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

# S4 method for 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.

Author

Sebastian Gibb

Details

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

Examples

Run this code

## 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)