JarrVis: Visualising Taxa-function relationships from meta-omic data

Abstract

High-throughput sequencing has necessitated and facilitated the development of various computational tools for dissecting the taxonomic structure and molecular function of microbial communities residing in diverse ecological niches. A wide variety of tools and protocols have been developed to process amplicon sequencing as well as meta-omic (metagenomic, metatranscriptomic and genomic) data to generate relative abundances of taxonomic groups or functional categories on a per-sample basis. A key output from many of these protocols is a stratified relative abundance table that specifies the taxonomic contribution to each function. However, there are a very few tools which can effectively visualize the different taxa-function relationships from these stratified outputs. Here we introduce an R Shiny application called JarrVis (Just Another stRatified Rpkm VISualizer) which can visualize the taxa-function relationships resulting from different types of microbiome data. JarrVis can visualize relationships between samples (which can be combined based on metadata categories), the taxa that are detected in these samples (at any given taxonomic level) and the functions encoded by these taxa in an interactive interface. We utilized JarrVis to visualize and examine taxa-function relationships in 1) a 16S amplicon time-series spanning 4 years with samples collected weekly, 2) functions associated with microbial cobalamin biosynthesis and uptake in metagenome-assembled genomes from marine metagenomes and 3) a set of metatrascriptomes from gut samples of patients with Crohns Disease, Ulcerative Colitis and non-IBD controls. Our analysis was able recapitulate already published taxa-function relationships as well as discover novel insights from these publicly available datasets. JarrVis and related scripts and data are available at https://github.com/dhwanidesai/JarrVis.