In PhanstielLab/BentoBox: Coordinate-Based Genomic Visualization Package for R

knitr::opts_chunk$set(
    fig.align = "center",
    fig.width = 3,
    fig.height = 3,
    collapse = TRUE,
    comment = "#>",
    warning = FALSE,
    message = FALSE
)
library(grid)
library(plotgardener)

plotgardener is designed to be flexibly compatible with typical Bioconductor classes and libraries of genomic data to easily integrate genomic data analysis and visualization. In addition to handling various genomic file types and R objects, many plotgardener functions can also handle GRanges or GInteractions objects as input data. Furthermore, plotgardener does not hard-code any genomic assemblies and can utilize TxDb, OrgDb, and BSgenome objects for various genomic annotations, including gene and transcript structures and names, chromosome sizes, and nucleotide sequences. Furthermore, all cytoband data for ideogram plots is retrieved from the UCSC Genome Browser through AnnotationHub. For standard genomic assemblies (i.e. hg19, hg38, mm10), plotgardener uses a set of default packages that can be displayed by calling defaultPackages():

defaultPackages("hg38")
defaultPackages("hg19")
defaultPackages("mm10")

To see which assemblies have defaults within plotgardener, call genomes():

genomes()

plotgardener functions default to an "hg38" assembly, but can be customized with any of the other genomic assemblies included or a assembly object. To create custom genomic assemblies and combinations of TxDb, orgDb, and BSgenome packages for use in plotgardener functions, we can use the assembly() constructor. For example, we can create our own TxDb from the current human Ensembl release:

library(GenomicFeatures)
TxDb.Hsapiens.Ensembl.GrCh38.103 <- makeTxDbFromEnsembl(
    organism =
        "Homo sapiens"
)

We can now create a new assembly with this TxDb and combinations of other Bioconductor packages. The Genome parameter can is a string to name or describe this assembly. Since the TxDb is now from ENSEMBL, we will change the gene.id field to "ENSEMBL" to map gene IDs and symbols between our TxDb and orgDb objects. Most gene ID types can be found by calling AnnotationDbi::keytypes() on an orgDb.

Ensembl38 <- assembly(
    Genome = "Ensembl.GRCh38.103",
    TxDb = TxDb.Hsapiens.Ensembl.GrCh38.103,
    OrgDb = "org.Hs.eg.db",
    BSgenome = "BSgenome.Hsapiens.NCBI.GRCh38",
    gene.id = "ENSEMBL", display.column = "SYMBOL"
)

This assembly object can now be easily passed into plotgardener functions through the assembly parameter to use custom genomic assembly configurations.

assembly objects are especially handy for changing the type of gene or transcript label of our gene and transcript plots. The default display.column = "SYMBOL", but we could change this value to other available keytypes in the orgDb we are using. For example, if we wanted to display the associated Ensembl IDs of an "hg19" assembly object, we would set display.column = "ENSEMBL":

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(org.Hs.eg.db)
new_hg19 <- assembly(
    Genome = "id_hg19",
    TxDb = "TxDb.Hsapiens.UCSC.hg19.knownGene",
    OrgDb = "org.Hs.eg.db",
    gene.id.column = "ENTREZID",
    display.column = "ENSEMBL"
)
pageCreate(
    width = 5, height = 1.25,
    showGuides = FALSE, xgrid = 0, ygrid = 0
)
genePlot <- plotGenes(
    chrom = "chr2", chromstart = 1000000, chromend = 20000000,
    assembly = new_hg19,
    x = 0.25, y = 0.25, width = 4.75, height = 1
)