makeVennDiagram: Make Venn Diagram from a list of peaks

In jianhong/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

Make Venn Diagram from a list of peaks

Description

Make Venn Diagram from two or more peak ranges, Also calculate p-value to determine whether those peaks overlap significantly.

Usage

makeVennDiagram(
  Peaks,
  NameOfPeaks,
  maxgap = -1L,
  minoverlap = 0L,
  totalTest,
  by = c("region", "feature", "base"),
  ignore.strand = TRUE,
  connectedPeaks = c("min", "merge", "keepAll", "keepFirstListConsistent"),
  method = c("hyperG", "permutation"),
  TxDb,
  plot = TRUE,
  ...
)

Arguments

Peaks	A list of peaks in GRanges format: See example below.
NameOfPeaks	Character vector to specify the name of Peaks, e.g., c("TF1", "TF2"). This will be used as label in the Venn Diagram.
maxgap, minoverlap	Used in the internal call to findOverlaps() to detect overlaps. See ?findOverlaps in the IRanges package for a description of these arguments.
totalTest	Numeric value to specify the total number of tests performed to obtain the list of peaks. It should be much larger than the number of peaks in the largest peak set.
by	"region", "feature" or "base", default = "region". "feature" means using feature field in the GRanges for calculating overlap, "region" means using chromosome range for calculating overlap, and "base" means calculating overlap in nucleotide level.
ignore.strand	Logical: when set to TRUE, the strand information is ignored in the overlap calculations.
connectedPeaks	If multiple peaks involved in overlapping in several groups, set it to "merge" will count it as only 1, while set it to "min" will count it as the minimal involved peaks in any connected peak group. "keepAll" will show all the orginal counts for each list while the final counts will be same as "min". "keepFirstListConsistent" will keep the counts consistent with first list.
method	method to be used for p value calculation. hyperG means hypergeometric test and permutation means peakPermTest.
TxDb	An object of TxDb.
plot	logical. If TRUE (default), a venn diagram is plotted.
...	Additional arguments to be passed to venn.diagram.

Details

For customized graph options, please see venn.diagram in VennDiagram package.

Value

A p.value is calculated by hypergeometric test or permutation test to determine whether the overlaps of peaks or features are significant.

Author(s)

Lihua Julie Zhu, Jianhong Ou

See Also

findOverlapsOfPeaks, 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, 
                fill=c("#009E73", "#F0E442"), # circle fill color
                col=c("#D55E00", "#0072B2"), #circle border color
                cat.col=c("#D55E00", "#0072B2"))

makeVennDiagram(list(peaks1, peaks2), NameOfPeaks=c("TF1", "TF2"),
                totalTest=100, 
                fill=c("#009E73", "#F0E442"), # circle fill color
                col=c("#D55E00", "#0072B2"), #circle border color
                cat.col=c("#D55E00", "#0072B2"))

###### 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))
}

jianhong/ChIPpeakAnno documentation built on Nov. 1, 2024, 8:55 a.m.