dba.plotVenn: Draw 2-way, 3-way, or 4-way Venn diagrams of overlaps
In DiffBind: Differential Binding Analysis of ChIP-Seq Peak Data

Description Usage Arguments Value Note Author(s) See Also Examples

Draws 2-way, 3-way, or 4-way Venn diagrams of overlaps

dba.plotVenn(DBA, mask, overlaps, label1, label2, label3, label4, main, sub, 
             contrast, method=DBA$config$AnalysisMethod, 
             th=DBA$config$th, bUsePval=DBA$config$bUsePval,
             bDB=TRUE, bNotDB, bAll=TRUE, bGain=FALSE, bLoss=FALSE,
             labelAttributes, DataType=DBA$config$DataType)

`DBA`	DBA object; if present, only the mask parameter will apply.
`mask`	mask or vector of peakset numbers indicating which peaksets to include in Venn diagram. Only 2 or 3 peaksets should be included. See `dba.mask`. Only one of mask or overlaps is used.
`overlaps`	overlap record, as computed by `dba.overlap(Report=DBA_OLAP_PEAKS)`. Only one of mask or overlaps is used.

`label1`	label for first peakset in diagram
`label2`	label for second peakset in diagram
`label3`	label for third peakset in diagram
`label4`	label for fourth peakset in diagram
`main`	main title for plot
`sub`	subtitle for plot
`contrast`	contrast number(s) to use for results-based plots. This can be a vector of contrast numbers. See `dba.show(DBA, bContrast=T)` to get contrast numbers.
`method`	if `contrast` is specified, include results from analyses using this method or methods: `DBA_DESEQ2` `DBA_DESEQ2_BLOCK` `DBA_EDGER` `DBA_EDGER_BLOCK` `DBA_ALL_METHODS` `DBA_ALL_BLOCK` `DBA_ALL_METHODS_BLOCK`
`th`	if `contrast` is specified, use this significance threshold; all sites with FDR (or p-values, see `bUsePval`) less than or equal to this value will be considered differentially bound (DB).
`bUsePval`	if `contrast` is specified, this logical indicates whether to use FDR (`FALSE`) or p-value (`TRUE`) for thresholding.
`bDB`	if `contrast` is specified, this logical indicates that peaksets should include Differentially Bound (DB) sites (respecting the `th`, `bUsePval`, and `fold` parameters).
`bNotDB`	if `contrast` is specified, this logical indicates that peaksets should include non-Differentially Bound (non-DB) sites (respecting the `th`, `bUsePval`, and `fold` parameters).
`bAll`	if `contrast` is specified, this logical indicates peaksets combining peaks with both positive and negative fold changes should be included.
`bGain`	if `contrast` is specified, this logical indicates that peaksets with only positive fold changes should be included.
`bLoss`	if `contrast` is specified, this logical indicates that peaksets with only negative fold changes should be included.
`labelAttributes`	if `label`s are not specified, use these attributes to create default labels: `DBA_ID` `DBA_TISSUE` `DBA_FACTOR` `DBA_CONDITION` `DBA_TREATMENT` `DBA_REPLICATE` `DBA_CONSENSUS` `DBA_CALLER` Only specified attributes that differ between peaksets will be used for labels; the ones that have the same value for all peaksets will be used as the default subtitle.

DataType

if bReturnPeaksets is set to TRUE, the class of object that peaksets should be returned as:

DBA_DATA_GRANGES
DBA_DATA_RANGEDDATA
DBA_DATA_FRAME

Can be set as default behavior by setting DBA$config$DataType.

Alternatively, this can be set to:

DBA_DATA_DBAOBJECT

to return a results-based DBA object, if a contrast is specified (see dba.report).

Either a list of peaksets is returned invisibly (as described in dba.overlap), or, if DataType=DBA_DATA_DBAOBJECT, a results-based DBA object.

When working with results overlaps (a least one contrast is specified), and results-oriented DBA object is generated internally (as described in dba.report). In some cases, it may be better to generate the DBA object explicitly (using dba.report or setting bReturnPeaksets=TRUE and DataType=DBA_DATA_DBAOBJECT). This include the case where several plots are being made of the same results set, and it takes a long time to generate the results-based DBA object, as well as the case where there are more than four results peaksets and a mask needs to be specified. I

This function relies on vennPlot in the systemPipeR package, written by Thomas Girke.

Rory Stark

dba.analyze, dba.overlap, dba.report, dba.plotPCA, vennPlot

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_counts)
tamoxifen <- dba.contrast(tamoxifen,design="~Tissue+Condition")
tamoxifen <- dba.analyze(tamoxifen,method=c(DBA_EDGER,DBA_DESEQ2))
dba.plotVenn(tamoxifen,contrast=1,method=DBA_ALL_METHODS,
             bAll=FALSE,bGain=TRUE,bLoss=TRUE)
par(mfrow=c(2,1))
dba.plotVenn(tamoxifen,contrast=1,method=DBA_ALL_METHODS,
             bAll=FALSE,bGain=TRUE,bLoss=FALSE)
dba.plotVenn(tamoxifen,contrast=1,method=DBA_ALL_METHODS,
             bAll=FALSE,bGain=FALSE,bLoss=TRUE)

data(tamoxifen_counts)
tamoxifen <- dba.contrast(tamoxifen,design=FALSE,block=DBA_TISSUE)
tamoxifen <- dba.contrast(tamoxifen,design="~Tissue + Condition",
                          contrast=c("Condition","Responsive","Resistant"))
tamoxifen <- dba.analyze(tamoxifen,method=DBA_ALL_METHODS)
dba.plotVenn(tamoxifen,contrast=1:2,method=c(DBA_DESEQ2,DBA_DESEQ2_BLOCK))
tamoxifen.db <- dba.report(tamoxifen,contrast=1:2,method=DBA_ALL_METHODS_BLOCK,
                           bDB=TRUE)
dba.plotVenn(tamoxifen.db,mask=1:2)
dba.plotVenn(tamoxifen.db,mask=3:6)