ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes

• Published in: BMC bioinformatics 2022-01, Vol.23 (1), p.33-33, Article 33
• Main Authors: Anand, Lakshay, Rodriguez Lopez, Carlos M
• Format: Article
• Language: English
• Subjects: Analysis; Annotations; Archives & records; Bioinformatics; Chromatin; Chromosome mapping; Chromosomes; Chromosomes - genetics; Computational Biology; Datasets; Diploids; DNA methylation; Economic aspects; Gene expression; Gene mapping; Genome; Genome visualization; Genomes; Genomic analysis; Genomics; Genotypes; High-throughput screening (Biochemical assaying); Homology; Innovations; JavaScript; Methods; Microsatellites; Multi-omics data visualization; Next-generation sequencing; Peptide mapping; Polyploidy; R package; Software; Technology application; Transcriptomics; Visualization
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-021-04556-z

The recent advancements in high-throughput sequencing have resulted in the availability of annotated genomes, as well as of multi-omics data for many living organisms. This has increased the need for graphic tools that allow the concurrent visualization of genomes and feature-associated multi-omics data on single publication-ready plots. We present chromoMap, an R package, developed for the construction of interactive visualizations of chromosomes/chromosomal regions, mapping of any chromosomal feature with known coordinates (i.e., protein coding genes, transposable elements, non-coding RNAs, microsatellites, etc.), and chromosomal regional characteristics (i.e. genomic feature density, gene expression, DNA methylation, chromatin modifications, etc.) of organisms with a genome assembly. ChromoMap can also integrate multi-omics data (genomics, transcriptomics and epigenomics) in relation to their occurrence across chromosomes. ChromoMap takes tab-delimited files (BED like) or alternatively R objects to specify the genomic co-ordinates of the chromosomes and elements to annotate. Rendered chromosomes are composed of continuous windows of a given range, which, on hover, display detailed information about the elements annotated within that range. By adjusting parameters of a single function, users can generate a variety of plots that can either be saved as static image or as HTML documents. ChromoMap's flexibility allows for concurrent visualization of genomic data in each strand of a given chromosome, or of more than one homologous chromosome; allowing the comparison of multi-omic data between genotypes (e.g. species, varieties, etc.) or between homologous chromosomes of phased diploid/polyploid genomes. chromoMap is an extensive tool that can be potentially used in various bioinformatics analysis pipelines for genomic visualization of multi-omics data.