MALDIquant (version 1.3)

plot-methods: Plots an AbstractMassObject object.

Description

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

Usage

## S3 method for class 'AbstractMassObject,missing':
plot(x, col="black", 
     xlab="mass", ylab="intensity", 
     type=ifelse(isMassPeaks(x), "h", "l"),
     xlim=c(ifelse(length(x@mass)>0, min(x@mass, na.rm=TRUE), 0),
            ifelse(length(x@mass)>0, max(x@mass, na.rm=TRUE), 1)),
     ylim=c(0, ifelse(length(x@intensity>0), max(x@intensity, na.rm=TRUE), 1)),
     main=x@metaData$name, sub=x@metaData$file, 
     cex.sub=0.75, col.sub="#808080", 
     abline.col="#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

abline.col

colour for horizontal line at y=0

...

arguments to be passed to plot

References

See website: http://strimmerlab.org/software/maldiquant/

See Also

AbstractMassObject,

Examples

## load library
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);