vennDiag: Plotting a Venn Diagram to compare hits

In RNAither: Statistical analysis of high-throughput RNAi screens

Description

Plots a Venn Diagram of up to three binary hit vectors.

Usage

vennDiag(header, listOfCols, listOfNames, plotTitle, showPlot)

Arguments

header	the header of a dataset file generated with generateDatasetFile
listOfCols	a list of binary hit vectors to compare
listOfNames	a list of character strings for the annotation of the Venn Diagram
plotTitle	the plot title
showPlot	0 or 1. 1 will open one or several plot windows in the R GUI, 0 will only save the plot(s) without opening windows

Value

The plot is saved in a pdf and a png file named after the experiment name specified in the header concatenated with the plotTitle.

The function returns the plot name.

See Also

Ttest, MannWhitney

Examples

data(exampleHeader, package="RNAither")

data(pValVec1, package="RNAither")
data(pValVec2, package="RNAither")
data(scoredDataset1, package="RNAither")
data(scoredDataset2, package="RNAither")

##for details on the generation of pValVec and scoredDataset, 
##see the examples of the functions Ttest and MannWhitney linked above.

scoredHits1 <- hitselectionPval(scoredDataset1, pValVec1, "SigIntensity", "pValue.ttest_l", 0.05, 
"GeneName", "pvalue_testfile1.txt")

scoredHits2 <- hitselectionPval(scoredDataset2, pValVec2, "SigIntensity", "pValue.mannwhitney_l", 0.05, 
"GeneName", "pvalue_testfile2.txt")

hitvector1 <- scoredHits1[[2]]
hitvector2 <- scoredHits2[[2]]

plot_name <- vennDiag(header, list(hitvector1, hitvector2), list("t test", "Mann-Whitney test"), 
"Venn diagram", 1)

RNAither documentation built on Nov. 8, 2020, 8:06 p.m.