How top do you pick 20 features in association.plot() function?

zellerlab / siamcat

R package for Statistical Inference of Associations between Microbial Communities And host phenoType

https://siamcat.embl.de/

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How top do you pick 20 features in association.plot() function? #41

Closed fernando-aq closed 1 year ago

fernando-aq commented 1 year ago

Hi, I am wondering how the top N features are selected in your association.plot(max.show = N) function?

Is it based on absolute fold change? or any other parameters?

jakob-wirbel commented 1 year ago

Hi @fernando-aq It depends on how you sort the table. By default, the features will be sorted by generalized fold change, so the N features with the largest absolute fold change will be chosen (if you have more than max.show significant features). You can also just extract the association results using associations(sc.obj) and then investigate the whole table with other R functions that you like Cheers, Jakob