plotDensity-methods {MSnbase} | R Documentation

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

### Description

These methods plot the distribution of several parameters of interest for the different precursor charges for `"MSnExp"` experiment.

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

### Arguments

`object` | An object of class `"MSnExp"` or and 'data.frame'. In the latter case, the data frame must have numerical columns named 'charge' and one of 'precursor.mz', 'peaks.count' or 'ionCount', depending on the `z` parameter. Such a data frame is typically generated using the `header` method on `"MSnExp"` object.
`z` | A character indicating which parameter's densitiy to plot. One of, possibly abreviated, "ionCount" (total ion count), "peaks.count" (peaks count) or "precursor.mz" (precursor MZ).
`log` | Logical, whether to log transform the data (default is 'FALSE').
`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 `plot2d` and `plotDensity` methods for other QC plots.

### Examples

    itraqdata
    plotDensity(itraqdata,z="ionCount")
    plotDensity(itraqdata,z="peaks.count")
    plotDensity(itraqdata,z="precursor.mz")

[Package MSnbase version 2.12.0 Index]