How to generate Beta diversity boxplot from phyloseq object?

Bioinformatics Asked on September 25, 2021

I am working with profiled metagenomic taxonomy abundance data. I want to generate beta diversity (bray-curtis) boxplot from a phyloseq object where two groups (control and test) will be shown. Something like this figure:

enter image description here

How can I make it? Can anyone share any code or tutorial?


One Answer

You could convert the phyloseq object to a dataframe and just plot it using base R or ggplot2. I'm not exactly sure what the bray curtis df will be called but you can access it using the @ notation then convert with data.frame e.g.

bray_for_plot <- data.frame([email protected])

Answered by adamsorbie on September 25, 2021

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