AttributeError: 'Ingest' object has no attribute '_pca_use_hvg' #3074
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?
Attempted label transfer using ingest, using the example code on the docs page
The fix is trivial (you must run sc.pp.pca(adata_ref) as well), but the error message is cryptic so I got stuck for a bit! I'll create the PR too.
Minimal code sample
import scanpy as sc
import pandas as pd
sc.settings.verbosity = 1 # verbosity: errors (0), warnings (1), info (2), hints (3)
sc.logging.print_versions()
sc.settings.set_figure_params(dpi=80, frameon=False, figsize=(3, 3), facecolor="white")
adata_ref = sc.datasets.pbmc3k_processed()
adata = sc.datasets.pbmc68k_reduced()
var_names = adata_ref.var_names.intersection(adata.var_names)
adata_ref = adata_ref[:, var_names]
adata = adata[:, var_names]
# start from scratch
del adata.obs["louvain"]
adata.uns = {}
adata_ref.uns = {}
# example code for ingest function:
sc.pp.neighbors(adata_ref)
sc.tl.umap(adata_ref)
sc.tl.ingest(adata, adata_ref, obs="louvain")Error output
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[11], line 23
21 sc.pp.neighbors(adata_ref)
22 sc.tl.umap(adata_ref)
---> 23 sc.tl.ingest(adata, adata_ref, obs="louvain")
File ~/miniconda3/envs/sc/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 ~/miniconda3/envs/sc/lib/python3.12/site-packages/scanpy/tools/_ingest.py:141, in ingest(adata, adata_ref, obs, embedding_method, labeling_method, neighbors_key, inplace, **kwargs)
138 labeling_method = labeling_method * len(obs)
140 ing = Ingest(adata_ref, neighbors_key)
--> 141 ing.fit(adata)
143 for method in embedding_method:
144 ing.map_embedding(method)
File ~/miniconda3/envs/sc/lib/python3.12/site-packages/scanpy/tools/_ingest.py:404, in Ingest.fit(self, adata_new)
401 self._obsm = _DimDict(adata_new.n_obs, axis=0)
403 self._adata_new = adata_new
--> 404 self._obsm["rep"] = self._same_rep()
File ~/miniconda3/envs/sc/lib/python3.12/site-packages/scanpy/tools/_ingest.py:371, in Ingest._same_rep(self)
369 adata = self._adata_new
370 if self._n_pcs is not None:
--> 371 return self._pca(self._n_pcs)
372 if self._use_rep == "X":
373 return adata.X
File ~/miniconda3/envs/sc/lib/python3.12/site-packages/scanpy/tools/_ingest.py:361, in Ingest._pca(self, n_pcs)
359 X = self._adata_new.X
360 X = X.toarray() if issparse(X) else X.copy()
--> 361 if self._pca_use_hvg:
362 X = X[:, self._adata_ref.var["highly_variable"]]
363 if self._pca_centered:
AttributeError: 'Ingest' object has no attribute '_pca_use_hvg'Versions
-----
anndata 0.10.7
scanpy 1.10.1
-----
PIL 10.3.0
anyio NA
arrow 1.3.0
asttokens NA
attr 23.2.0
attrs 23.2.0
babel 2.14.0
brotli 1.1.0
certifi 2024.02.02
cffi 1.16.0
charset_normalizer 3.3.2
colorama 0.4.6
comm 0.2.2
cycler 0.12.1
cython_runtime NA
dateutil 2.9.0
debugpy 1.8.1
decorator 5.1.1
defusedxml 0.7.1
executing 2.0.1
fastjsonschema NA
fqdn NA
h5py 3.11.0
idna 3.7
igraph 0.10.8
ipykernel 6.29.3
ipywidgets 8.1.2
isoduration NA
jedi 0.19.1
jinja2 3.1.3
joblib 1.4.0
json5 0.9.25
jsonpointer 2.4
jsonschema 4.21.1
jsonschema_specifications NA
jupyter_events 0.10.0
jupyter_server 2.14.0
jupyterlab_server 2.27.0
kiwisolver 1.4.5
legacy_api_wrap NA
leidenalg 0.10.2
llvmlite 0.42.0
markupsafe 2.1.5
matplotlib 3.8.4
matplotlib_inline 0.1.7
mpl_toolkits NA
natsort 8.4.0
nbformat 5.10.4
numba 0.59.1
numpy 1.26.4
overrides NA
packaging 24.0
pandas 1.5.3
parso 0.8.4
pickleshare 0.7.5
platformdirs 4.2.0
prometheus_client NA
prompt_toolkit 3.0.42
psutil 5.9.8
pure_eval 0.2.2
pycparser 2.22
pydev_ipython NA
pydevconsole NA
pydevd 2.9.5
pydevd_file_utils NA
pydevd_plugins NA
pydevd_tracing NA
pygments 2.17.2
pynndescent 0.5.12
pyparsing 3.1.2
pythonjsonlogger NA
pytz 2024.1
referencing NA
requests 2.31.0
rfc3339_validator 0.1.4
rfc3986_validator 0.1.1
rpds NA
scipy 1.13.0
send2trash NA
session_info 1.0.0
six 1.16.0
sklearn 1.4.2
sniffio 1.3.1
socks 1.7.1
stack_data 0.6.2
texttable 1.7.0
threadpoolctl 3.4.0
tornado 6.4
tqdm 4.66.2
traitlets 5.14.3
umap 0.5.5
uri_template NA
urllib3 2.2.1
wcwidth 0.2.13
webcolors 1.13
websocket 1.7.0
yaml 6.0.1
zmq 26.0.2
-----
IPython 8.22.2
jupyter_client 8.6.1
jupyter_core 5.7.2
jupyterlab 4.1.6
notebook 7.1.3
-----
Python 3.12.3 | packaged by conda-forge | (main, Apr 15 2024, 18:38:13) [GCC 12.3.0]
Linux-5.4.0-150-generic-x86_64-with-glibc2.27
-----
Session information updated at 2024-05-22 17:19