PeakML.bubbleplot {mzmatch.R}R Documentation

PeakML.bubbleplot

Description

This function generates "bubble" plot of XC/MS experimental data. This graphical interpretation is suitable for quick assesing of data quality.

Usage

PeakML.bubbleplot(xcmsset, peakidentifications, samples = NULL, samples2 = NULL, DB1string = NULL, bubbletype = "filled", plottype = "identified", outputfile = "bubbleplot.pdf", cor.threshold = 0.7, rtrange = NULL, mzrange = NULL, intensity.threshold.min = NULL, intensity.threshold.max = NULL, strict.relation.select = TRUE, scale = "max", logbase = 10, integral.val = "maxint", bubblesize = 3, smalllegend=FALSE)

Arguments

xcmsset

The XCMS set structure containing the data to be written to the PeakML file.

peakidentifications

Matrix of peak attributes extracted by mzmatch software and PeakML.xcms.read function.

samples

Which samples should be plotted.

samples2

If 'plottype' is "correlation" sample name to correlate with should be given.

DB1string

Name of database file which should be used main data base for coloring

bubbletype

Values: "open" or "closed".

plottype

"identified","compare" or "correlation"

outputfile

Name of output file in which graphical output shoud be generated (pdf format).

cor.threshold

If 'plottype' is 'correlation', threshold for correlated peaks can be set with this value.

rtrange

Numeric vector with two elements indicating RT range at which bublle plot should be plotted.

mzrange

Numeric vector with two elements indicating m/z range at which bublle plot should be plotted.

intensity.threshold.min

Minimum intensity threshold cut-off value.

intensity.threshold.max

Maximum intensity threshold cut-off value.

strict.relation.select

Restric relation classes for related peaks matching.

scale

Set scaling which to use before plotting.

logbase

If logaritmical scaling is used, log base can be defined.

integral.val

Which value to use for circle size, max intensity - 'maxo', or peak integral - 'into'

bubblesize

Scaling factor for bubble size, it depends on scaling which is used.

smalllegend

Defaults to FALSE. If is set to TRUE, legend is plotted only for unidentified,identified and their related features.

Value

Graphical output in pdf file.

Author(s)

Andris Jankevics (a.jankevics@rug.nl) Richard Scheltema (r.a.scheltema@rug.nl)

References

PeakML/mzMatch - a file format, Java library, R library and tool-chain for mass spectrometry data analysis. In preparation.

See Also

PeakML.xcms.read


[Package mzmatch.R version 2.0-6 Index]