Sushi (version 1.10.0)

zoombox: Adds a zoom box to a plot

Description

This function is used on the second plot of a zoom in

Usage

zoombox(zoomregion = NULL, lty = 2, lwd = 1, col = "black", topextend = 2, passthrough = FALSE)

Arguments

zoomregion

Region of another zoom on this plot. Only required if this plot has another zoomregion on it.

lty

line type for box. See par

lwd

line width. See See par

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

Examples

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)