plotFragmentMatching {synapter} | R Documentation

## Plot fragment matching results.

### Description

This method plots the results of the fragment matching procedure (`fragmentMatching`). A single plot contains two panels. The upper panel shows the identification fragments and the lower one the MS2 spectrum of the quantitation run. Common peaks are drawn in a slightly darker colour and with a point on the top.

### Arguments

`object` | Object of class `"Synapter"` .
`key` | `character`, value to look for.
`column` | `character`, name of the column in which `plotFragmentMatching` looks for `key`.
`...` | Further arguments passed to internal functions.

### Methods

`signature(object = "Synapter", key = "character", column = "character", verbose = "logical", ...)`

  Plots identification fragments against quantitation spectra. The `...` arguments are passed to the internal functions. Currently `legend.cex`, `fragment.cex`, and most of the `plot.default` arguments (like `xlim`, `ylim`, `main`, `xlab`, `ylab`, ...) are supported. `legend.cex` and `fragment.cex` control the size of the legend and fragments labels (default: `0.5`). Please see `par` for details about `cex`. If `verbose = TRUE` a progress bar is shown.

### Author(s)

Sebastian Gibb <mail@sebastiangibb.de>

### See Also

`fragmentMatching`

[Package synapter version 2.16.0 Index]