plotBedpe: plots data stored in bed file format
In dphansti/Sushi: Tools for visualizing genomics data

plots data stored in bed file format

plotBedpe(bedpedata, chrom, chromstart, chromend, heights, color = "black",
  colorby = NULL, colorbycol = NULL, colorbyrange = NULL, border = NULL,
  lwdby = NULL, lwdrange = c(1, 5), offset = 0, flip = FALSE, lwd = 1,
  xaxt = "n", yaxt = "n", bty = "n", plottype = "loops",
  maxrows = 10000, height = 0.3, ymax = 1.04, ...)

`bedpedata`	bed paired end data to be plotted
`chrom`	chromosome of region to be plotted
`chromstart`	start position
`chromend`	end position
`heights`	single value or vector specifying the height of the arches to be plotted (only valid when plottype is set to "loops" )
`color`	single value or vector specifying colors of bedpe elements
`colorby`	vector to scale colors by
`colorbycol`	palette to apply color scale to (only valid when colorby is not NULL)
`colorbyrange`	the range of values to apply the color scale to. Values outside that range will be set to the limits of the range.
`lwdby`	vector to scale line widths by
`lwdrange`	the range of values to apply the line width scale to. Values outside that range will be set to the limits of the range.
`offset`	offset of bedpe elements from the x-axis
`flip`	TRUE/FALSE whether the plot should be flipped over the x-axis
`lwd`	linewidth for bedpe elements (only valid when colorby is not NULL)
`xaxt`	A character which specifies the x axis type. See `par`
`yaxt`	A character which specifies the y axis type. See `par`
`bty`	A character string which determined the type of box which is drawn about plots. See `par`
`plottype`	type of plot (acceptable values are 'loops', 'ribbons', or 'lines')
`maxrows`	The maximum number of rows to plot on the y-axis
`height`	the height of the boxes at either end of a bedpe element if plottype is set to 'lines'. Typical vaues range form 0 to 1. (only valid when plottype is set to 'lines')
`ymax`	fraction of max y value to set as height of plot. Only applies when plottype is set to 'loops' or 'ribbons'
`...`	values to be passed to `plot`

data(Sushi_5C.bedpe)

chrom            = "chr11"
chromstart       = 1650000
chromend         = 2350000
pbpe = plotBedpe(Sushi_5C.bedpe,chrom,chromstart,chromend,heights = Sushi_5C.bedpe$score,offset=0,flip=FALSE,bty='n',
lwd=1,plottype="ribbons",colorby=Sushi_5C.bedpe$samplenumber,colorbycol=topo.colors,border="black")
labelgenome(chrom, chromstart,chromend,side=1,scipen=20,n=3,scale="Mb",line=.18,chromline=.5,scaleline=0.5)
legend("topright",inset =0.01,legend=c("K562","HeLa","GM12878"),col=c(topo.colors(3)),pch=19,bty='n',text.font=2)
axis(side=2,las=2,tcl=.2)
mtext("Z-score",side=2,line=1.75,cex=.75,font=2)