plot_transcripts: Plot transcripts for each partner gene in a fusion event.

In stianlagstad/chimeraviz: Visualization tools for gene fusions

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

plot_transcripts(
  fusion,
  edb = NULL,
  bamfile = NULL,
  which_transcripts = "exonBoundary",
  non_ucsc = TRUE,
  ylim = c(0, 1000),
  reduce_transcripts = 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.
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".
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".
ylim	Limits for the coverage y-axis.
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.

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 <- 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_transcripts(
  fusion = fusion,
  edb = edb,
  bamfile = bamfile5267,
  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 = 500, height = 500)
# Plot!
plot_transcripts(
  fusion = fusion,
  edb = edb,
  bedgraphfile = bedgraphfile,
  non_ucsc = TRUE)
# Close device
dev.off()

stianlagstad/chimeraviz documentation built on Dec. 3, 2023, 8:11 p.m.