plot.genominator.coverage {Genominator} | R Documentation

## Create coverage plot

### Description

S3 method to plot `genominator.coverage` object. Shows coverage as a function of plotting effort.

### Usage

    ## S3 method for class 'genominator.coverage'
    plot(x, type = "l", col = NULL,
      draw.totals = TRUE, draw.legend = TRUE, legend.location = NULL, ...)

### Arguments

`x` | An object of class `genominator.coverage`, as returned by `computeCoverage`.
`type` | Plot type. See `plot`.
`col` | Vector of plotting colors.
`draw.totals` | Logical indicating whether totals should be drawn.
`draw.legend` | Logical indicating whether legend should be drawn.
`legend.location` | Vector giving x and y coordinates of legend position.
`...` | Additional arguments for lower-level functions.

### Value

This method is used for its side effect.

### Author(s)

James Bullard bullard@berkeley.edu, Kasper Daniel Hansen khansen@jhsph.edu

### See Also

See `Genominator` vignette for more information. See also `computeCoverage`.

### Examples

    ed <- ExpData(system.file(package = "Genominator", "sample.db"),
                  tablename = "raw")
    data("yeastAnno")
    a <- computeCoverage(ed, yeastAnno, effort = 2^(5:18),
                         cutoff = function(x, ...) x > 1)
    plot(a, lwd = 5, col = "grey")
    plot(a, draw.totals = FALSE)
    ygroups <- rep(c("mut", "wt"), c(2,2))
    b <- computeCoverage(ed, yeastAnno, grups = ygroups,
                         effort = 2^(5:18), cutoff = function(x, ...) x > 1)
    plot(b)
    b <- computeCoverage(ed, yeastAnno, groups = ygroups,
                         effort = 2^(5:18), cutoff = function(x, ...) x > 3,
                         smooth = function(probs) {
                           probs = probs + min(probs[probs!=0])
                           probs = probs/sum(probs)
                         })
    plot(b)

[Package Genominator version 1.36.0 Index]