plotClustAlignment-clusterAlignment-method: plotClustAlignment

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

plotClustAlignment

Description

Plotting functions for GCMS data objects

Usage

## S4 method for signature 'clusterAlignment'
plotClustAlignment(object, alignment = 1, ...)

Arguments

object	clusterAlignment object.
alignment	the set of alignments to plot
...	further arguments passed to image. See also plotAlignment

Details

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

Value

plot the pairwise alignment

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

plotAlignment

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, peak detection results
pd <- peaksDataset(cdfFiles[1:2], mz=seq(50,550), rtrange=c(7.5,8.5))
pd <- addAMDISPeaks(pd, eluFiles[1:2])

ca <- clusterAlignment(pd, gap=0.5, D=0.05, df=30, metric=1, type=1)
plotClustAlignment(ca, run = 1)
plotClustAlignment(ca, run = 2)
plotClustAlignment(ca, run = 3)

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