Hi there,
Thanks for these wonderful packages and scverse ecosystem. This is part 1/2 of an error I’m facing. I’m a Python and scverse beginner so I’m struggling to understand the error messages generated in Python - thanks for your patience! 
Expected output:
A plot similar to the one in here
Code used:
ir.pl.vdj_usage(
adata[
adata.obs["cc_aa_identity"].isin(["25", "13", "1119"]), :
],
max_ribbons=None,
max_segments=100,
fig_kws={"figsize": [4,4]},
)
Error:
---------------------------------------------------------------------------
NotImplementedError Traceback (most recent call last)
Cell In[297], line 2
1 # doesn't work
----> 2 ir.pl.vdj_usage(
3 adata[
4 adata.obs["cc_aa_identity"].isin(["25", "13", "1119"]), :
5 ],
6 max_ribbons=None,
7 max_segments=100,
8 fig_kws={"figsize": [4,4]},
9 )
11 # ir.pl.vdj_usage(
12 # adata,
13 # full_combination=False,
(...)
16 # fig_kws={"figsize": [4, 4]},
17 # )
File ~/miniconda3/envs/scirpy/lib/python3.11/site-packages/scirpy/pl/_vdj_usage.py:108, in vdj_usage(adata, vdj_cols, normalize_to, ax, max_segments, max_labelled_segments, max_ribbons, barwidth, draw_bars, full_combination, fig_kws, airr_mod, airr_key, chain_idx_key)
95 chains, airr_variables = zip(
96 *[
97 (f"{arm}_{chain}", airr_variable)
(...)
100 strict=False,
101 )
103 tmp_obs = (
104 params.get_obs([normalize_to]).reindex(params.adata.obs_names)
105 if isinstance(normalize_to, str)
106 else params.adata.obs
107 )
--> 108 df = get_airr(params, airr_variables, chains).assign(
109 # make sure this also works with mudata columns:
110 cell_weights=_normalize_counts(tmp_obs, normalize_to) if isinstance(normalize_to, bool | str) else normalize_to
111 )
112 for col in df.columns:
113 if col.startswith("VJ") or col.startswith("VDJ"):
File ~/miniconda3/envs/scirpy/lib/python3.11/site-packages/scirpy/get/__init__.py:60, in airr(adata, airr_variable, chain, airr_mod, airr_key, chain_idx_key)
57 if not multiple_chains:
58 chain = [chain] # type: ignore
59 return pd.DataFrame(
---> 60 {
61 f"{tmp_chain}_{tmp_var}": _airr_col(
62 params.airr,
63 params.chain_indices,
64 tmp_var,
65 cast(ChainType, tmp_chain),
66 )
67 for tmp_chain, tmp_var in itertools.product(chain, airr_variable)
68 },
69 index=params.adata.obs_names,
70 )
71 else:
72 return pd.Series(
73 _airr_col(params.airr, params.chain_indices, airr_variable, cast(ChainType, chain)),
74 index=params.adata.obs_names,
75 )
File ~/miniconda3/envs/scirpy/lib/python3.11/site-packages/scirpy/get/__init__.py:62, in <dictcomp>(.0)
57 if not multiple_chains:
58 chain = [chain] # type: ignore
59 return pd.DataFrame(
60 {
61 f"{tmp_chain}_{tmp_var}": _airr_col(
---> 62 params.airr,
63 params.chain_indices,
64 tmp_var,
65 cast(ChainType, tmp_chain),
66 )
67 for tmp_chain, tmp_var in itertools.product(chain, airr_variable)
68 },
69 index=params.adata.obs_names,
70 )
71 else:
72 return pd.Series(
73 _airr_col(params.airr, params.chain_indices, airr_variable, cast(ChainType, chain)),
74 index=params.adata.obs_names,
75 )
File ~/miniconda3/envs/scirpy/lib/python3.11/site-packages/scirpy/util/__init__.py:213, in DataHandler.airr(self)
211 """Reference to the awkward array with AIRR information."""
212 if self._airr_key is not None:
--> 213 return cast(ak.Array, self.adata.obsm[self._airr_key])
214 else:
215 raise AttributeError("DataHandler was initialized wihtout airr information")
File ~/miniconda3/envs/scirpy/lib/python3.11/site-packages/anndata/_core/aligned_mapping.py:149, in AlignedViewMixin.__getitem__(self, key)
148 def __getitem__(self, key: str) -> V:
--> 149 return as_view(
150 _subset(self.parent_mapping[key], self.subset_idx),
151 ElementRef(self.parent, self.attrname, (key,)),
152 )
File ~/miniconda3/envs/scirpy/lib/python3.11/functools.py:909, in singledispatch.<locals>.wrapper(*args, **kw)
905 if not args:
906 raise TypeError(f'{funcname} requires at least '
907 '1 positional argument')
--> 909 return dispatch(args[0].__class__)(*args, **kw)
File ~/miniconda3/envs/scirpy/lib/python3.11/site-packages/anndata/_core/views.py:370, in as_view_awkarray(array, view_args)
365 # TODO: See https://github.com/scverse/anndata/pull/647#discussion_r963494798_ for more details and
366 # possible strategies to stack behaviors.
367 # A better solution might be based on xarray-style "attrs", once this is implemented
368 # https://github.com/scikit-hep/awkward/issues/1391#issuecomment-1412297114
369 if type(array).__name__ != "Array":
--> 370 raise NotImplementedError(
371 "Cannot create a view of an awkward array with __array__ parameter. "
372 "Please open an issue in the AnnData repo and describe your use-case."
373 )
374 array = ak.with_parameter(array, _PARAM_NAME, (parent_key, attrname, keys))
375 array = ak.with_parameter(array, "__list__", "AwkwardArrayView")
NotImplementedError: Cannot create a view of an awkward array with __array__ parameter. Please open an issue in the AnnData repo and describe your use-case.
adata
AnnData object with n_obs × n_vars = 3618 × 16185
obs: 'orig.ident', 'nCount_RNA', 'nFeature_RNA', 'decontX_contamination', 'seqType', ... 'contigCellBarcode', 'barcode', 'CTgene', 'CTnt', 'CTaa', 'CTstrict', 'Frequency', 'cloneType', 'ident', 'receptor_type', 'receptor_subtype', 'chain_pairing', 'cc_aa_identity', 'cc_aa_identity_size', 'clone_id', 'clone_id_size', 'VJ_1_junction_aa', 'VDJ_1_junction_aa', 'VJ_2_junction_aa', 'VDJ_2_junction_aa', 'clonal_expansion', 'VJ_1_v_call', 'VDJ_1_v_call', 'VJ_2_v_call', 'VDJ_2_v_call', 'VJ_1_j_call', 'VDJ_1_j_call', 'VJ_2_j_call', 'VDJ_2_j_call'
var: 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'highly_variable_nbatches', 'highly_variable_intersection'
uns: 'X_name', 'chain_indices', 'hvg', 'log1p', 'chain_pairing_colors', 'ir_dist_aa_identity', 'ir_dist_nt_identity', 'cc_aa_identity', 'clonotype_network', 'PatientID_colors', 'clone_id', 'seuratClusters_colors', 'sampleSource_colors', 'repertoire_overlap'
obsm: 'airr', 'chain_indices', 'X_clonotype_network'
layers: 'logcounts'
session info:
Click to view session information
-----
anndata 0.10.8
awkward 2.6.9
matplotlib 3.9.2
natsort 8.4.0
numpy 2.0.2
pandas 2.2.3
scanpy 1.10.3
scipy 1.14.1
scirpy 0.18.1.dev8+g7817ce8
seaborn 0.13.2
session_info 1.0.0
tcrdist NA
-----
Click to view modules imported as dependencies
Levenshtein 0.26.0
PIL 11.0.0
adjustText 1.2.0
asttokens NA
awkward_cpp NA
charset_normalizer 3.4.0
comm 0.2.2
cycler 0.12.1
cython_runtime NA
dateutil 2.9.0.post0
debugpy 1.8.7
decorator 5.1.1
executing 2.1.0
feather 0.4.1
fishersapi 1.0
fsspec 2024.9.0
h5py 3.12.1
hierdiff NA
igraph 0.11.6
importlib_metadata NA
ipykernel 6.29.5
jedi 0.19.1
jinja2 3.1.4
joblib 1.4.2
kiwisolver 1.4.7
legacy_api_wrap NA
llvmlite 0.43.0
markupsafe 3.0.1
matplotlib_inline 0.1.7
mpl_toolkits NA
mudata 0.3.1
networkx 3.4.1
numba 0.60.0
olga NA
packaging 24.1
parasail 1.3.4
parmap NA
parso 0.8.4
patsy 0.5.6
pexpect 4.9.0
platformdirs 4.3.6
pooch v1.8.2
progress 1.6
prompt_toolkit 3.0.48
psutil 6.0.0
ptyprocess 0.7.0
pure_eval 0.2.3
pwseqdist NA
pyarrow 17.0.0
pydev_ipython NA
pydevconsole NA
pydevd 3.1.0
pydevd_file_utils NA
pydevd_plugins NA
pydevd_tracing NA
pygments 2.18.0
pyparsing 3.2.0
pytz 2024.2
rapidfuzz 3.10.0
six 1.16.0
sklearn 1.5.2
squarify NA
stack_data 0.6.3
statsmodels 0.14.4
tcrsampler NA
texttable 1.7.0
threadpoolctl 3.5.0
tornado 6.4.1
tqdm 4.66.5
tracerlib NA
traitlets 5.14.3
typing_extensions NA
wcwidth 0.2.13
yaml 6.0.2
zipdist NA
zipp NA
zmq 26.2.0
zoneinfo NA
-----
IPython 8.28.0
jupyter_client 8.6.3
jupyter_core 5.7.2
-----
Python 3.11.10 | packaged by conda-forge | (main, Oct 16 2024, 01:27:36) [GCC 13.3.0]
Linux-3.10.0-1160.118.1.el7.x86_64-x86_64-with-glibc2.17
-----
Session information updated at 2024-10-18 12:13