bc3_2 conda-forge
zeromq 4.3.5 h9f5b81c_6 conda-forge
zipp 3.20.2 pyhd8ed1ab_0 conda-forge
zstandard 0.23.0 py312h15fbf35_1 conda-forge
zstd 1.5.6 hb46c0d2_0 conda-forge
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