plotBed: plots data stored in bed file format
In PhanstielLab/Sushi: Tools for visualizing genomics data

plots data stored in bed file format

plotBed(beddata, chrom, chromstart, chromend, type = "region",
  colorby = NULL, colorbycol = NULL, colorbyrange = NULL,
  rownumber = NULL, row = "auto", height = 0.4, plotbg = "white",
  wiggle = 0.02, splitstrand = FALSE, numbins = 200, binsmoothing = 10,
  palettes = topo.colors, rowlabels = NULL, rowlabelcol = "dodgerblue2",
  rowlabelfont = 2, rowlabelcex = 1, maxrows = 1e+06,
  color = "dodgerblue4", xaxt = "none", yaxt = "none", xlab = "",
  ylab = "", xaxs = "i", yaxs = "i", bty = "n", border = NA, ...)

`beddata`	genomic data to be plotted (in bed format)
`chrom`	chromosome of region to be plotted
`chromstart`	start position
`chromend`	end position
`type`	type of plot ('region','circles','density')
`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.
`rownumber`	vector giving the row numbers of each bed element to be plotted.
`row`	How row number should be determined. Appropriate values are 'auto' or 'supplied'
`height`	Value, typically between 0 and 1, that sets the height of each bed element
`plotbg`	The background color of the plot
`wiggle`	the fraction of the plot to leave blank on either side of each element to avoid overcrowding.
`splitstrand`	TRUE/FALSE indicating whether reverse strnad bed elements shold be plotted below the x axis. (only valid when row is set to 'auto')
`numbins`	The number of bins to divide the region into when type is set to density (only valid when type is set to 'density')
`binsmoothing`	umber of bins to sum together when type is set to density (only valid when type is set to 'density')
`palettes`	list of color palettes used for density plots. Each row can have a unique palette. number of palettes is less than the number of rows then only the first palette is used (only valid when type is set to 'density')
`rowlabels`	labels for the y-axis
`rowlabelcol`	color of the y-axis labels
`rowlabelfont`	font of the y-axis labels
`rowlabelcex`	font size of the y-axis labels
`maxrows`	The maximum number of rows to plot on the y-axis
`color`	single color or vector of colors to use to plot the points or regions (not valid when type is set to 'density')
`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`
`bty`	A character string which determined the type of box which is drawn about plots. See `par`
`border`	border color drawn around each bed element or density bin. Set to 'n' for none.
`...`	values to be passed to other functions

data(Sushi_ChIPSeq_severalfactors.bed)
chrom            = "chr15"
chromstart      = 72800000
chromend         = 73100000
Sushi_ChIPSeq_severalfactors.bed$color = heat.colors(max(Sushi_ChIPSeq_severalfactors.bed$row))[Sushi_ChIPSeq_severalfactors.bed$row]
plotBed(beddata    = Sushi_ChIPSeq_severalfactors.bed,chrom = chrom,chromstart = chromstart,chromend =chromend,
        rownumber  = Sushi_ChIPSeq_severalfactors.bed$row, type = "circles",color=Sushi_ChIPSeq_severalfactors.bed$color,row="given",plotbg="grey95",
        rowlabels=unique(Sushi_ChIPSeq_severalfactors.bed$name),rowlabelcol=unique(Sushi_ChIPSeq_severalfactors.bed$color),rowlabelcex=0.75)

Sushi_ChIPSeq_severalfactors.bed$color = heat.colors(max(Sushi_ChIPSeq_severalfactors.bed$row))[Sushi_ChIPSeq_severalfactors.bed$row]

plotBed(beddata    = Sushi_ChIPSeq_severalfactors.bed,chrom = chrom,chromstart = chromstart,chromend =chromend,
        rownumber  = Sushi_ChIPSeq_severalfactors.bed$row, type = "region",color=Sushi_ChIPSeq_severalfactors.bed$color,row="given",plotbg="grey95",
        rowlabels=unique(Sushi_ChIPSeq_severalfactors.bed$name),rowlabelcol=unique(Sushi_ChIPSeq_severalfactors.bed$color),rowlabelcex=0.75)

colors = c("dodgerblue1","firebrick2","violet","yellow",
        "dodgerblue1","firebrick2","violet","yellow",
        "dodgerblue1","firebrick2","violet")
plotBed(beddata    = Sushi_ChIPSeq_severalfactors.bed,chrom = chrom,chromstart = chromstart,chromend =chromend,
         rownumber  = Sushi_ChIPSeq_severalfactors.bed$row, type = "density",row="supplied",
         rowlabels=unique(Sushi_ChIPSeq_severalfactors.bed$name),rowlabelcol=colors,rowlabelcex=0.75,
         palettes=list(
         colorRampPalette(c("black",colors[1])),
         colorRampPalette(c("black",colors[2])),
         colorRampPalette(c("black",colors[3])),
         colorRampPalette(c("black",colors[4])),
         colorRampPalette(c("black",colors[5])),
         colorRampPalette(c("black",colors[6])),
         colorRampPalette(c("black",colors[7])),
         colorRampPalette(c("black",colors[8])),
         colorRampPalette(c("black",colors[9])),
         colorRampPalette(c("black",colors[10])),
         colorRampPalette(c("black",colors[11]))))