MALDIquant (version 1.5)

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,
    mass,
    labels,
    digits=3, underline=TRUE, 
    verticalOffset=abs(diff(par("usr")[3:4]))*0.01,
    absoluteVerticalPos,
    adj=c(0.5, 0), cex=0.7,
    avoidOverlap=FALSE,
    arrowLength=0, arrowLwd=0.5, arrowCol=1,
    ...)

Arguments

object

MassPeaks object.

index

integer/logical, indices of peaks to label.

mass

numeric, mass of peaks to label.

labels

character, use labels instead of mass values as peak label.

digits

integer, number of decimal places.

underline

logical, underline peak values?

verticalOffset

numeric, move label vertically (relative to peak height).

absoluteVerticalPos

numeric, absolute y value for the label. If missing verticalOffset is used.

adj

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

cex

numeric, font size, see par.

avoidOverlap

logical, try to find label coordinates to avoid overlap.

arrowLength, arrowLwd, arrowCol

arrow parameters, possible vectors. NA values in arrowCol cause the arrow to be omitted, see arrows.

...

arguments to be passed to text.

See Also

MassPeaks, plot,AbstractMassObject,missing-method

Examples

## load library
library("MALDIquant");

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

## plot peaks
plot(p);

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

## label all peaks in mass range 15 to 20 
labelPeaks(p, mass=15:20, underline=FALSE);

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


## real example
data("fiedler2009subset");

## a simplified preprocessing
r <- removeBaseline(fiedler2009subset[[1]]);
p <- detectPeaks(r);
plot(p);

## label highest peaks (top 10) and avoid label overlap
top10 <- sort(intensity(p), decreasing=TRUE, index.return=TRUE)$ix[1:10];
labelPeaks(p, index=top10, avoidOverlap=TRUE, digits=1);

## use own labels and rotate by 90 degree
plot(p);
labelPeaks(p, index=top10, labels=paste("TOP", 1:10), underline=FALSE, 
           srt=90, adj=c(0, 0.5), col=2);