zoombox {Sushi} | R Documentation

## 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)

[Package Sushi version 1.28.0 Index]