plot_fusion_transcripts_graph {chimeraviz} | R Documentation

## Graph plot of possible fusion transcripts.

### Description

This function takes a fusion object and a TranscriptDb object and plots a graph showing the possible fusion transcripts.

### Usage

    plot_fusion_transcripts_graph(
      fusion,
      edb = NULL,
      which_transcripts = "exonBoundary",
      rankdir = "TB"
    )

### Arguments

`fusion` | The Fusion object to plot.
`edb` | The edb object that will be used to fetch 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".
`rankdir` | Choose whether the graph should be plotted from left to right ("LR"), or from top to bottom ("TB"). This parameter is given to Rgraphviz::plot().

### Value

Creates a fusion transcripts graph 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)
    # 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_transcripts_graph(
      fusion = fusion,
      edb = edb)
    # Close device
    dev.off()

[Package chimeraviz version 1.12.3 Index]