zoombox {Sushi} | R Documentation |
This function is used on the second plot of a zoom in
zoombox(zoomregion = NULL, lty = 2, lwd = 1, col = "black", topextend = 2, passthrough = FALSE)
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 |
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)