Description Usage Arguments Value Note Author(s) References See Also Examples
Ploting function of 25 way Venn diagrams from 'VENNset' objects or count set vectors. A useful feature is the possiblity to combine the counts from several Venn comparisons with the same number of label sets in a single Venn diagram.
1  vennPlot(x, mymain = "Venn Diagram", mysub = "default", setlabels = "default", yoffset = seq(0, 10, by = 0.34), ccol = rep(1, 31), colmode = 1, lcol = c("#FF0000", "#008B00", "#0000FF", "#FF00FF", "#CD8500"), lines = c("#FF0000", "#008B00", "#0000FF", "#FF00FF", "#CD8500"), mylwd = 3, diacol = 1, type = "ellipse", ccex = 1, lcex = 1, sepsplit = "_", ...)

x 

mymain 
Main title of plot. 
mysub 
Subtitle of plot. Default 
setlabels 
The argument 
yoffset 
The results from several Venn comparisons can be combined in a single Venn diagram
by assigning to 
ccol 
Character or numeric 
colmode 
See argument 
lcol 
Character or numeric 
lines 
Character or numeric 
mylwd 
Defines line width of shapes used in plot. 
diacol 
See argument 
type 
Defines shapes used to plot 4way Venn diagram. Default 
ccex 
Controls font size for count values. 
lcex 
Controls font size for set labels. 
sepsplit 
Character used to separate sample labels in Venn counts. 
... 
Additional arguments to pass on. 
Venn diagram plot.
The functions provided here are an extension of the Venn diagram resources on this site: http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual#TOCVennDiagrams
Thomas Girke
See examples in 'The Electronic Journal of Combinatorics': http://www.combinatorics.org/files/Surveys/ds5/VennSymmExamples.html
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60  ## Sample data
setlist < list(A=sample(letters, 18), B=sample(letters, 16),
C=sample(letters, 20), D=sample(letters, 22),
E=sample(letters, 18), F=sample(letters, 22))
## 2way Venn diagram
vennset < overLapper(setlist[1:2], type="vennsets")
vennPlot(vennset)
## 3way Venn diagram
vennset < overLapper(setlist[1:3], type="vennsets")
vennPlot(vennset)
## 4way Venn diagram
vennset < overLapper(setlist[1:4], type="vennsets")
vennPlot(list(vennset, vennset))
## Pseudo 4way Venn diagram with circles
vennPlot(vennset, type="circle")
## 5way Venn diagram
vennset < overLapper(setlist[1:5], type="vennsets")
vennPlot(vennset)
## Alternative Venn count input to vennPlot (not recommended!)
counts < sapply(vennlist(vennset), length)
vennPlot(counts)
## 6way Venn comparison as bar plot
vennset < overLapper(setlist[1:6], type="vennsets")
olBarplot(vennset, mincount=1)
## Bar plot of standard intersect counts
interset < overLapper(setlist, type="intersects")
olBarplot(interset, mincount=1)
## Accessor methods for VENNset/INTERSECTset objects
names(vennset)
names(interset)
setlist(vennset)
intersectmatrix(vennset)
complexitylevels(vennset)
vennlist(vennset)
intersectlist(interset)
## Coerce VENNset/INTERSECTset object to list
as.list(vennset)
as.list(interset)
## Pairwise intersect matrix and heatmap
olMA < sapply(names(setlist),
function(x) sapply(names(setlist),
function(y) sum(setlist[[x]] %in% setlist[[y]])))
olMA
heatmap(olMA, Rowv=NA, Colv=NA)
## Presenceabsence matrices for large numbers of sample sets
interset < overLapper(setlist=setlist, type="intersects", complexity=2)
(paMA < intersectmatrix(interset))
heatmap(paMA, Rowv=NA, Colv=NA, col=c("white", "gray"))

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