plotCoverage {chimera} | R Documentation |
A function to plot the coverage of a fusion gene.
plotCoverage(fset, plot.type=c("exons","junctions"), junction.spanning=20, fusion.only=FALSE, xlab="nts", ylab="Coverage", main="", col.box1="red", col.box2="green", ybox.lim=c(-4,-1))
fset |
A fSet object |
plot.type |
exons plot exons coverage as junctions plot coverage of junction between exons |
junction.spanning |
number of nucleotides located upstream and downstream the junction/fusion location |
fusion.only |
if TRUE only fusion coverage is plotted |
xlab |
x-axis label |
ylab |
y-axis label |
main |
Plot title |
col.box1 |
color of the box describing the first gene |
col.box2 |
color of the box describing the second gene |
ybox.lim |
y range defining the height of the box representing the exons |
Raffaele A Calogero
tmp <- importFusionData("fusionmap", paste(find.package(package="chimera"),"/examples/mcf7.FMFusionReport", sep=""), org="hg19") fusion.names <- fusionName(tmp) fusion.names myset <- tmp[[13]] trs <- chimeraSeqs(myset, type="transcripts") myset <- addRNA(myset , trs) tmp.seq <- fusionRNA(myset) myset <- addGA(myset, paste(path.package(package="chimera"),"/examples/mcf7_trs_accepted_hits.bam",sep="")) ga <- fusionGA(myset) plotCoverage(myset, plot.type="exons", col.box1="red", col.box2="green", ybox.lim=c(-4,-1)) plotCoverage(myset, plot.type="junctions", col.box1="red", col.box2="yellow", ybox.lim=c(-4,-1)) plotCoverage(myset, fusion.only=TRUE, col.box1="red", col.box2="yellow", ybox.lim=c(-4,-1))