plot_fusion_reads: Create a plot of the reads supporting the given fusion.

Description Usage Arguments Details Value See Also Examples

View source: R/plot_fusion_reads.R

Description

This function takes a Fusion object and plots the reads supporting the fusion on top of the fusion sequence (fusion@junction_sequence), provided that add_fusion_reads_alignment() has been run earlier in order to add fusion reads alignment data to the fusion object.

Usage

1
plot_fusion_reads(fusion, show_all_nucleotides = TRUE, nucleotide_amount = 10)

Arguments

fusion

The Fusion object to plot.

show_all_nucleotides

Boolean indicating whether or not to show all nucleotides. If FALSE, then only nucleotide_amount amount of nucleotides will be shown on each end of the fusion junction. If TRUE, then the whole fusion junction sequence will be shown.

nucleotide_amount

The number of nucleotides to show on each end of the fusion junction sequence. Defaults to 10. Only applicable if show_all_nucleotides is set to TRUE.

Details

Note that the package used for plotting, Gviz, is strict on chromosome names. If the plot produced doesn't show the reads, the problem might be solved by naming the fusion sequence "chrNA".

Value

Creates a fusion reads plot.

See Also

add_fusion_reads_alignment

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
# Load data
defuseData <- system.file(
  "extdata",
  "defuse_833ke_results.filtered.tsv",
  package="chimeraviz")
fusions <- import_defuse(defuseData, "hg19", 1)
# Find the specific fusion we have aligned reads for
fusion <- get_fusion_by_id(fusions, 5267)
bamfile <- system.file(
  "extdata",
  "5267readsAligned.bam",
  package="chimeraviz")
# Add the bam file of aligned fusion reads to the fusion object
fusion <- add_fusion_reads_alignment(fusion, bamfile)
# Temporary file to store the plot
pngFilename <- tempfile(
  pattern = "fusionPlot",
  fileext = ".png",
  tmpdir = tempdir())
# Calculate image size based on supporting reads and lenght of junction
# sequence.
imageWidth <- (nchar(partner_gene_junction_sequence(upstream_partner_gene(fusion))) +
  nchar(partner_gene_junction_sequence(downstream_partner_gene(fusion)))) * 15
imageHeight <- (fusion_split_reads_count(fusion)+fusion_spanning_reads_count(fusion)) * 20
# Open device
png(pngFilename, width = imageWidth, height = imageHeight)
# Now we can plot
plot_fusion_reads(fusion)
# Close device
dev.off()

chimeraviz documentation built on April 29, 2020, 5:38 a.m.