plot_fusion: Plot a fusion event with transcripts, coverage and ideograms.

In stianlagstad/chimeraviz: Visualization tools for gene fusions

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()

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