plot-methods function

Plots an AbstractMassObject object.

This is an overloaded method to allow plotting of an AbstractMassObject object. methods

## S4 method for signature 'AbstractMassObject,missing'
plot(x, col="black",
   xlab=expression(italic(m/z)), ylab="intensity",
   type=ifelse(isMassPeaks(x), "h", "l"),
   xlim=c(ifelse(length(x@mass), min(x@mass, na.rm=TRUE), 0),
      ifelse(length(x@mass), max(x@mass, na.rm=TRUE), 1)),
   ylim=c(0, ifelse(length(x@intensity), max(x@intensity, na.rm=TRUE), 1)),
   main=x@metaData$name, sub=x@metaData$file,
   cex.sub=0.75, col.sub="#808080", ...)

Arguments

• x: MassSpectrum object.
• col: line colour, see par.
• xlab: title for the x-axis, see title.
• ylab: title for the y-axis, see title.
• type: type of plot: see plot.
• xlim: the x limits (x1, x2) of the plot, see plot.default.
• ylim: the y limits (y1, y2) of the plot, see plot.default.
• main: title for the plot, see title.
• sub: sub title for the plot, see title.
• cex.sub: sub title font size, see par.
• col.sub: sub title color, see par.
• ...: arguments to be passed to plot.

Author(s)

Sebastian Gibb mail@sebastiangibb.de

See Also

AbstractMassObject

Website: https://strimmerlab.github.io/software/maldiquant/

Examples

## load package
library("MALDIquant")

## create a MassSpectrum object by default constructor
s <- createMassSpectrum(mass=1:100, intensity=rnorm(100)^2,
                        metaData=list(name="example"))

## show some details
s

## plot spectrum
plot(s)