zoomsregion: Adds a zoom region to a plot
In PhanstielLab/Sushi: Tools for visualizing genomics data

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

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zoomsregion(region, chrom = NULL, genome = NULL, space = 0.01,
  padding = 0.005, col = NA, zoomborder = "black", lty = 2, lwd = 1,
  extend = 0, wideextend = 0.1, offsets = c(0, 0), highlight = FALSE)

`region`	chromosome start and stop to zoom in on
`chrom`	chromosome of region to be plotted
`genome`	A genome object (2 columns: column 1 = chromosome name, column 2 = length of chromosome). Set to NULL if adding zoom to a plot with only a singe chromosome.
`space`	the space in between each chromosome as a fraction of the width of the plot. Only used when adding a zoomsregion to a plot with multiple chromosomes (e.g. a Manhattan plot)
`padding`	The minimum size of a zoom region (as a fraction of the plot width). If the specified zoom region is too small it will zoom on a region twice this wide cerntered on te specified zoom region.
`col`	Color of the zoom region
`zoomborder`	Color of the border of the zoom region
`lty`	line type of zoom region border. See `plot`
`lwd`	line type of zoom region border. See `plot`
`extend`	single value or vector of 2 values specifying how far the zoom region extend above and below the plot region (as a fraction of the plot height). Note this valu only applies to the narrow portion of the zoom region.
`wideextend`	Value specifying how below the plot region (as a fraction of the plot height) the wide portion of the zoom window starts. Only applicable if highlight is set to FALSE.
`offsets`	vector of 2 values specifying offsets to the left and right side of the wide portion of the zoom window. It may be neccesary to adjust these by trial and error for more complicated layouts. Only applicable if highlight is set to FALSE.
`highlight`	TRUE/FALSE indicating if you are adding a highlight region as opposed to a zoom in. Highlight regions simply draw a box around the region of interest

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)