plot_fusion_transcript {chimeraviz} | R Documentation

## Plot possible fusion transcripts based on annotation.

### Description

This function takes a fusion object and an ensembldb object and plots the reduced version of the fusion transcript. This transcript consist of the "mashed together" version of all possible fusion transcripts based on known annotations. If a bamfile is specified, the fusion transcript will be plotted with coverage information.

### Usage

    plot_fusion_transcript(
      fusion,
      edb = NULL,
      bamfile = NULL,
      which_transcripts = "exonBoundary",
      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.
`which_transcripts` | 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".
`bedgraphfile` | A bedGraph file to use instead of the bamfile to plot coverage.

### Details

Note that the transcript database used (the edb object) must have the same seqnames as any bamfile used. Otherwise the coverage data will be wrong.

### Value

Creates a fusion transcript plot.

### Examples

    # Load data and example fusion event
    defuse833ke <- system.file(
      "extdata",
      "defuse_833ke_results.filtered.tsv",
      package="chimeraviz")
    fusions <- import_defuse(defuse833ke, "hg19", 1)
    fusion <- get_fusion_by_id(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!
    plot_fusion_transcript(
      fusion = fusion,
      bamfile = bamfile5267,
      edb = edb)
    # 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 <- import_defuse(defuse833ke, "hg19", 1)
    fusion <- get_fusion_by_id(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!
    plot_fusion_transcript(
      fusion = fusion,
      bamfile = bamfile5267,
      edb = edb)
    # Close device
    dev.off()

[Package chimeraviz version 1.16.1 Index]