Refactor BasePlot not to create a dataframe representation of the data

What kind of feature would you like to request?

Additional function parameters / changed functionality / changed defaults?

Please describe your wishes

See #3717 for what prompted me to look at this code.

Currently BasePlot creates a in-memory copy as a dataframe of the main data of interest (obsm, X, layers etc.):

scanpy/src/scanpy/plotting/_baseplot_class.py

Lines 148 to 157 in 0b82c93

    
           self.categories, self.obs_tidy = _prepare_dataframe( 
        
               adata, 
        
               self.var_names, 
        
               groupby, 
        
               use_raw=use_raw, 
        
               log=log, 
        
               num_categories=num_categories, 
        
               layer=layer, 
        
               gene_symbols=gene_symbols, 
        
           )

I believe this to be unnecessary as this dataframe is only ever used for groupby operations, for which we have a zero-copy solution in https://scanpy.readthedocs.io/en/latest/generated/scanpy.get.aggregate.html

Thus we should

Refactor Baseplot not to create a copy
Use the https://scanpy.readthedocs.io/en/latest/generated/scanpy.get.aggregate.html for aggregation
Ensure this doesn't affect performance
Integrate (feat): sc.get.aggregate via dask #3700

I'd like to work on this issue, will submit a PR soon.

@dorzhey

wooo great thanks @dorzhey !

@ilan-gold

Hi @ilan-gold @flying-sheep noticed this has bounced across a few milestones and doesn't currently show a linked PR. Is this still something you'd want a contribution on, given the _v2/holoviz plotting work in progress? Happy to pick it up if so, or take a pointer elsewhere if this one's lower priority now.

Ah sorry for no reaction. We still take contributions. The plan is that the old plotting module becomes a very lightly maintained extra package at some point

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Refactor `BasePlot` not to create a dataframe representation of the data #3718

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	self.categories, self.obs_tidy = _prepare_dataframe(
	adata,
	self.var_names,
	groupby,
	use_raw=use_raw,
	log=log,
	num_categories=num_categories,
	layer=layer,
	gene_symbols=gene_symbols,
	)

Refactor BasePlot not to create a dataframe representation of the data #3718

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What kind of feature would you like to request?

Please describe your wishes

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dorzhey commented on Jul 29, 2025

ilan-gold commented on Jul 29, 2025

srikarjy commented on Aug 6, 2026

flying-sheep commented on Oct 2, 2026

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Refactor `BasePlot` not to create a dataframe representation of the data #3718