GOVenn {GOplot}

Venn diagram of differentially expressed genes.

Description

The function compares lists of differentially expressed genes and illustrates possible relations.Additionally it represents the variety of gene expression patterns within the intersection in small pie charts with three segements. Clockwise are shown the number of commonly up- regulated, commonly down- regulated and contra- regulated genes.

Usage

GOVenn(data1, data2, data3, title, label, lfc.col, circle.col, plot = T)

Arguments

data1

A data frame consisting of two columns: ID, logFC

data2

A data frame consisting of two columns: ID, logFC

data3

A data frame consisting of two columns: ID, logFC

title

The title of the plot

label

A character vector to define the legend keys

lfc.col

A character vector determining the background colors of the pie segments representing up- and down- regulated genes

circle.col

A character vector to assign clockwise colors for the circles

plot

If TRUE only the venn diagram is plotted. Otherwise the function returns a list with two items: the actual plot and a list containing the overlap entries (default= TRUE)

Details

The plot argument can be used to adjust the amount of information that is returned by calling the function. If you are only interested in the actual plot of the venn diagram, plot should be set to TRUE. Sometimes you also want to know the elements of the intersections. In this case plot should be set to FALSE and the function call will return a list of two items. The first item, that can be accessed by $plot, contains the plotting information. Additionally, a list ($table) will be returned containing the elements of the various overlaps.

Examples

## Not run: 
#Load the included dataset
data(EC)

#Generating the circ object
circ<-circular_dat(EC$david, EC$genelist)

#Selecting terms of interest
l1<-subset(circ,term=='heart development',c(genes,logFC))
l2<-subset(circ,term=='plasma membrane',c(genes,logFC))
l3<-subset(circ,term=='tissue morphogenesis',c(genes,logFC))

GOVenn(l1,l2,l3, label=c('heart development','plasma membrane','tissue morphogenesis'))

## End(Not run)