View source: R/plot_breakpoints.R
plot_breakpoints | R Documentation |
Function to plot breakpoints of a gene in a sample/cohort
plot_breakpoints( domainDataFrame = NULL, exons, geneposition = c("Left", "Right"), sampleid = NULL, fusionname = NULL, leftBreakpoint = NULL, rightBreakpoint = NULL, base_size = 12 )
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 |
ggplot of gene and breakpoints
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")
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