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aertslab / pycisTopic

pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
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NameError: name 'subset_list' is not defined #124

Open w1973145618 opened 6 months ago

w1973145618 commented 6 months ago

Describe the bug A clear and concise description of what the bug is.

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 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

Expected behavior I reinstalled pycisTopic yesterday to fix a bug: NameError: name ‘Tuple’ is not defined, but now I’ve encountered a new bug.

SeppeDeWinter commented 6 months ago

Hi @w1973145618

Yes, that was my bad. It should be fixed now https://github.com/aertslab/pycisTopic/commit/284c5a53cc7e2f2e85b76f68f0612e0c0a98d29a.

Could you try reinstalling?

All the best,

Seppe