plot_breakpoints: Function to plot breakpoints of a gene in a sample/cohort

In d3b-center/annoFuse: annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions

Function to plot breakpoints of a gene in a sample/cohort

Description

Function to plot breakpoints of a gene in a sample/cohort

Usage

plot_breakpoints(
  domainDataFrame = NULL,
  exons,
  geneposition = c("Left", "Right"),
  sampleid = NULL,
  fusionname = NULL,
  leftBreakpoint = NULL,
  rightBreakpoint = NULL,
  base_size = 12
)

Arguments

domainDataFrame	A dataframe from star fusion or arriba standardized to run through the filtering steps and get_Pfam_domain() function to get pfam domain annotation per gene
exons	exon level information from gtf availbale in the package exonsToPlot.RDS
geneposition	Position of gene in the fusion allowed values are Left (Gene1A) or Right (Gene1B)
sampleid	id (if multiple provide a character vector) from Sample column of standardized fusion file format
fusionname	value from FusionName column of standardized fusion file format (Gene1A–Gene1B)
leftBreakpoint	If a specific breakpoint needs to be plotted then provide genomic coordinate as LeftBreakpoint
rightBreakpoint	If a specific breakpoint needs to be plotted then provide genomic coordinate as RightBreakpoint
base_size	base size for text in plot ; default is 12

Value

ggplot of gene and breakpoints

Examples

out_annofuse <- system.file("extdata", "PutativeDriverAnnoFuse.tsv", package = "annoFuseData")
sfc <- read.delim(out_annofuse)
exons <- readRDS(system.file("extdata", "exonsToPlot.RDS", package = "annoFuseData"))
bioMartDataPfam <-
  readRDS(system.file("extdata", "pfamDataBioMart.RDS", package = "annoFuseData"))
domainDataFrame <- get_Pfam_domain(
  standardFusioncalls = sfc,
  bioMartDataPfam = bioMartDataPfam,
  keepPartialAnno = TRUE
)
left <- plot_breakpoints(
  sampleid = "BS_044XZ8ST",
  domainDataFrame = domainDataFrame,
  exons = exons,
  geneposition = "Left",
  fusionname = "ANTXR1--BRAF",
  leftBreakpoint = "2:69193415"
)
right <- plot_breakpoints(
  sampleid = "BS_044XZ8ST",
  domainDataFrame = domainDataFrame,
  exons = exons,
  geneposition = "Right",
  fusionname = "ANTXR1--BRAF",
  rightBreakpoint = "7:140787584"
)
ggpubr::ggarrange(left, right, align = "h")

d3b-center/annoFuse documentation built on Oct. 2, 2024, 4:17 a.m.