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Last data update: 2014.03.03 |
Make Venn Diagram from a list of peaksDescriptionMake Venn Diagram from two or more peak ranges, Also calculate p-value to determine whether those peaks overlap significantly. Usage
makeVennDiagram(Peaks, NameOfPeaks, maxgap = 0L, minoverlap = 1L,
totalTest, by = c("region", "feature", "base"),
ignore.strand = TRUE, connectedPeaks = c("min",
"merge", "keepAll"), method = c("hyperG",
"permutation"), TxDb, ...)
Arguments
DetailsFor customized graph options, please see venn.diagram in VennDiagram package. ValueIn addition to a Venn Diagram produced, a p.value is calculated by hypergeometric test to determine whether the peaks or features are overlapped significantly. Author(s)Lihua Julie Zhu, Jianhong Ou See AlsofindOverlapsOfPeaks, venn.diagram, peakPermTest Examples
if (interactive()){
peaks1 <- GRanges(seqnames=c("1", "2", "3"),
IRanges(start=c(967654, 2010897, 2496704),
end=c(967754, 2010997, 2496804),
names=c("Site1", "Site2", "Site3")),
strand="+",
feature=c("a","b","f"))
peaks2 = GRanges(seqnames=c("1", "2", "3", "1", "2"),
IRanges(start = c(967659, 2010898,2496700,
3075866,3123260),
end = c(967869, 2011108, 2496920,
3076166, 3123470),
names = c("t1", "t2", "t3", "t4", "t5")),
strand = c("+", "+", "-", "-", "+"),
feature=c("a","b","c","d","a"))
makeVennDiagram(list(peaks1, peaks2), NameOfPeaks=c("TF1", "TF2"),
totalTest=100,scaled=FALSE, euler.d=FALSE)
makeVennDiagram(list(peaks1, peaks2), NameOfPeaks=c("TF1", "TF2"),
totalTest=100)
###### 4-way diagram using annotated feature instead of chromosome ranges
makeVennDiagram(list(peaks1, peaks2, peaks1, peaks2),
NameOfPeaks=c("TF1", "TF2","TF3", "TF4"),
totalTest=100, by="feature",
main = "Venn Diagram for 4 peak lists",
fill=c(1,2,3,4))
}
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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> library(ChIPpeakAnno)
Loading required package: grid
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: Biostrings
Loading required package: XVector
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: VennDiagram
Loading required package: futile.logger
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ChIPpeakAnno/makeVennDiagram.Rd_%03d_medium.png", width=480, height=480)
> ### Name: makeVennDiagram
> ### Title: Make Venn Diagram from a list of peaks
> ### Aliases: makeVennDiagram
> ### Keywords: graph
>
> ### ** Examples
>
> #if (interactive()){
> peaks1 <- GRanges(seqnames=c("1", "2", "3"),
+ IRanges(start=c(967654, 2010897, 2496704),
+ end=c(967754, 2010997, 2496804),
+ names=c("Site1", "Site2", "Site3")),
+ strand="+",
+ feature=c("a","b","f"))
> peaks2 = GRanges(seqnames=c("1", "2", "3", "1", "2"),
+ IRanges(start = c(967659, 2010898,2496700,
+ 3075866,3123260),
+ end = c(967869, 2011108, 2496920,
+ 3076166, 3123470),
+ names = c("t1", "t2", "t3", "t4", "t5")),
+ strand = c("+", "+", "-", "-", "+"),
+ feature=c("a","b","c","d","a"))
> makeVennDiagram(list(peaks1, peaks2), NameOfPeaks=c("TF1", "TF2"),
+ totalTest=100,scaled=FALSE, euler.d=FALSE)
$p.value
TF1 TF2 pval
[1,] 1 1 6.184292e-05
$vennCounts
TF1 TF2 Counts
[1,] 0 0 95
[2,] 0 1 2
[3,] 1 0 0
[4,] 1 1 3
attr(,"class")
[1] "VennCounts"
>
> makeVennDiagram(list(peaks1, peaks2), NameOfPeaks=c("TF1", "TF2"),
+ totalTest=100)
$p.value
TF1 TF2 pval
[1,] 1 1 6.184292e-05
$vennCounts
TF1 TF2 Counts
[1,] 0 0 95
[2,] 0 1 2
[3,] 1 0 0
[4,] 1 1 3
attr(,"class")
[1] "VennCounts"
>
> ###### 4-way diagram using annotated feature instead of chromosome ranges
>
> makeVennDiagram(list(peaks1, peaks2, peaks1, peaks2),
+ NameOfPeaks=c("TF1", "TF2","TF3", "TF4"),
+ totalTest=100, by="feature",
+ main = "Venn Diagram for 4 peak lists",
+ fill=c(1,2,3,4))
$p.value
TF1 TF2 TF3 TF4 pval
[1,] 0 0 1 1 3.586889e-03
[2,] 0 1 0 1 2.550223e-07
[3,] 0 1 1 0 3.586889e-03
[4,] 1 0 0 1 3.586889e-03
[5,] 1 0 1 0 6.184292e-06
[6,] 1 1 0 0 3.586889e-03
$vennCounts
TF1 TF2 TF3 TF4 Counts
[1,] 0 0 0 0 95
[2,] 0 0 0 1 0
[3,] 0 0 1 0 0
[4,] 0 0 1 1 0
[5,] 0 1 0 0 0
[6,] 0 1 0 1 2
[7,] 0 1 1 0 0
[8,] 0 1 1 1 0
[9,] 1 0 0 0 0
[10,] 1 0 0 1 0
[11,] 1 0 1 0 1
[12,] 1 0 1 1 0
[13,] 1 1 0 0 0
[14,] 1 1 0 1 0
[15,] 1 1 1 0 0
[16,] 1 1 1 1 2
attr(,"class")
[1] "VennCounts"
> #}
>
>
>
>
>
> dev.off()
null device
1
>
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