RobVolPlot: Outlier-Robust Volcano Plot for Identifying Influential...

In nishithkumarpaul/Rvolcano: Robust Volcano Plot: Identification of Influential Metabolites in the Presence of Outliers

Description

This function draws a volcano plot using the robust fold change value and the p-value obtained from robust t-test.

Usage

RobVolPlot(folds, pvals, cexcutoff = 0.7, cexlab = 0.5, 
plimit = 0.05, fclimit = 2, xlab = "log2 Robust Fold Change",
tab ylab = "-log10 Robust t-Test P-value", main = "Robust Volcano Plot", ...)

Arguments

folds	A vector of fold changes with metabolite names.
pvals	A vector of corresponding p-values with metabolite names.
cexcutoff	Font size of the cut-off labels.
cexlab	Font size of the variable labels.
plimit	A numeric indicating the p value cutoff. The default is set to 0.05.
fclimit	A numeric indicating the lower fold cutoff. The default is set to 2.
xlab	x-axis label.
ylab	y-axis label.
main	Plot title.
...	Other graphical parameters.

Author(s)

Nishith Kumar <[e-mail]>

Examples

data(DummyFullData)
##Calculation of fold change values
fcval<-foldChngCalc(DummyFullData,nSampG1=20,nSampG2=20)
##Calculation of p-values
pval<-NULL
for (i in 1:dim(DummyFullData)[1]){
pval[i]<-p.valcalc(DummyFullData[i,1:20],DummyFullData[i,21:40])
}
##Robust volcano plot
RobVolPlot(fcval,pval , cexcutoff = 0.7, cexlab = 0.8, plimit = .05,fclimit = 2) 

nishithkumarpaul/Rvolcano documentation built on May 19, 2019, 10:49 p.m.