labelPeaks-methods: Draws peak labels to plot.

In MALDIquant: Quantitative Analysis of Mass Spectrometry Data

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

## S4 method for signature '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, srt=0,
  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.
srt	numeric, the label rotation in degrees.
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.

Details

Please note that avoidOverlap = TRUE is just supported for srt %% 90 == 0 (means srt has to be a multiple of 90 degree).

Author(s)

Sebastian Gibb

See Also

MassPeaks, plot,AbstractMassObject,missing-method

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

Examples

## load package
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)

MALDIquant documentation built on Sept. 11, 2024, 6:15 p.m.