NameError: name 'Tuple' is not defined

[w1973145618]

Describe the bug

To Reproduce
imputed_acc_obj = impute_accessibility(
cistopic_obj,
selected_cells=None,
selected_regions=None,
scale_factor=10**6
)

Error output

NameError Traceback (most recent call last)
Cell In[66], line 3
1 from typing import Tuple
----> 3 imputed_acc_obj = impute_accessibility(
4 cistopic_obj,
5 selected_cells=None,
6 selected_regions=None,
7 scale_factor=10**6
8 )

File ~/anaconda3/Git/pycisTopic/src/pycisTopic/diff_features.py:387, in impute_accessibility(cistopic_obj, selected_cells, selected_regions, scale_factor, chunk_size, project)
377 topic_region = topic_region.to_numpy().astype(np.float32)
379 log.info("Imputing region accessibility")
381 def calculate_imputed_accessibility(
382 topic_region: np.ndarray,
383 cell_topic: np.ndarray,
384 region_names: list,
385 scale_factor: Optional[int],
386 chunk_size: int
--> 387 ) -> Tuple[np.ndarray, list]:
388 """
389 Calculate imputed accessibility in chunks of chunk_size.
390
(...)
411
412 """
413 output_chunk_end = 0

[SeppeDeWinter]

Hi @w1973145618

I fixed this error some days ago, 5416709

Can you try reinstalling pycisTopic?

All the best,

Seppe

[w1973145618]

Hi @w1973145618

I fixed this error some days ago, 5416709

Can you try reinstalling pycisTopic?

All the best,

Seppe

Dear Seppe:
I am happy for you tell me how to do. I followed your method: I reinstalled pycisTopic from GitHub to fix the bug: NameError: name ‘Tuple’ is not defined.This is work. However, now I’ve encountered new problems. I will show you the new problem I’ve encountered.

New bug1：

Describe the bug
NameError: name 'subset_list' is not defined

To Reproduce
plot_metadata(
cistopic_obj,
reduction_name='UMAP',
variables=['log10_unique_fragments_count', 'tss_enrichment', 'Doublet_scores_fragments', 'fraction_of_fragments_in_peaks'],
target='cell', num_columns=4,
text_size=10,
dot_size=5)

Error output
NameError Traceback (most recent call last)
Cell In[48], line 1
----> 1 plot_metadata(
2 cistopic_obj,
3 reduction_name='UMAP',
4 variables=['log10_unique_fragments_count', 'tss_enrichment', 'Doublet_scores_fragments', 'fraction_of_fragments_in_peaks'],
5 target='cell', num_columns=4,
6 text_size=10,
7 dot_size=5)

File ~/anaconda3/Git/pycisTopic/src/pycisTopic/clust_vis.py:571, in plot_metadata(cistopic_obj, reduction_name, variables, target, remove_nan, show_label, show_legend, cmap, dot_size, text_size, alpha, seed, color_dictionary, figsize, num_columns, selected_features, save)
566 plt.subplot(num_rows, num_columns, i)
567 i = i + 1
568 plt.scatter(
569 embedding.iloc[o, 0],
570 embedding.iloc[o, 1],
--> 571 c=subset_list(var_data, o),
572 cmap=cmap,
573 s=dot_size,
574 alpha=alpha,
575 )
576 plt.xlabel(embedding.columns[0])
577 plt.ylabel(embedding.columns[1])

NameError: name 'subset_list' is not defined

New bug2：

Describe the bug
NameError: name 'sparse' is not defined

To Reproduce
plot_imputed_features(
cistopic_obj,
reduction_name='UMAP',
imputed_data=imputed_acc_obj,
features=[markers_dict[x].index.tolist()[0] for x in ['BG', 'GC', 'INH_SST', 'COP']],
scale=False,
num_columns=4
)

Error output
NameError Traceback (most recent call last)
Cell In[78], line 1
----> 1 plot_imputed_features(
2 cistopic_obj,
3 reduction_name='UMAP',
4 imputed_data=imputed_acc_obj,
5 features=[markers_dict[x].index.tolist()[0] for x in ['BG', 'GC', 'INH_SST', 'COP']],
6 scale=False,
7 num_columns=4
8 )

File ~/anaconda3/Git/pycisTopic/src/pycisTopic/clust_vis.py:823, in plot_imputed_features(cistopic_obj, reduction_name, imputed_data, features, scale, cmap, dot_size, alpha, selected_cells, figsize, num_columns, save)
821 except BaseException:
822 feature_data = sklearn.preprocessing.scale(feature_data, axis=1)
--> 823 if isinstance(feature_data, sparse.csr_matrix):
824 color_data = pd.DataFrame(
825 feature_data.transpose().todense(), index=embedding.index.tolist()
826 )
827 else:

NameError: name 'sparse' is not defined

[SeppeDeWinter]

Hi @w1973145618

Yes that was my bad as well. It should be fixed now: 284c5a5.

Can you try reinstalling?

All the best,

Seppe