plot2d-methods {MSnbase} | R Documentation

## The 'plot2d' method for 'MSnExp' quality assessment

### Description

These methods plot the retention time vs. precursor MZ for the whole `"MSnExp"` experiment. Individual dots will be colour-coded to describe individual spectra's peaks count, total ion count, precursor charge (MS2 only) or file of origin.

The methods make use the `ggplot2` system. An object of class 'ggplot' is returned invisibly.

### Arguments

`object` | An object of class `"MSnExp"` or a `data.frame`. In the latter case, the data frame must have numerical columns named 'retention.time' and 'precursor.mz' and one of 'tic', 'file', 'peaks.count' or 'charge', depending on the `z` parameter. Such a data frame is typically generated using the `header` method on `"MSnExp"` object.
`z` | A character indicating according to what variable to colour the dots. One of, possibly abreviated, "ionCount" (total ion count), "file" (raw data file), "peaks.count" (peaks count) or "charge" (precursor charge).
`alpha` | Numeric [0,1] indicating transparence level of points.
`plot` | A logical indicating whether the plot should be printed (default is 'TRUE').

### Methods

`signature(object = "MSnExp", ...)`

  Plots a 'MSnExp' summary.

`signature(object = "data.frame", ...)`

  Plots a summary of the 'MSnExp' experiment described by the data frame.

### Author(s)

Laurent Gatto <lg390@cam.ac.uk>

### See Also

The `plotDensity` and `plotMzDelta` methods for other QC plots.

### Examples

    itraqdata
    plot2d(itraqdata,z="ionCount")
    plot2d(itraqdata,z="peaks.count")
    plot2d(itraqdata,z="charge")

[Package MSnbase version 2.6.4 Index]