zoombox: Adds a zoom box to a plot

In Sushi: Tools for visualizing genomics data

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)

Example output

Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric

Loading required package: biomaRt

Sushi documentation built on Nov. 8, 2020, 7:48 p.m.