On 10/20/2009 06:10 PM, Mao Jianfeng wrote:
Dear R-help listers,
I am now asking for helps on how to draw stacked ellipses to
illustrate the shared and specific of multiple objects using R.
My problem comes from my population genetics study. Now, I genotyped
three species, and I get known about the amount of shared and specific
haplotypes in each of the species and their combinations. I want to
illustrate this result in three stack ellipses, with the shared and
unique area of the stack ellipses were annotated with the relative
amount.
my data is as followed:
------------------------------------------------------------
hap.type hap.dis.num hap.dis.per types
hap.Pd 8 27.5862069 Pd specific
hap.Pt 6 20.68965517 Pt specific
hap.Py 9 31.03448276 Py specific
hap.PdPt 3 10.34482759 PdPt shared
hap.PdPy 3 10.34482759 PdPy shared
hap.PtPy 0 0 PtPy shared
hap.3P 0 0 3 species shared
-------------------------------------------------------------
Several individuals of 3 species (Pd, Pt, Py) were genotyped, the
summary of haplotype distribution in species level were contained in
the forward dataset.
Could you please give any direction on this graphical problem? Thank
you in advance.
Hi Mao,
I can't help you with ellipses, but intersectDiagram in the plotrix
package may do what you want in a different way. Try this:
library(plotrix)
hapIntList<-
getIntersectList(3,xnames=c("hap.Pd","hap.Pt","hap.Py"))
# enter the data as follows
#Number of elements in hap.Pd - 1: 27.586
#Number of elements in hap.Pt - 1: 20.689
#Number of elements in hap.Py - 1: 31.034
#Number of elements in hap.Pdhap.Pt - 1: 10.345
#Number of elements in hap.Pdhap.Py - 1: 10.345
#Number of elements in hap.Pthap.Py - 1: 0
#Number of elements in hap.Pdhap.Pthap.Py - 1: 0
#Total number of elements - 1: 99.999
# this is a small bug that I have fixed and will
# not be necessary from v2.7-2 onward
class(hapIntList)<-"intersectList"
intersectDiagram(hapIntList)
I'm quite interested in whether this is of any use to you, as I had not
even thought of this particular use for intersectDiagram.
Jim
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