plotImage: Plot of images of GCMS data

In rromoli/flagme: Analysis of Metabolomics GC/MS Data

Plot of images of GCMS data

Description

Image plots (i.e. 2D heatmaps) of raw GCMS profile data

Usage

## S4 method for signature 'peaksDataset'
plotImage(
  object,
  run = 1,
  rtrange = c(11, 13),
  main = NULL,
  mzrange = c(50, 200),
  SCALE = log2,
  ...
)

Arguments

object	a peaksDataset object
run	index of the run to plot an image for
rtrange	vector of length 2 giving start and end of the X-axis (retention time)
main	main title (auto-constructed if not specified)
mzrange	vector of length 2 giving start and end of the Y-axis (mass-to-charge ratio)
SCALE	function called to scale the data (default: log2)
...	further arguments passed to the image command

Details

For peakDataset objects, each TIC is scale to the maximum value (as specified by the how.near and max.near values). The many parameters gives considerable flexibility of how the TICs can be visualized.

For peakAlignment objects, the similarity matrix is plotted and optionally, the set of matching peaks. clusterAlignment objects are just a collection of all pairwise peakAlignment objects.

Author(s)

Mark Robinson

References

Mark D Robinson (2008). Methods for the analysis of gas chromatography - mass spectrometry data PhD dissertation University of Melbourne.

See Also

plot, peaksDataset

Examples

require(gcspikelite)

# paths and files
gcmsPath<-paste(find.package("gcspikelite"),"data",sep="/")
cdfFiles<-dir(gcmsPath,"CDF",full=TRUE)
eluFiles<-dir(gcmsPath,"ELU",full=TRUE)

# read data
pd<-peaksDataset(cdfFiles[1],mz=seq(50,550),rtrange=c(7.5,8.5))

# image plot
plotImage(pd,run=1,rtrange=c(7.5,8.5),main="")

rromoli/flagme documentation built on Feb. 10, 2023, 12:59 a.m.