olBarplot | R Documentation |
Generates bar plots of the intersect counts of VENNset
and
INTERSECTset
objects generated by the overLapper
function. It is
an alternative to Venn diagrames (e.g. vennPlot
) that scales to larger numbers
of label sets. By default the bars in the plot are colored and grouped by complexity
levels of the intersect sets.
olBarplot(x, mincount = 0, complexity="default", myxlabel = "default", myylabel="Counts", mytitle = "default", ...)
x |
Object of class |
mincount |
Sets minimum number of counts to consider in the bar plot. Default |
complexity |
Allows user to limit the bar plot to specific complexity levels of intersects
by specifying the chosen ones with an integer vector. Default
|
myxlabel |
Defines label of x-axis. |
myylabel |
Defines label of y-axis. |
mytitle |
Defines main title of plot. |
... |
Allows to pass on additional arguments to |
Bar 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
overLapper
, vennPlot
## Sample data: list of vectors with object labels 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"))
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