genoPlot {genoset} | R Documentation

## Plot data along the genome

### Description

Plot location data and chromosome boundaries from a GenoSet or GRanges object against data from a numeric or Rle. Specifying a chromosome name and optionally a 'xlim' will zoom into one chromosome region. If more than one chromosome is present, the chromosome boundaries will be marked. Alternatively, for a numeric x and a numeric or Rle y, data in y can be plotted at genome positions x. In this case, chromosome boundaries can be taken from the argument locs. If data for y-axis comes from a Rle lines are plotted representing segments. X-axis tickmarks will be labeled with genome positions in the most appropriate units.

### Usage

    genoPlot(x, y, ...)

    ## S4 method for signature 'numeric,numeric'
    genoPlot(x, y, add = FALSE, xlab = "",
      ylab = "", col = "black", locs = NULL, ...)

    ## S4 method for signature 'numeric,Rle'
    genoPlot(x, y, add = FALSE, xlab = "",
      ylab = "", col = "red", locs = NULL, lwd = 2, xlim = NULL, ...)

    ## S4 method for signature 'GenoSetOrGenomicRanges,ANY'
    genoPlot(x, y, chr = NULL,
      add = FALSE, pch = ".", xlab = "", ylab = "", ...)

### Arguments

`x` | GenoSet (or descendant) or GRanges
`y` | numeric or Rle
`...` | Additional plotting args
`add` | Add plot to existing plot
`xlab` | character, label for x-axis of plot
`ylab` | character, label for y-axis of plot
`col` | character, color to plot lines or points
`locs` | GRanges, like rowRanges slot of GenoSet
`lwd` | numeric, line width for segment plots from an Rle
`xlim` | integer, length two, bounds for genome positions. Used in conjunction with 'chr' to subset data for plotting.
`chr` | Chromosome to plot, NULL by default for full genome
`pch` | character or numeric, printing character, see points

### Value

TRUE

### Methods

`signature(x = 'GenoSetOrGenomicRanges', y = 'ANY')`

  Plot feature locations and data from one sample.

`signature(x = 'numeric', y = 'numeric')`

  Plot numeric location and a vector of numeric data.

`signature(x = 'numeric', y = 'Rle')`

  Plot numeric location and a vector of Rle data. Uses lines for Rle runs.

### See Also

Other 'genome plots': `genomeAxis`

### Examples

    data(genoset,package='genoset')
    genoPlot( x=genoset.ds,y=genoset.ds[,1,'lrr'] )
    genoPlot( genoPos(genoset.ds), genoset.ds[,1,'lrr'], locs=rowRanges(genoset.ds) ) # The same
    genoPlot( 1:10, Rle(c(rep(0,5),rep(3,4),rep(1,1))) )

[Package genoset version 1.43.0 Index]