How to set the circle size same proportion of the number of peaks when there are more than 2 sets using `makeVennDiagram`?

[danli349]

Hello,

library(ChIPpeakAnno)

Control_Menin <- toGRanges("peaks/changeformat/4934_Control_Menin_peaks.narrowPeak",
                               format="narrowPeak", header=FALSE)
Control_Menin$score <- as.numeric(Control_Menin$score)
Control_Menin_reduce <- reduce(Control_Menin, drop.empty.ranges=FALSE, min.gapwidth=1L,
                      with.revmap=FALSE,
                      with.inframe.attrib=FALSE, ignore.strand=FALSE)

Control_Set1a <- toGRanges("peaks/changeformat/4934_Control_Set1a_peaks.narrowPeak",
                           format="narrowPeak", header=FALSE)
Control_Set1a$score <- as.numeric(Control_Set1a$score)
Control_Set1a_reduce <- reduce(Control_Set1a, drop.empty.ranges=FALSE, min.gapwidth=1L,
                               with.revmap=FALSE,
                               with.inframe.attrib=FALSE, ignore.strand=FALSE)

MLL4_MERGED <- toGRanges("peaks/changeformat/SICER_HOMER_MLL4_MERGED.bed",
                             format="BED", header=FALSE)
MLL4_MERGED$score <- as.numeric(MLL4_MERGED$score)
MLL4_MERGED_reduce <- reduce(MLL4_MERGED, drop.empty.ranges=FALSE, min.gapwidth=1L,
                                 with.revmap=FALSE,
                                 with.inframe.attrib=FALSE, ignore.strand=FALSE)

ol <- findOverlapsOfPeaks(Control_Menin_reduce, Control_Set1a_reduce, MLL4_MERGED_reduce)
makeVennDiagram(ol, NameOfPeaks=c("Control_Menin", "Control_Set1a",
                                  "MLL4_MERGED"),
                fill=c("#CC79A7", "#56B4E9", "#F0E442"),
                col=c("#D55E00", "#0072B2", "#E69F00"), 
                cat.col=c("#D55E00", "#0072B2", "#E69F00"))

When there are only 2 sets, makeVennDiagram show the circle size in the same proportion as the number of peaks. But when there are 3 sets or more, makeVennDiagram show the circle size all the same.

How to set the circle size in the same proportion as the number of peaks when there are more than 2 sets using makeVennDiagram? Thanks

[hukai916]

I bet it rather challenging to make proportional Venn Diagrams with more than 2 sets. It is mathematically not possible in my mind.

[danli349]

@hukai916 How about if we can use ovals instead of only round circles? Thanks

[jianhong]

Hi @danli349 , Thank you for your question. Just above the section Generate_annotation_data, there is documentation to plot the Venn by Vennerable package. I copied the doc here:

Alternatively, users have the option to use other tools to plot Venn diagram. The following code demonstrates how to use a third party R package Vernerable with the output from the function findOverlapsOfPeaks.

#     install.packages("Vennerable", repos="http://R-Forge.R-project.org",
#                     type="source")
#     library(Vennerable)
#     venn_cnt2venn <- function(venn_cnt){
#         n <- which(colnames(venn_cnt)=="Counts") - 1
#         SetNames=colnames(venn_cnt)[1:n]
#         Weight=venn_cnt[,"Counts"]
#         names(Weight) <- apply(venn_cnt[,1:n], 1, base::paste, collapse="")
#         Venn(SetNames=SetNames, Weight=Weight)
#     }
#
#     v <- venn_cnt2venn(ol$venn_cnt)
#     plot(v)

[hukai916]

@hukai916 How about if we can use ovals instead of only round circles? Thanks

It is possible with ovals @danli349, this R package can do that: https://cran.r-project.org/web/packages/eulerr/vignettes/introduction.html

Just follow @jianhong's documentation and draw with your favorable third-party plotting tools.

[danli349]

@hukai916 @jianhong That is awesome. Thanks a lot.