gelmap: This function draws a simple pseudo-gelmap.

In sgibb/MALDIquantTools: Additional tools for MALDIquant

Description

This function draws a simple pseudo-gelmap.

Usage

gelmap(x, col = gray((255:1)/255), rowLabels, dendrogram,
  dendrogramRatio = 1/5, xlab = "mass", cex.axis = 0.75, ...)

Arguments

x	an 'intensityMatrix'.
col	gelmap colours.
rowLabels	labels of rows.
dendrogram	a dendrogram which is plotted on the left of the gelmap.
dendrogramRatio	ratio of width of dendrogram to gelmap.
xlab	a label for the x axis.
cex.axis	magnification to be used for axis annotation (relative to current setting of cex).
...	further arguments passed to image.

See Also

intensityMatrix

Examples

library("MALDIquant")
library("MALDIquantTools")
data(fiedler2009subset)

## select some tumor/control subset
spectra <- fiedler2009subset[9:16]

## run preprocessing
spectra <- transformIntensity(spectra, method="sqrt")
spectra <- smoothIntensity(spectra, method="MovingAverage", halfWindowSize=2)
spectra <- removeBaseline(spectra, method="SNIP")
spectra <- calibrateIntensity(spectra, method="TIC")
peaks <- detectPeaks(spectra)
peaks <- binPeaks(peaks)

## create labels
tumor <- sapply(peaks, function(x)grepl(pattern="tumor", x=metaData(x)$file))
fullName <- sapply(peaks, function(x)metaData(x)$fullName)
rowLabels <- paste(fullName, " (", ifelse(tumor, "T", "C"), ")", sep="")

## run clustering and create dendrogram
iM <- intensityMatrix(peaks, spectra)
d <- dist(iM, method="euclidean")
d <- as.dendrogram(hclust(d, method="complete"), hang=-1)

## plot gelmap
gelmap(iM, rowLabels=rowLabels, dendrogram=d, xlab="mass [Da]")

sgibb/MALDIquantTools documentation built on Oct. 18, 2019, 8:02 p.m.