vennPlot {systemPipeR} | R Documentation |
Ploting function of 2-5 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.
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 4-way 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#TOC-Venn-Diagrams
Thomas Girke
See examples in 'The Electronic Journal of Combinatorics': http://www.combinatorics.org/files/Surveys/ds5/VennSymmExamples.html
overLapper
, olBarplot
## 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)) ## 2-way Venn diagram vennset <- overLapper(setlist[1:2], type="vennsets") vennPlot(vennset) ## 3-way Venn diagram vennset <- overLapper(setlist[1:3], type="vennsets") vennPlot(vennset) ## 4-way Venn diagram vennset <- overLapper(setlist[1:4], type="vennsets") vennPlot(list(vennset, vennset)) ## Pseudo 4-way Venn diagram with circles vennPlot(vennset, type="circle") ## 5-way 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) ## 6-way 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) ## Presence-absence 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"))