[BioC] Set plot title and background in makeVennDiagram (ChIPpeakAnno)

Zhu, Lihua (Julie) Julie.Zhu at umassmed.edu
Sat Sep 15 05:03:44 CEST 2012


Thanks to Jianhong, options from package VennDiagram are now available in ChIPpeakAnno:::makeVennDiagram (version 2.5.12).  You can specify the title using main and background color using fill. For more options, please type ?venn.diagram.

Here is an example by Jianhong,

peaks1 = RangedData(IRanges(start = c(967654, 2010897, 2496704),
    end = c(967754, 2010997, 2496804), names = c("Site1", "Site2", "Site3")),
    space = c("1", "2", "3"), strand=as.integer(1),feature=c("a","b","f"))
peaks2 = RangedData(IRanges(start = c(967659, 2010898,2496700,3075866,3123260),
    end = c(967869, 2011108, 2496920, 3076166, 3123470),
    names = c("t1", "t2", "t3", "t4", "t5")),
    space = c("1", "2", "3", "1", "2"), strand = c(1, 1, -1,-1,1), feature=c("a","b","c","d","a"))
makeVennDiagram(RangedDataList(peaks1,peaks2, peaks1, peaks2), NameOfPeaks=c("TF1", "TF2","TF3", "TF4"),
     totalTest=100,useFeature=TRUE, main="Venn Diagram",
    col = "transparent",fill = c("cornflowerblue", "green", "yellow", "darkorchid1"),
    alpha = 0.50,label.col = c("orange", "white", "darkorchid4", "white", "white", "white", "white", "white", "darkblue", "white", "white", "white", "white", "darkgreen", "white"), cat.col = c("darkblue", "darkgreen", "orange", "darkorchid4"))

Best regards,


On 9/13/12 9:41 AM, "António Miguel de Jesus Domingues" <amjdomingues at gmail.com> wrote:

Hi Julie,


If it is not asking too much and how much work it takes, but adding colours to the background of the circles would also be nice for presentations and papers. Basically some possibilities along the lines of the R package VennDiagram (http://www.biomedcentral.com/1471-2105/12/35)

Good package you've developed btw.


On 13 September 2012 15:35, Zhu, Lihua (Julie) <Julie.Zhu at umassmed.edu> wrote:

Thanks for the great suggestion! Currently makeVennDiagram only supports
limited plotting options, i.e., cex and count.col. I will add the title in
my to do list.

Best regards,


On 9/13/12 9:03 AM, "António Miguel de Jesus Domingues"
<amjdomingues at gmail.com> wrote:

> Hi Bioconducters,
> I am comparing 2 list of ChIP peaks obtained with different peak callers
> and would like to change some of the graphical options of the plot created
> by makeVennDiagram. Crucially I would like to add a title to the plot.
> Is there any way to change the graphical options of makeVennDiagram?
> Cheers,
> António

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