r - Venn Diagram from GRanges -

i have granges objects these( showing 2 of four):

> upmd_hf3a   granges object 398117 ranges , 2 metadata columns:        seqnames                 ranges strand |        type       ncg           <rle>              <iranges>  <rle> | <character> <integer>    [1]     chr1       [     1, 714170]      * |         pmd       280    [2]     chr1       [714171, 732041]      * |      notpmd       103    [3]     chr1       [732042, 762741]      * |         pmd       109    [4]     chr1       [762742, 796127]      * |      notpmd       264    [5]     chr1       [796128, 859047]      * |         pmd       829    ...      ...                    ...    ... .         ...       ... [398113]     chr9 [140133051, 140174235]      * |      notpmd      1725 [398114]     chr9 [140174236, 140176229]      * |         pmd       187 [398115]     chr9 [140176230, 140187041]      * |      notpmd       219 [398116]     chr9 [140967724, 140973103]      * |      notpmd       152 [398117]     chr9 [140973104, 141042747]      * |         pmd      1145  seqinfo: 93 sequences unspecified genome  > upmd_hf3b granges object 334247 ranges , 2 metadata columns:        seqnames                 ranges strand |        type       ncg           <rle>              <iranges>  <rle> | <character> <integer>    [1]     chr1       [     1, 712661]      * |         pmd       274    [2]     chr1       [712662, 734889]      * |      notpmd       116    [3]     chr1       [734890, 770103]      * |         pmd       152    [4]     chr1       [770104, 794246]      * |      notpmd       163    [5]     chr1       [794247, 859587]      * |         pmd       855    ...      ...                    ...    ... .         ...       ... [334243]     chr9 [137315552, 137325053]      * |      notpmd       265 [334244]     chr9 [138776843, 138782261]      * |         pmd       119 [334245]     chr9 [138782262, 138854249]      * |      notpmd      1899 [334246]     chr9 [139633630, 139648757]      * |         pmd       391 [334247]     chr9 [140835156, 140917488]      * |         pmd      1169 ------- seqinfo: 93 sequences unspecified genome 

i have used methylseekr create (predict paritally methylated domains-pmds) these granges objects. want plot venn diagram pmd (for column "type") regions these granges objects show overlap. can please me ? lot in advance

it easier if have granges separately:

library(chippeakanno) peaks1 <- granges("chr1", iranges(seq(1, 100, 5), width=2), "+") peaks2 <- granges("chr1", iranges(seq(2, 20, 3), width=2), "+") peaks3 <- granges("chr1", iranges(seq(10, 50, 4), width=2), "+") res <- makevenndiagram(peaks=list(peaks1, peaks2, peaks3),                        nameofpeaks=c("tf1", "tf2", "tf3")) 

but if have them single granges stratified type metadata, make grangeslist , plot this:

peaks1$type<-"tf1" peaks2$type<-"tf2" peaks3$type<-"tf3" gr <- c(peaks1, peaks2, peaks3) # data  grl <- splitaslist(gr, gr$type) res <- makevenndiagram(peaks=grl, nameofpeaks=names(grl)) 

if want nice , colorful venn diagram, check https://github.com/js229/vennerable/blob/master/readme.md install venerable (i not rforge) , this:

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, paste, collapse="")   venn(setnames=setnames, weight=weight) } v <- venn_cnt2venn(res$venncounts) plot(v)