peakPlots-methods {xcms} | R Documentation

## 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

### 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.

### Methods

`signature(object = "xcmsSet")`

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

### See Also

`xcmsRaw-class`, `findPeaks`, `split.screen`

[Package xcms version 3.6.2 Index]