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

plots data stored in bed file format

plotBedgraph(signal, chrom, chromstart, chromend, range = NULL,
  color = SushiColors(2)(2)[1], lwd = 1, linecolor = NA,
  addscale = FALSE, overlay = FALSE, rescaleoverlay = FALSE,
  transparency = 1, flip = FALSE, xaxt = "none", yaxt = "none",
  xlab = "", ylab = "", xaxs = "i", yaxs = "i", bty = "n",
  ymax = 1.04, colorbycol = NULL, ...)

`signal`	signal track data to be plotted (in bedgraph format)
`chrom`	chromosome of region to be plotted
`chromstart`	start position
`chromend`	end position
`range`	y-range to plpt ( c(min,max) )
`color`	color of signal track
`lwd`	color of line outlining signal track. (only valid if linecol is not NA)
`linecolor`	color of line outlining signal track. use NA for no outline
`addscale`	TRUE/FALSE whether to add a y-axis
`overlay`	TRUE / FALSE whether this data should be plotted on top of an existing plot
`rescaleoverlay`	TRUE/FALSE whether the new plot shold be rescaled based on the maximum value to match the existing plot (only valid when overlay is set to 'TRUE')
`transparency`	Value between 0 and 1 indication the degree of transparency of the plot
`flip`	TRUE/FALSE whether the plot should be flipped over the x-axis
`xaxt`	A character which specifies the x axis type. See `par`
`yaxt`	A character which specifies the y axis type. See `par`
`xlab`	Label for the x-axis
`ylab`	Label for the y-axis
`xaxs`	Must be set to 'i' for appropriate integration into Sushi plots. See `par`
`yaxs`	Must be set to 'i' for appropriate integration into Sushi plots. See `par` plottype
`bty`	A character string which determined the type of box which is drawn about plots. See `par`
`ymax`	fraction of max y value to set as height of plot.
`colorbycol`	palette to use to shade the signal track plot. Only applicable when overlay is set to FALSE.
`...`	values to be passed to `plot`

data(Sushi_ChIPSeq_CTCF.bedgraph)
data(Sushi_DNaseI.bedgraph)

chrom            = "chr11"
chromstart       = 1955000
chromend         = 1965000

plotBedgraph(Sushi_ChIPSeq_CTCF.bedgraph,chrom,chromstart,chromend,transparency=.50,flip=FALSE,color="blue",linecol="blue")
plotBedgraph(Sushi_DNaseI.bedgraph,chrom,chromstart,chromend,transparency=.50,flip=FALSE,color="#E5001B",linecol="#E5001B",overlay=TRUE,rescaleoverlay=TRUE)
labelgenome(chrom,chromstart,chromend,side=1,scipen=20,n=3,line=.18,chromline=.5,scaleline=0.5,scale="Mb")

transparency = 0.5
col1 = col2rgb("blue")
finalcolor1 = rgb(col1[1],col1[2],col1[3],alpha=transparency * 255,maxColorValue = 255)
col2 = col2rgb("#E5001B")
finalcolor2 = rgb(col2[1],col2[2],col2[3],alpha=transparency * 255,maxColorValue = 255)

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)