MSnbase: plotDensity-methods – R documentation

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plotDensity-methods

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>

Examples

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

MSnbase

Base Functions and Classes for Mass Spectrometry and Proteomics

v2.16.1

Artistic-2.0

Authors

Laurent Gatto, Johannes Rainer and Sebastian Gibb with contributions from Guangchuang Yu, Samuel Wieczorek, Vasile-Cosmin Lazar, Vladislav Petyuk, Thomas Naake, Richie Cotton, Arne Smits, Martina Fisher, Ludger Goeminne, Adriaan Sticker and Lieven Clement.

Initial release