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:
How can I make it? Can anyone share any code or tutorial?
Thanks,
dpc
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(phylo_obj@bray)
Answered by adamsorbie on September 25, 2021
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