plotTranscripts {chimeraviz} | R Documentation

## Plot transcripts for each partner gene in a fusion event.

### Description

This function takes a fusion object and an ensembldb object and plots transcripts for both genes, showing which parts of each genes are included in the fusion event. If the bamfile parameter is set, then the coverage is plotted beneath the transcripts.

### Usage

    plotTranscripts(fusion, edb = NULL, bamfile = NULL,
      whichTranscripts = "exonBoundary", nonUCSC = TRUE, ylim = c(0, 1000),
      reduceTranscripts = FALSE, bedgraphfile = NULL)

### Arguments

`fusion` | The Fusion object to plot.
`edb` | The edb object that will be used to fetch data.
`bamfile` | The bamfile with RNA-seq data.
`whichTranscripts` | This character vector decides which transcripts are to be plotted. Can be "exonBoundary", "withinExon", "withinIntron", "intergenic", or a character vector with specific transcript ids. Default value is "exonBoundary".
`nonUCSC` | Boolean indicating whether or not the bamfile used has UCSC- styled chromosome names (i.e. with the "chr" prefix). Setting this to true lets you use a bamfile with chromosome names like "1" and "X", instead of "chr1" and "chrX".
`ylim` | Limits for the coverage y-axis.
`reduceTranscripts` | Boolean indicating whether or not to reduce all transcripts into a single transcript for each partner gene.
`bedgraphfile` | A bedGraph file to use instead of the bamfile to plot coverage.

### Value

Creates a fusion transcripts plot.

### Examples

    # Load data and example fusion event
    defuse833ke <- system.file(
      "extdata",
      "defuse_833ke_results.filtered.tsv",
      package="chimeraviz")
    fusions <- importDefuse(defuse833ke, "hg19", 1)
    fusion <- getFusionById(fusions, 5267)
    # Load edb
    edbSqliteFile <- system.file(
      "extdata",
      "Homo_sapiens.GRCh37.74.sqlite",
      package="chimeraviz")
    edb <- ensembldb::EnsDb(edbSqliteFile)
    # bamfile with reads in the regions of this fusion event
    bamfile5267 <- system.file(
      "extdata",
      "fusion5267and11759reads.bam",
      package="chimeraviz")
    # Temporary file to store the plot
    pngFilename <- tempfile(
      pattern = "fusionPlot",
      fileext = ".png",
      tmpdir = tempdir())
    # Open device
    png(pngFilename, width = 500, height = 500)
    # Plot!
    plotTranscripts(
      fusion = fusion,
      edb = edb,
      bamfile = bamfile5267,
      nonUCSC = TRUE)
    # Close device
    dev.off()

    # Example using a .bedGraph file instead of a .bam file:
    # Load data and example fusion event
    defuse833ke <- system.file(
      "extdata",
      "defuse_833ke_results.filtered.tsv",
      package="chimeraviz")
    fusions <- importDefuse(defuse833ke, "hg19", 1)
    fusion <- getFusionById(fusions, 5267)
    # Load edb
    edbSqliteFile <- system.file(
      "extdata",
      "Homo_sapiens.GRCh37.74.sqlite",
      package="chimeraviz")
    edb <- ensembldb::EnsDb(edbSqliteFile)
    # bedgraphfile with coverage data from the regions of this fusion event
    bedgraphfile <- system.file(
      "extdata",
      "fusion5267and11759reads.bedGraph",
      package="chimeraviz")
    # Temporary file to store the plot
    pngFilename <- tempfile(
      pattern = "fusionPlot",
      fileext = ".png",
      tmpdir = tempdir())
    # Open device
    png(pngFilename, width = 500, height = 500)
    # Plot!
    plotTranscripts(
      fusion = fusion,
      edb = edb,
      bedgraphfile = bedgraphfile,
      nonUCSC = TRUE)
    # Close device
    dev.off()

[Package chimeraviz version 1.4.3 Index]