plot_fusion {chimeraviz} | R Documentation

## Plot a fusion event with transcripts, coverage and ideograms.

### Description

This function creates a plot with information about transcripts, coverage, location and more.

### Usage

    plot_fusion(
      fusion,
      edb = NULL,
      bamfile = NULL,
      which_transcripts = "exonBoundary",
      ylim = c(0, 1000),
      non_ucsc = TRUE,
      reduce_transcripts = FALSE,
      bedgraphfile = NULL
    )

    plot_fusion_separate(
      fusion,
      edb,
      bamfile = NULL,
      which_transcripts = "exonBoundary",
      ylim = c(0, 1000),
      non_ucsc = TRUE,
      reduce_transcripts = FALSE,
      bedgraphfile = NULL
    )

    plot_fusion_together(
      fusion,
      edb,
      bamfile = NULL,
      which_transcripts = "exonBoundary",
      ylim = c(0, 1000),
      non_ucsc = TRUE,
      reduce_transcripts = FALSE,
      bedgraphfile = NULL
    )

### Arguments

`fusion` | The Fusion object to plot.
`edb` | The ensembldb 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".
`ylim` | Limits for the coverage y-axis.
`non_ucsc` | 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".
`reduce_transcripts` | 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.

### Details

plot_fusion() will dispatch to either plot_fusion_separate() or plot_fusion_together(). plot_fusion_separate() will plot the fusion gene partners in separate graphs shown next to each other, while plot_fusion_together() will plot the fusion gene partners in the same graph with the same x-axis. plot_fusion() will dispatch to plot_fusion_together() if the fusion gene partners are on the same strand, same chromosome and are close together (<=50,000 bp apart).

### Value

Creates a fusion 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 = 1000, height = 750)
    # Plot!
    plot_fusion(
      fusion = fusion,
      bamfile = bamfile5267,
      edb = edb,
      non_ucsc = 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 <- 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 = 1000, height = 750)
    # Plot!
    plot_fusion(
      fusion = fusion,
      bedgraphfile = bedgraphfile,
      edb = edb,
      non_ucsc = TRUE)
    # Close device
    dev.off()

[Package chimeraviz version 1.12.3 Index]