xcms (version 1.48.0)

peakPlots-methods: Plot a grid of a large number of peaks

Description

Plot extracted ion chromatograms for many peaks simultaneously, indicating peak integration start and end points with vertical grey lines.

Arguments

object

the xcmsRaw object

peaks

matrix with peak information as produced by findPeaks

figs

two-element vector describing the number of rows and the number of columns of peaks to plot, if missing then an approximately square grid that will fit the number of peaks supplied

width

width of chromatogram retention time to plot for each peak

Methods

signature(object = "xcmsSet")

plotPeaks(object, peaks, figs, width = 200)

Details

This function is intended to help graphically analyze the results of peak picking. It can help estimate the number of false positives and improper integration start and end points. Its output is very compact and tries to waste as little space as possible. Each plot is labeled with rounded m/z and retention time separated by a space.

See Also

xcmsRaw-class, findPeaks, split.screen