MALDIquant (version 0.3)

labelPeaks-methods: Draws peak labels to plot.

Description

labelPeaks draws the corresponding mass values on top of the peaks stored in a MassPeaks object to a plot.

Usage

## S3 method for class 'MassPeaks':
labelPeaks(object, index,
    digits=3, underline=TRUE, 
    verticalOffset=ceiling(max(object@intensity)/200), 
    adj=c(0.5, 0), cex=0.7, family="sans", 
    ...)

Arguments

object

MassPeaks object

index

vector, index of peaks to label

digits

integer, number of decimal places

underline

logical, underline peak values?

verticalOffset

numeric, move label vertically

adj

numeric, adjust text to the left, center, right and top, center, bottom; see text

cex

numeric, font size, see par

family

name of font family, see par

...

arguments to be passed to text

See Also

MassPeaks, plot,AbstractMassSpectrumData,missing-method

Examples

## load library
library("MALDIquant");

## create a MassPeaks object from scratch
p <- new("MassPeaks", mass=1:20, intensity=sample(x=100:10000, size=20), 
         metaData=list(name="unrealistic example"));

## plot peaks
plot(p);

## label the first 5 peaks
labelPeaks(p, index=1:5);

## label all peaks in mass range 15 to 20 
## (index=15:20 would be easier but sometimes you don't know the correct values)
labelPeaks(p, index=which(mass(p) >= 15 & mass(p) <= 20), underline=FALSE);

## label highest peaks (top 5)
top5 <- intensity(p) %in% sort(intensity(p), decreasing=TRUE)[1:5];
labelPeaks(p, index=top5, col="red");