plotBedpe {Sushi} | R Documentation

## plots data stored in bed file format

### Description

plots data stored in bed file format

### Usage

    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, ...)

### Arguments

`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`

### Examples

    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)

[Package Sushi version 1.28.0 Index]