Visualizing Standalone Dendrogram and Merging Similar Nodes
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- Python
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Description
I would like to visualize a dendrogram from scanpy.pl.heatmap() without the heatmap, grouped by louvain clusters. It would be nice to have the louvain clusters as the x-axis and the y-axis representative of OOBE or some other metric for cluster scores (similar to Seurat).
Is there some obvious method for doing this that I have not seen? I realize that adata.uns['dendrogram'] contains dendrogram information; however, I am unsure of how to use the information to generate a dendrogram within scanpy.
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First steps
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Research direction
Start by reading scanpy.pl.heatmap() and the dendrogram information stored in adata.uns['dendrogram']; the issue does not name a source file or test. Clarify how standalone visualization should group louvain clusters and represent cluster scores, then define completion around producing the requested dendrogram without the heatmap.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, data-visualization
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100