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pamRespectsDendro parameter error #12

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daniel-spies opened this issue Dec 15, 2023 · 0 comments
Open

pamRespectsDendro parameter error #12

daniel-spies opened this issue Dec 15, 2023 · 0 comments

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@daniel-spies
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daniel-spies commented Dec 15, 2023

Hi there, thanks for the great tool!

I just wanted to report that if the pamRespectsDendro is set to false cutreeHybrid crashes as it seems to not find df_apply even thought it's loaded when importing dynamicTreeCut

from dynamicTreeCut.dynamicTreeCut import cutreeHybrid
clusters = cutreeHybrid(link, distM=distance, minClusterSize=min_module_size, pamRespectsDendro=False)['labels'] 

will result in the following error:

..cutHeight not given, setting it to 0.8541350079439015  ===>  99% of the (truncated) height range in dendro.
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/spies.daniel/.conda/envs/cellrank/lib/python3.9/site-packages/dynamicTreeCut/dynamicTreeCut.py", line 775, in cutreeHybrid
    nearest = df_apply.apply(np.argmin, UnassdToClustDist, 1)
NameError: name 'df_apply' is not defined

apparently this is linked to potential NaNs as with another dataset it actually worked without any fuss

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