Description Usage Arguments Examples
This function is used on the second plot of a zoom in
1 2 |
zoomregion |
Region of another zoom on this plot. Only required if this plot has another zoomregion on it. |
lty |
line type for box. See |
lwd |
line width. See See |
col |
Color for zoombox line |
topextend |
How far to exted the lines above the current plot (as a fraction of the plot height) |
passthrough |
TRUE / FALSE whether or not to pass the zoom though this plot. If set to FALSE no horizontal line is drawn on the botoom of the plot |
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 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 | data(Sushi_DNaseI.bedgraph)
data(Sushi_ChIPSeq_CTCF.bedgraph)
# make a layout for all of the plots
layout(matrix(c(1,1,
2,2)
,2, 2, byrow = TRUE))
par(mgp=c(3, .3, 0))
par(mar=c(3,4,2,1))
chrom = "chr11"
chromstart = 1650000
chromend = 2350000
zoomregion1 = c(1955000,1965000)
plotBedgraph(Sushi_DNaseI.bedgraph,chrom,chromstart,chromend,transparency=1.0,color="#5900E5",lwd=1,linecol="#5900E5")
zoomsregion(zoomregion1,col=NA,zoomborder="black",lty=2,lwd=1,extend=c(0.01,0.09),wideextend=0.10,offsets=c(0,0))
labelgenome(chrom,chromstart,chromend,side=1,scipen=20,n=4,line=.18,chromline=.5,scaleline=0.5,scale="Mb")
axis(side=2,las=2,tcl=.2)
mtext("Read Depth",side=2,line=1.75,cex=.75,font=2)
# plot dnaseI data
plotBedgraph(Sushi_DNaseI.bedgraph,chrom,zoomregion1[1],zoomregion1[2],transparency=.50,flip=FALSE,color="#E5001B",linecol="#E5001B")
# plot chip-seq data
plotBedgraph(Sushi_ChIPSeq_CTCF.bedgraph,chrom,zoomregion1[1],zoomregion1[2],transparency=.30,flip=FALSE,color="blue",linecol="blue",overlay=TRUE,rescaleoverlay=TRUE)
# add zoombox
zoombox(zoomregion = NULL,lwd = 1,col="black")
axis(side=2,las=2,tcl=.2)
mtext("Read Depth",side=2,line=1.75,cex=.75,font=2)
# add the genome labels
labelgenome(chrom,zoomregion1[1],zoomregion1[2],side=1,scipen=20,n=3,line=.18,chromline=.5,scaleline=0.5,scale="Mb")
# set the legend colors
transparency = 0.5
col1 = col2rgb("blue")
finalcolor1 = rgb(col1[1],col1[2],col1[3],alpha=transparency * 255,max = 255)
col2 = col2rgb("#E5001B")
finalcolor2 = rgb(col2[1],col2[2],col2[3],alpha=transparency * 255,max = 255)
# add legend
legend("topright",inset=0.025,legend=c("DnaseI","ChIP-seq (CTCF)"),fill=c(finalcolor1,finalcolor2),border=c("blue","#E5001B"),text.font=2,cex=0.75)
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