plot.genominator.coverage: Create coverage plot

In Genominator: Analyze, manage and store genomic data

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 [e-mail], Kasper Daniel Hansen [e-mail]

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)

Genominator documentation built on Oct. 31, 2019, 8:56 a.m.