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

statistics

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

How to generate Beta diversity boxplot from phyloseq object?

One Answer

Add your own answers!

Related Questions

mBED has time complexity $O(n lg n)$, claimed by Clustal Omega paper, why?

Sequence alignment using BWT

differential analysis of chip-seq data

Generating 3D coordinates error

Seurat DE t.test

Coronavirus RNA structures?

calculating nucleotide frequency per column

Is it possible for coronavirus or SARS to be synthetic?

Extract sequences from partial Header

Subsetting from seurat object based on orig.ident?

Is there a way to measure cell line similarity using python?

P-value correction when evaluating correlation between gene and miRNA expression

Separating peaks of chip-seq with specific length

How to run MaxQuant in command line mode?

Why does the FASTA sequence for coronavirus look like DNA, not RNA?

How to extract metadata from NCBI’s experiment?

Viral Metagenomics

How to map short sequences to long reads, recovering all multiply-mapped high-quality matches

How identifiable are human omics data and how to mitigate their identifying features?

How to get transcriptome FASTA file for viruses for Kallisto pseudo-alignment?

Ask a Question