plotAlignment-peaksAlignment-method: plotAlignment

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

plotAlignment

Description

Plotting functions for GCMS data objects

Usage

## S4 method for signature 'peaksAlignment'
plotAlignment(
  object,
  xlab = "Peaks - run 1",
  ylab = "Peaks - run 2",
  plotMatches = TRUE,
  matchPch = 19,
  matchLwd = 3,
  matchCex = 0.5,
  matchCol = "black",
  col = colorpanel(50, "white", "green", "navyblue"),
  breaks = seq(0, 1, length = 51),
  ...
)

Arguments

object	a clusterAlignment object
xlab	x-axis label
ylab	y-axis label
plotMatches	logical, whether to plot matches
matchPch	match plotting character
matchLwd	match line width
matchCex	match character expansion factor
matchCol	match colour
col	vector of colours for colourscale
breaks	vector of breaks for colourscale
...	further arguments passed to image

Details

Plot an object of peaksAlignment

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 an object of class peaksAlignment

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

peaksAlignment plotAlignment

Examples

require(gcspikelite)
files <- list.files(path = paste(find.package("gcspikelite"), "data",
                    sep = "/"),"CDF", full = TRUE)
data <- peaksDataset(files[1:2], mz = seq(50, 550), rtrange = c(7.5, 8.5))
## create settings object
mfp <- xcms::MatchedFilterParam(fwhm = 10, snthresh = 5)
cwt <- xcms::CentWaveParam(snthresh = 3, ppm = 3000, peakwidth = c(3, 40),
 prefilter = c(3, 100), fitgauss = FALSE, integrate = 2, noise = 0,
 extendLengthMSW = TRUE, mzCenterFun = "wMean")
data <- addXCMSPeaks(files[1:2], data, settings = mfp)
data
## image plot
plotChrom(data, rtrange = c(7.5,8.5), plotPeaks = TRUE, plotPeakLabels =TRUE)

## align two chromatogram
pA <- peaksAlignment(data@peaksdata[[1]], data@peaksdata[[2]],
                     data@peaksrt[[1]], data@peaksrt[[2]], D = 50,
                     compress = FALSE, type = 1, metric = 1,
                     gap = 0.5)
plotAlignment(pA)

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