plot_fusion_transcript_with_protein_domain {chimeraviz} | R Documentation

## Plot a specific fusion transcript with protein domain annotations

### Description

This function takes a fusion object, an ensembldb object, a bedfile with protein domain data and two specific transcript ids. The function plots the specific fusion transcript along with annotations of protein domains. If a bamfile is specified, the fusion transcript will be plotted with coverage information.

### Usage

    plot_fusion_transcript_with_protein_domain(
      fusion,
      edb = NULL,
      bamfile = NULL,
      bedfile = NULL,
      gene_upstream_transcript = "",
      gene_downstream_transcript = "",
      plot_downstream_protein_domains_if_fusion_is_out_of_frame = FALSE
    )

### 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.
`bedfile` | The bedfile with protein domain data.
`gene_upstream_transcript` | The transcript id for the upstream gene.
`gene_downstream_transcript` | The transcript id for the downstream gene.
`plot_downstream_protein_domains_if_fusion_is_out_of_frame` | Setting this to true makes the function plot protein domains in the downstream gene even though the fusion is out of frame.

### 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 with annotations of protein domains.

### 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)
    # Select transcripts
    gene_upstream_transcript <- "ENST00000434290"
    gene_downstream_transcript <- "ENST00000370031"
    # 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")
    # bedfile with protein domains for the transcripts in this example
    bedfile <- system.file(
      "extdata",
      "protein_domains_5267.bed",
      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_with_protein_domain(
      fusion = fusion,
      edb = edb,
      bamfile = bamfile5267,
      bedfile = bedfile,
      gene_upstream_transcript = gene_upstream_transcript,
      gene_downstream_transcript = gene_downstream_transcript,
      plot_downstream_protein_domains_if_fusion_is_out_of_frame = TRUE)
    # Close device
    dev.off()

[Package chimeraviz version 1.12.3 Index]