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microbiome / miaViz

Microbiome Analysis Plotting and Visualization
https://microbiome.github.io/miaViz
Artistic License 2.0
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Default ranks #88

Closed antagomir closed 4 months ago

antagomir commented 1 year ago

In plotAbundance() the default rank is set to rank = taxonomyRanks(x)[1].

This can be confusing since the data is aggregated to higher than original level without user intervention.

Perhaps better to have no rank specified by default (using the highest resolution data available): rank=NULL?

himmil commented 1 year ago

If the default for rank is set to NULL, then plotAbundance() has an identical default function to plotExpression() from scater. Is it a problem?

antagomir commented 1 year ago

I dont think it is a problem. It is nevertheless a different function, with some microbiome-specific extensions (I think). The defaults can be the same and that might even be beneficial, for comparison.

antagomir commented 7 months ago

@himmil could you check this with Noah for a practice.