Description Usage Arguments Value Author(s) References See Also
View source: R/PeakML.bubbleplot.R
This function generates "bubble" plot of XC/MS experimental data. This graphical interpretation is suitable for quick assesing of data quality.
1 | 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)
|
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. |
Graphical output in pdf file.
Andris Jankevics (a.jankevics@rug.nl) Richard Scheltema (r.a.scheltema@rug.nl)
PeakML/mzMatch - a file format, Java library, R library and tool-chain for mass spectrometry data analysis. In preparation.
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