vennplot: vennplot

In YuLab-SMU/ChIPseeker: ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

vennplot

Description

plot the overlap of a list of object

Usage

vennplot(Sets, by = "gplots", ...)

Arguments

Sets	a list of object, can be vector or GRanges object
by	one of gplots, ggVennDiagram or Vennerable
...	extra parameters using ggVennDiagram. Details see ggVennDiagram

Details

There are two ways to plot, which users can specify through 'by'.

The first way is to use 'gplots' packages, by setting 'by = gplots'. This method is default method. The venn plot produced through this way has no color.

The second way is to use 'ggVennDiagram' packages, by setting 'by = ggVennDiagram'. The venn plot produced through this way has colors which can be defined by users using ggplot2 grammar e.g.(scale_fill_distiller()). And users can specify any details, like digital number, text size and showing percentage or not, by inputting '...' extra parameters.

Value

venn plot that summarize the overlap of peaks from different experiments or gene annotation from different peak files.

Author(s)

G Yu

Examples

## example not run
## require(TxDb.Hsapiens.UCSC.hg19.knownGene)
## txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
## peakfiles <- getSampleFiles()
## peakAnnoList <- lapply(peakfiles, annotatePeak)
## names(peakAnnoList) <- names(peakfiles)
## genes= lapply(peakAnnoList, function(i) as.data.frame(i)$geneId)
## vennplot(genes)

YuLab-SMU/ChIPseeker documentation built on Nov. 2, 2024, 1:45 p.m.