TypeError: 'NoneType' object is not callable

[sun-fei2026]

Dear team,
When I run the data.plt.paga_plot, it shows: "TypeError: 'NoneType' object is not callable." What could be the possible reasons?
Thanks,
sunfei

data.plt.paga_plot(
... adjacency='connectivities_tree', # keyword to use for paga or paga tree
... threshold=0.01, # prune edges lower than threshold
... layout='fr' # the method to layout each node
... )
Traceback (most recent call last):
File "", line 1, in
File "/home/sunfei/.conda/envs/stereo_env/lib/python3.8/site-packages/stereo/plots/decorator.py", line 52, in wrapped
fig: Figure = func(*args, **kwargs)
TypeError: 'NoneType' object is not callable
stereo_env.version
'1.6.2'

The full code that I executed is shown below：
import os
import stereo as stereo_env
import warnings
warnings.filter
warnings('ignore')

base_dir = "/mnt/sdb/sunfei/stomics/Y01502PD/Mouse_Brain/feature_expression"
os.chdir(base_dir)

read data

data = stereo_env.io.read_h5ad('/mnt/sdb/sunfei/stomics/Multi_Sample/06.Time_Series_analysis/AnnData_075/Embyro_E9.5.h5ad')

preprocessing

data.tl.cal_qc()
data.tl.raw_checkpoint()
data.tl.normalize_total(target_sum=1e4)
data.tl.log1p()

hvg

data.tl.highly_variable_genes(min_mean=0.0125, max_mean=3, min_disp=0.5, res_key='highly_variable_genes', n_top_genes=None)

data.tl.scale(zero_center=False)

embedding

data.tl.pca(use_highly_genes=True, hvg_res_key='highly_variable_genes', n_pcs=20, res_key='pca', svd_solver='arpack')
data.tl.neighbors(pca_res_key='pca', n_pcs=30, res_key='neighbors', n_jobs=-1)
data.tl.umap(pca_res_key='pca', neighbors_res_key='neighbors', res_key='umap')

data.tl.paga(groups='annotation', neighbors_key='neighbors')

data.tl.result['paga']

#PAGA可视化
data.plt.paga_plot(
adjacency='connectivities_tree', # keyword to use for paga or paga tree
threshold=0.01, # prune edges lower than threshold
layout='fr' # the method to layout each node
)

[wanruiwen-genomics-cn]

Dear @sun-fei2026,

Thank you for reporting this issue!

Short answer: This is a bug in the plot function registration mechanism in PlotCollection.__getattr__. When the internal lookup for paga_plot returns None, it gets incorrectly wrapped by the download decorator, leading to the TypeError: 'NoneType' object is not callable error.

---

Assessment

• Type: bug
• Severity: medium
• Affected module: stereo/plots/plot_collection.py

What Is Happening

When you call data.plt.paga_plot(...), Python invokes PlotCollection.__getattr__('paga_plot') to dynamically resolve the plot function. This method calls PlotBase.get_attribute_helper() to look up the paga_plot method from the PlotPaga class.

If get_attribute_helper() returns None (which can happen if the PlotPaga class was not properly loaded — for example, due to a partial import failure in stereo/plots/__init__.py), the code in __getattr__ still applies the download decorator to the None value. This creates a wrapper function around None. When the wrapper is later called, it tries to execute None(*args, **kwargs), resulting in the TypeError: 'NoneType' object is not callable error at line 52 of decorator.py.

Is This Expected?

No. The code should check that the resolved function is not None before wrapping it with the download decorator, and should raise a clear AttributeError instead.

Recommended Workflow

Step 1: Update to a version with this fix once it is merged. The fix adds a proper None check in PlotCollection.__getattr__ so that a missing plot function produces a clear error message instead of the confusing TypeError.

Step 2: As a workaround, verify that all optional dependencies for the plots module are installed (particularly igraph, networkx, etc.) and ensure there are no import errors when loading Stereopy.

Notes

• The root cause is a missing guard in PlotCollection.__getattr__ that allows download(None) to be called.
• The paga_plot function itself (in stereo/plots/plot_paga.py) is correctly implemented — the issue is in the dynamic resolution layer.
• A fix PR will be submitted shortly.

Maintainer Note

The fix is localized to stereo/plots/plot_collection.py in the __getattr__ method. The None check must be added before the download decorator is applied. The get_attribute_helper method in plot_base.py should also be reviewed to ensure it fails loudly rather than returning None silently.

Please let us know if you have further questions!

Best regards,
Stereopy Maintainer

[wanruiwen-genomics-cn]

A fix has been submitted: #456

This PR addresses the root cause described above by adding a proper None check in PlotCollection.__getattr__ before the download decorator is applied. Please review when convenient.