How to make alpha diversity boxplot?
How to make alpha diversity boxplot? I am trying to perform alpha diversity and I performed scatter plot for shannon measure,How can I make boxplot??
meta.physeq = sample_data(meta)
tax <- otu_table(tax,taxa_are_rows=FALSE)
physeq.alpha = phyloseq(ASV, tax, meta.physeq)
sample_data(physeq.alpha)$shannon.physeq <- estimate_richness(physeq.alpha, measures="Shannon")
plot_richness(physeq.alpha, measures="Shannon")
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Use
plot_richness()directly with your phyloseq object instead estimate_richness, define "x=Treatment", with your groups-treatments, etc.so no boxplot function? what do you mean by x=Treatment? do you mean groups of meta data? please write your code to make it clearer to me
yes, you need a function from ggplot2.