VolcanoPlot: Volcano plot
In NormalizeMets: Analysis of Metabolomics Data

Description Usage Arguments Author(s) Examples

Produces a volcano plot given fold changes and p-values.

VolcanoPlot(coef, pvals, cexcutoff = 0.7, cexlab = 0.5, pointsize = 0.9,
  plimit = 0.05, coeflimit = 1, negcontrol = NULL, poscontrol = NULL,
  saveplot = FALSE, plotname = "VolcanoPlot", savetype = c("png", "bmp",
  "jpeg", "tiff", "pdf"), xlab = "Coefficients", ylab = "-log(p-value)",
  labelunderlim = FALSE, labelsig = FALSE, interactiveplot = TRUE,
  saveinteractiveplot = FALSE,
  interactiveplotname = "interactiveVolcanPlot", interactiveonly = FALSE,
  main = "Volcano Plot", fclabel = "", chooselegend = NULL,
  vlines = TRUE, tolabel = NULL, ...)

`coef`	A vector of coefficients with metabolite names.
`pvals`	A vector of corresponding p-values.
`cexcutoff`	Font size of the cut-off labels.
`cexlab`	Font size of the variable labels.
`pointsize`	A numeric indicating the size of the points on the graph.
`plimit`	A numeric indicating the p value cutoff. The default is set to 0.05.
`coeflimit`	A numeric indicating the lower fold cutoff. The default is set to 2.
`negcontrol`	A vector with the names of the metabolites used as negative controls, to be coloured differently.
`poscontrol`	A vector with the names of the metabolites used as positive controls, to be coloured differently.
`saveplot`	A logical indicator whether to save the produced plot.
`plotname`	A character string indicating the name to be used for saving the plot.
`savetype`	The required format for the plot to be saved in. Threre is a choice of `"png","bmp","jpeg","tiff","pdf"` type files.
`xlab`	x-axis label.
`ylab`	y-axis label.
`labelunderlim`	A logical indicating whether to label points that are not significant.
`labelsig`	A logical indicating whether all significant points should be labeled.
`interactiveplot`	A logical indication whether an interactive plot should be shown.
`saveinteractiveplot`	A logical indication whether the interactive plot produced should be saved as a `.html` file.
`interactiveplotname`	A character string indicating the name to be used for saving the interactive plot.
`interactiveonly`	A boolean whether only an interactive version of the plot is required
`main`	Plot title.
`fclabel`	An optional character sting to label the vertical coefficient cutoff.
`chooselegend`	Defualt to `NULL`. For internal use in other functions in the package.
`vlines`	A logical indicating whether to show vertical coefficient cutoff lines.
`tolabel`	A list of metabolite names on the graph to be labeled
`...`	Other graphical parameters. See `par`.

Alysha M De Livera, Gavriel Olshansky

 data("alldata_eg")
logdata<-LogTransform(alldata_eg$featuredata)
sampledata<-alldata_eg$sampledata
metabolitedata<-alldata_eg$metabolitedata
imp <-  MissingValues(logdata$featuredata,sampledata,metabolitedata,
                     feature.cutof=0.8, sample.cutoff=0.8, method="knn")
featuredata<-imp$featuredata
qcmets<-which(metabolitedata[,1]=="IS")
factormat<-model.matrix(~gender +Age , sampledata)

#Linear model fit with ordinary statistics with ruv2
ordFit_ruv2<-LinearModelFit(featuredata=featuredata,
                           factormat=factormat,
                           ruv2=TRUE, qcmets=qcmets,
                           k=2)
#Volcano plot
VolcanoPlot(coef=ordFit_ruv2$coefficients[,3], 
           pval=ordFit_ruv2$p.value[,3],
           cexlab = 0.8, 
           interactiveplot = TRUE, 
           coeflimit = 0.05,
           xlab="Coef",
           negcontrol= rownames(ordFit_ruv2$coefficients)
           [which(metabolitedata[,2]==1)],
           poscontrol= c("m74", "m161"),
           interactiveonly = TRUE)