Skip to contents

The 'plot2d' method for 'MSnExp' quality assessment

plot2d-methods.Rd

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.

See also

The plotDensity and plotMzDelta methods for other QC plots.

Author

Laurent Gatto

Examples

itraqdata
#> MSn experiment data ("MSnExp")
#> Object size in memory: 1.9 Mb
#> - - - Spectra data - - -
#>  MS level(s): 2 
#>  Number of spectra: 55 
#>  MSn retention times: 19:09 - 50:18 minutes
#> - - - Processing information - - -
#> Data loaded: Wed May 11 18:54:39 2011 
#> Updated from version 0.3.0 to 0.3.1 [Fri Jul  8 20:23:25 2016] 
#>  MSnbase version: 1.1.22 
#> - - - Meta data  - - -
#> phenoData
#>   rowNames: 1
#>   varLabels: sampleNames sampleNumbers
#>   varMetadata: labelDescription
#> Loaded from:
#>   dummyiTRAQ.mzXML 
#> protocolData: none
#> featureData
#>   featureNames: X1 X10 ... X9 (55 total)
#>   fvarLabels: spectrum ProteinAccession ProteinDescription
#>     PeptideSequence
#>   fvarMetadata: labelDescription
#> experimentData: use 'experimentData(object)'
plot2d(itraqdata,z="ionCount")

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

plot2d(itraqdata,z="charge")