data(tamoxifen_peaks)
par(mfrow=c(2,2))
# 2-way Venn
dba.plotVenn(tamoxifen,6:7)
dba.plotVenn(tamoxifen,tamoxifen$masks$ZR75)
# 3-way Venn (done two different ways)
dba.plotVenn(tamoxifen,tamoxifen$masks$MCF7&tamoxifen$masks$Responsive)
olaps <- dba.overlap(tamoxifen,tamoxifen$masks$MCF7&tamoxifen$masks$Responsive)
dba.plotVenn(tamoxifen,overlaps=olaps,
label1="Rep 1",label2="Rep 2",label3="Rep 3",main="MCF7 (Responsive) Replicates")
#Venn of overlaps
Responsive=dba(tamoxifen,tamoxifen$masks$Responsive)
Responsive
Responsive <- dba.peakset(Responsive,1:3,sampID="MCF7")
Responsive <- dba.peakset(Responsive,4:5,sampID="T47D")
Responsive <- dba.peakset(Responsive,6:7,sampID="ZR75")
par(mfrow=c(1,1))
dba.plotVenn(Responsive,Responsive$masks$Consensus)
#4-way overlap
data(tamoxifen_peaks)
tamoxifen <- dba.peakset(tamoxifen, consensus=DBA_TISSUE)
par(mfrow=c(1,1))
dba.plotVenn(tamoxifen,tamoxifen$masks$Consensus,main="Tissue consensus overlaps")
#Venns of differentially bound sites
data(tamoxifen_analysis)
tamoxifen <- dba.contrast(tamoxifen,categories=DBA_CONDITION,block=tamoxifen$masks$MCF7)
tamoxifen <- dba.analyze(tamoxifen,method=c(DBA_EDGER,DBA_DESEQ2))
dba.plotVenn(tamoxifen,contrast=1,method=DBA_ALL_METHODS_BLOCK)
dba.plotVenn(tamoxifen,contrast=1,method=DBA_ALL_BLOCK,bAll=FALSE,bGain=TRUE,bLoss=TRUE)
par(mfrow=c(2,1))
dba.plotVenn(tamoxifen,contrast=1,method=DBA_ALL_BLOCK,bAll=FALSE,bGain=TRUE,bLoss=FALSE)
dba.plotVenn(tamoxifen,contrast=1,method=DBA_ALL_BLOCK,bAll=FALSE,bGain=FALSE,bLoss=TRUE)
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