plot-methods {MALDIquant}

Plots an AbstractMassObject object.

Description

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

Usage

## 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 [e-mail]

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)