plot_fusion_transcript_with_protein_domain: Plot a specific fusion transcript with protein domain...

In stianlagstad/chimeraviz: Visualization tools for gene fusions

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()

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