I'm using vame 0.5.0 from the main branch. vame.community() is not working as expected, where Cohort Community Bag and the Hierarchy list isn't outputted.
Some changes to improve this function:
-Increase the figure size to be twice as wide to improve visibility.
-Comment out Lines 497-511 in community_analysis.py. For now, let's only support creating the cohort-level dendrogram.
(These last two bullets are to reproduce the original dendrogram outputs)
-Remove all blue circles and text that isn't a leaf.
-Leaf node size should be proportional to motif usage.
luiztauffer
commented
2 weeks ago
I'm using vame 0.5.0 from the main branch. vame.community() is not working as expected, where Cohort Community Bag and the Hierarchy list isn't outputted.
Some changes to improve this function: -Increase the figure size to be twice as wide to improve visibility. -Comment out Lines 497-511 in community_analysis.py. For now, let's only support creating the cohort-level dendrogram. (These last two bullets are to reproduce the original dendrogram outputs) -Remove all blue circles and text that isn't a leaf. -Leaf node size should be proportional to motif usage.
The expected dendrogram figure should look like this. This was created from the original VAME. Cohort_Balanced_Dendrogram.pdf
Here are some sample outputs of the current function :