Heatmap does not respect Ordered Categorical
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Description
I am trying to plot a heatmap to visualize genes that peak at different temporal clusters. I am passing the groupby parameter as the original leiden label transformed into an Ordered Categorical. However, the pl.heatmap API displays the clusters in alphabetic order.
My code and the relative results follows:
# Order of the lineage
lin = ('0', '3', '1', '2', '6', '4')
# Genes to plot
top = ['Malat1', 'Ctdnep1', 'Atxn10', 'Fhl2', 'Etf1']
# Reordering leiden labels using Categorical data type
adata.obs['leiden_res0.6'] = adata.obs['leiden_res0.6'].cat.reorder_categories(list(lin), ordered=True)
# Plotting
sc.pl.heatmap(adata, var_names=top, groupby='leiden_res0.6', cmap='viridis')
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Research direction
Start by reproducing the supplied sc.pl.heatmap example with the ordered categorical leiden_res0.6 and inspect the heatmap implementation's groupby handling. Confirm that the plotted cluster order follows the categorical order rather than alphabetical order, then verify the behavior with the relevant heatmap tests if present.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data-visualization
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100