plotRelCon: Boxplot or Histogram of Posterior distributions of Relative...

In batman: Bayesian AuTomated Metabolite Analyser for NMR spectra

Description

This function plots the posterior distributions of relative concentrations, and saves the figure to pdf file. The file name is in the format of "spec_i_RelCon_j1toj2.pdf", where i are the spectrum numbers and j1 and j2 are the order numbers of fitted metabolites in the order of their input in file metaboliteList.csv. The figure file will not be overwritten if it already exists. A prefix can be added to file name for new saves.

Usage

 plotRelCon(BM, metaName, plotHist = FALSE, breaks, 
            saveFig = TRUE, saveFigDir = BM$outputDir, 
            prefixFig, rerun = FALSE, overwriteFig = FALSE,
            showPlot)

Arguments

BM	batman output data frame.
metaName	Only multiplets belonging to the named Metabolite will be shown. Only one metabolite name can be given. If missing, all metabolites will be plotted.
plotHist	If plotHist = TRUE, the ppm shift posteriors will be displayed as histogram. The default is FALSE.
breaks	A single number to set the number of bins for the histogram. If missing from the input, it is set to the data length divided by 3.
saveFig	Save figure(s) to pdf file(s) if set TRUE. The default is TRUE.
saveFigDir	Save figure(s) in this directory. The default is output directory of BM.
prefixFig	Add prefix to each saved figure name. The default is no prefix.
rerun	Set to FALSE to plot batman result, and TRUE to plot batmanrerun result.
overwriteFig	Overwrite saved figure file in pdf format if overwriteFig = TRUE. If set to FALSE, a new figure file with system time as postfix will be created. The default is FALSE.
showPlot	If set FALSE, no plot will be shown on display, the pdf file(s) for the figure plot(s) will be created in output folder. If missing from input, for windows and osx operating systems, it will be set to TRUE, for the rest operating systems, it will be set to FALSE automatically.

See Also

batman, batmanrerun

Examples

library(batman)
## Run BATMAN and then plot relative concentration
if(interactive()) 
{
bm<-batman()
## Plot relative concentrations
plotRelCon(bm)
}

batman documentation built on May 2, 2019, 6:13 p.m.