Plot gene region

Visualize the gene model for a gene of interest, or for all genes in a provided region, and/or show one or more coverage tracks based on bigwig file(s).

plotGeneRegion(
  gtf = "",
  granges = NULL,
  chr = "",
  start = NA_real_,
  end = NA_real_,
  showgene = "",
  bigwigFiles = "",
  bigwigCond = "",
  geneTrackTitle = "Genes",
  transcriptIdColumn = "transcript_id",
  geneIdColumn = "gene_id",
  geneSymbolColumn = "gene_name",
  lowerPadding = 0.15,
  upperPadding = 0.05,
  colorByStrand = FALSE,
  featureColors = c(plusmain = "#0E14D0", minusmain = "#D0350E", plusother = "#9E9BEB",
    minusother = "#DA907E"),
  condColors = NULL,
  scaleDataTracks = FALSE,
  plotTitle = NULL,
  ...
)

Arguments

gtf

Character scalar, path to gtf file (tested with Ensembl/Gencode files).

granges

GRanges object, typically generated from a GTF file using the prepareGTF function. This is an alternative to providing the link to the gtf file directly, and will take precedence over the gtf argument if provided.

chr

Character scalar, name of the chromosome to show.

start, end

Numeric scalars, start and end position of the region to show.

showgene

Character scalar, the gene ID/name to display. Will take precedence over positional range specification if provided.

bigwigFiles

Named character vector, paths to bigwig files.

bigwigCond

Named character vector, the grouping of the bigwig files (used for coloring of the coverage tracks).

geneTrackTitle

Character scalar, name of the gene track.

transcriptIdColumn

Character scalar, the column in the gtf file that contains the transcript ID. Passed to prepareGTF.

geneIdColumn

Character scalar, the column in the gtf file that contains the gene ID. Passed to prepareGTF.

geneSymbolColumn

Character scalar, the column in the gtf file that contains the gene symbol (if available). Set to "" if not available (in which case the gene IDs will be used in its place). Passed to prepareGTF.

lowerPadding, upperPadding

Numeric scalars, setting the amount of padding in the lower and upper range of the plot, respectively. For example, a value of 0.05 will expand the range by 0.05 * (max coordinate - min coordinate) in the specified direction.

colorByStrand

Logical scalar, determining whether gene features are colored by the annotated strand.

featureColors

Named character vector of length 4, with elements plusmain, minusmain, plusother, minusother, giving the colors to use for the features if colorByStrand is TRUE.

condColors

Either NULL or a named character vector (with the same names as the unique values of bigwigCond), giving the colors to use for the coverage tracks if bigwigCond is provided.

scaleDataTracks

Logical scalar, indicating whether the data tracks should be scaled to have the same y-axis limits.

plotTitle

Character scalar, the title of the final plot. If NULL (the default), it will be automatically defined based on the displayed gene or region.

...

Additional arguments to be passed to Gviz::plotTracks.

Details

The gene annotation can be provided either as a path to a gtf file, or as a GRanges object (generated using the prepareGTF function to ensure compatibility). The region to display can be determined either by specifying a gene (ID or symbol) or by specifying a viewing range (chromosome, start and end positions).

Author

Charlotte Soneson

Examples

if (requireNamespace("Gviz", quietly = TRUE)) {
    gtffile <- system.file("extdata/plotGeneRegion/mm10_ensembl98.gtf", 
                           package = "swissknife")
    plotGeneRegion(gtf = gtffile, 
                   showgene = "Tnfaip3")
               
    bwf <- system.file("extdata/plotGeneRegion/mnase_mm10.bw", 
                       package = "swissknife")
    names(bwf) <- "bwf1"
    plotGeneRegion(gtf = gtffile, 
                   bigwigFiles = bwf,
                   chr = "chr10", start = 20000000, end = 20005000)
    plotGeneRegion(bigwigFiles = bwf,
                   chr = "chr10", start = 20000000, end = 20005000)
               
    bwf2 <- c(bwf, bwf)
    names(bwf2) <- c("bwf1", "bwf2")
    bwc2 <- c("c1", "c2")
    names(bwc2) <- names(bwf2)
    plotGeneRegion(gtf = gtffile, bigwigFiles = bwf2, bigwigCond = bwc2, 
                   showgene = "Map3k5")
}