.getOL<-(x, retVals=){
((x)>5){
("max length of x is 5...")
}
OL=()
index<-1
##start with 1 on one comparisons:
(i 1:(x)){
(i < (x)){
(j in (i+1):(x)){
OL[index]]<-x[i]][which(x[i]] %in% x[j]])]
(OL)[index]<-("n",i,j)
index<-index+1
}
}
}
((x)>2){
##Now three way comparisons
(i 1:(x)){
(i<(x)){
(j in (i+1):(x)){
(j<(x)){
tmp<-x[i]][which(x[i]] %in% x[j]])]
(k in (j+1):(x)){
OL[index]]<-tmp[which(tmp %in% x[k]])]
(OL)[index]<-("n",i,j,k)
index<-index+1
}
}
}
}
}
}
((x)>3){
##Now for the four way comparisons
(i 1:(x)){
(i<(x)){
(j in (i+1):(x)){
(j<(x)){
tmp<-x[i]][which(x[i]] %in% x[j]])]
(k in (j+1):(x)){
(k<(x)){
tmp<-tmp[which(tmp %in% x[k]])]
(d in (k+1):(x)){
OL[index]]<-tmp[which(tmp %in% x[d]])]
(OL)[index]<-("n",i,j,k,d)
index<-index+1
}
}
}
}
}
}
}
}
((x) == 5){
##Now for the final comparison:
tmp<-x[1]]
(i 2:(x)){
tmp<-tmp[which(tmp %in% x[i]])]
}
OL[index]]<-tmp
(OL)[index]<-"n12345"
}
((retVals)){
OL<-((OL))
}
##If we're returning the values, we need to remove values that are found in multiple overlaps (for instance, n13, and n135)
((retVals)){
##Set up a tmp list
tmp<-()
##Loop through Overlaps
(i 1:(OL)){
(i<(OL)){
##Now set up a second tmp list of only the following entries of OL - this only works because the further overlaps (i.e. n135) are downstream of the earlier overlaps (i.e. n13)
tmp2<-OL(i+1):(OL)]
tmp[i]]<-OL[i]][which(!OL[i]] %in% (tmp2))]
(tmp)[i]<-(OL)[i]
}
(i == (OL)){
tmp[i]]<-OL[i]]
(tmp)[i]<-(OL)[i]
}
}
OL<-tmp
}
(OL)
}
.nonOL<-(x, OL){
OLgenes<-((OL))
y<-()
(i 1:(x)){
y[i]]<-x[i]][which(!x[i]] %in% OLgenes)]
(y)[i]<-("Only",i, sep="_")
}
(y)
}
.makeNames<-(x){
y<-x
(i 1:(x)){
(i < (x)){
(j in (i+1):(x)){
y<-(y, (x[i],x[j],sep="_"))
}
}
}
((x)>2){
(i 1:(x)){
(i<(x)){
(j in (i+1):(x)){
(j<(x)){
(k in (j+1):(x)){
y<-(y, (x[i],x[j],x[k], sep="_"))
}
}
}
}
}
}
((x)>3){
(i 1:(x)){
(i<(x)){
(j in (i+1):(x)){
(j<(x)){
(k in (j+1):(x)){
(k<(x)){
(d in (k+1):(x)){
y<-(y, (x[i],x[j],x[k],x[d],sep="_"))
}
}
}
}
}
}
}
}
((x) == 5){
y<-(y, (x[1],x[2],x[3],x[4],x[5], sep="_"))
}
(y)
}
#' Make a Venn diagram
#'
#' Make a Venn diagram from a named list of genes. Uses functions from the VennDiagram package.
#'
#' @param x A named list (max length of 5) of characters (genes) to plot in a Venn Diagram
#' @param title Character indicating the title of the plot. Default="Venn Diagram"
#' @param cols Character indicating the RColorBrewer palette name or list of colours (hex, name, rgb()) to be used. Default is "Dark2"
#' @param lty Line type (1=solid line, 2=dashed line, default="blank")
#' @param scale Boolean indicating if circles should be scaled to size (works only for 2 or 3-way Venn diagrams). Default=FALSE.
#' @param retVals Boolean indicating if the overlaps should be returned (default=FALSE)
#' @return An image of a Venn diagram showing overlaps between groups
#' @export
<-(x, ="Venn Diagram", cols="Dark2", lty="blank", =, retVals=){
(VennDiagram, quietly=)
y<-.getOL(x)
()
((=(2,1, heights=((0.25, 10),"null"))))
venn<-
((x) == 1){
venn<-draw.single.venn(area=(x),
fill=BinfTools::(cols)[1:(x)],
lty=lty,
=(x))
}
((x) == 2){
venn<-draw.pairwise.venn(area1=(x[1]]),
area2=(x[2]]),
cross.area=y$n12,
fill=BinfTools::(cols)[1:(x)],
lty=lty,
= (x),
scaled=,
euler.d=)
}
((x) == 3){
(()){
("overrideTriple", , envir=)
}
venn<-draw.triple.venn(area1=(x[1]]),
area2=(x[2]]),
area3=(x[3]]),
n12=y$n12,
n23=y$n23,
n13=y$n13,
n123=y$n123,
fill=BinfTools::(cols)[1:(x)],
lty=lty,
= (x),
scaled=,
euler.d=)
(()){
(overrideTriple, pos=".GlobalEnv")
}
}
((x) == 4){
venn<-draw.quad.venn(area1=(x[1]]),
area2=(x[2]]),
area3=(x[3]]),
area4=(x[4]]),
n12=y$n12, n13=y$n13, n14=y$n14,
n23=y$n23, n24=y$n24, n34=y$n34,
n123=y$n123, n124=y$n124, n134=y$n134, n234=y$n234,
n1234=y$n1234,
fill=BinfTools::(cols)[1:(x)],
lty=lty,
=(x))
}
((x) == 5){
venn<-draw.quintuple.venn(area1=(x[1]]), area2=(x[2]]),
area3=(x[3]]), area4=(x[4]]), area5=(x[5]]),
n12=y$n12, n13=y$n13, n14=y$n14, n15=y$n15, n23=y$n23, n24=y$n24,
n25=y$n25, n34=y$n34, n35=y$n35, n45=y$n45, n123=y$n123, n124=y$n124,
n125=y$n125, n134=y$n134, n135=y$n135, n145=y$n145, n234=y$n234, n235=y$n235,
n245=y$n245, n345=y$n345, n1234=y$n1234, n1235=y$n1235, n1245=y$n1245,
n1345=y$n1345, n2345=y$n2345, n12345=y$n12345,
fill=BinfTools::(cols)[1:(x)],
lty=lty,
=(x))
}
(, vp=(layout.pos.row=1))
((retVals)){
res<-.getOL(x, retVals=retVals)
res<-(.nonOL(x, res), res)
(res)<-.makeNames((x))
res<-res[which((res)>0)]
(res)
}
}
