plotBed {Sushi} | R Documentation

## plots data stored in bed file format

### Description

plots data stored in bed file format

### Usage

    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, ...)

### Arguments

`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

### Examples

    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]))))

[Package Sushi version 1.30.0 Index]