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Tan Hui Hui Jenny

2005-Jun-09 00:15 UTC

[R] How to plot more than 3 sets in Venn Diagrams?

I'm trying to plot Venn diagrams with more than 3 sets (5 actually) in order
to describe graphically the genetic variation between populations.
 
I tried the limma library but realised it can only plot 3 sets.
 
Is there any solution? Of course I could plot the chart manually but it'll
take too long (have other datasets)..... One of my dataset is given below.
 
THanks for any advice. 
 
j
 
	AA	 CH	 EA	 IN	 MY	
[1,]	 0	 0	 0	 1	 0	
[2,]	 1	 0	 0	 0	 0	
[3,]	 1	 0	 0	 0	 0	
[4,]	 0	 0	 0	 0	 1	
[5,]	 1	 0	 0	 0	 0	
[6,]	 1	 0	 0	 0	 0	
[7,]	 1	 0	 0	 0	 0	
[8,]	 1	 0	 0	 1	 0	
[9,]	 1	 0	 0	 0	 0	
[10,]	 1	 0	 0	 0	 0	
[11,]	 1	 0	 0	 0	 0	
[12,]	 0	 0	 0	 0	 1	
[13,]	 1	 0	 0	 0	 0	
[14,]	 0	 0	 1	 0	 0	
[15,]	 1	 0	 0	 0	 0	
[16,]	 0	 0	 1	 0	 0	
[17,]	 1	 0	 0	 0	 0	
[18,]	 0	 0	 0	 1	 0	
[19,]	 1	 0	 0	 1	 0	
[20,]	 0	 0	 1	 0	 0	
[21,]	 0	 1	 0	 0	 0	
[22,]	 1	 0	 0	 0	 0	
[23,]	 0	 0	 1	 0	 0	
[24,]	 1	 0	 1	 1	 1	
[25,]	 0	 1	 0	 0	 0	
[26,]	 1	 0	 0	 0	 0	
[27,]	 1	 0	 0	 0	 0	
[28,]	 0	 0	 0	 1	 0	
[29,]	 0	 0	 0	 1	 0	
[30,]	 1	 0	 0	 0	 0	
[31,]	 1	 0	 0	 0	 0	
[32,]	 0	 0	 0	 1	 0	
[33,]	 0	 0	 0	 1	 0	
[34,]	 0	 1	 0	 0	 0	
[35,]	 1	 0	 0	 0	 0	
[36,]	 0	 0	 0	 1	 0	
[37,]	 0	 0	 1	 1	 0	
[38,]	 1	 0	 0	 1	 0	
[39,]	 0	 0	 0	 1	 0	
[40,]	 0	 0	 0	 1	 0	
[41,]	 0	 1	 0	 0	 0	
[42,]	 1	 0	 0	 0	 0	
[43,]	 0	 0	 0	 1	 0	
[44,]	 0	 0	 1	 0	 0	
[45,]	 1	 0	 0	 0	 0	
[46,]	 1	 0	 0	 0	 0	
[47,]	 0	 0	 0	 1	 0	
[48,]	 1	 0	 0	 0	 0	
[49,]	 0	 0	 0	 1	 0	
[50,]	 0	 0	 1	 0	 0	
[51,]	 0	 0	 0	 1	 0	
[52,]	 1	 0	 0	 0	 0	
[53,]	 0	 0	 0	 1	 0	
[54,]	 1	 0	 0	 0	 0	
[55,]	 0	 1	 0	 0	 0

Duncan Murdoch

2005-Jun-09 02:11 UTC

head link

[R] How to plot more than 3 sets in Venn Diagrams?

Tan Hui Hui Jenny wrote:> I'm trying to plot Venn diagrams with more than 3 sets (5 actually) in
order to describe graphically the genetic variation between populations.
>  
> I tried the limma library but realised it can only plot 3 sets.
>  
> Is there any solution? Of course I could plot the chart manually but
it'll take too long (have other datasets)..... One of my dataset is given
below.
The general Venn diagrams with more than 3 sets are ugly.  You can't use 
circles, you need strange shapes to get all the 2^n-1 possible subsets.

Duncan Murdoch

Gabor Grothendieck

2005-Jun-09 03:10 UTC

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[R] How to plot more than 3 sets in Venn Diagrams?

If the data you posted is prototypical of your datasets then note that:

- it has two disconnected components of 1 and 4 sets
- there are only 8 unique rows out of 32
- 5 of these 8 are the regions that contain only the non-intersecting
  portion of each of the 5 sets
> unique(mydata)   AA CH EA IN MY
1   0  0  0  1  0
2   1  0  0  0  0
4   0  0  0  0  1
8   1  0  0  1  0
14  0  0  1  0  0
21  0  1  0  0  0
24  1  0  1  1  1
37  0  0  1  1  0

Thus these are not very interesting Venn diagrams as they are
quite sparse.  Perhaps you would be better off to represent them 
as bipartite graphs with a node for each row and a node for each 
column with the edges corresponding to the ones.  The RGraphViz 
package (or graphViz, itself, locatable via google) could be used for 
that.


On 6/8/05, Tan Hui Hui Jenny <medp9193 at nus.edu.sg>
wrote:> I'm trying to plot Venn diagrams with more than 3 sets (5 actually) in
order to describe graphically the genetic variation between populations.
> 
> I tried the limma library but realised it can only plot 3 sets.
> 
> Is there any solution? Of course I could plot the chart manually but
it'll take too long (have other datasets)..... One of my dataset is given
below.
> 
> THanks for any advice.
> 
> j
> 
>        AA       CH      EA      IN      MY
> [1,]     0       0       0       1       0
> [2,]     1       0       0       0       0
> [3,]     1       0       0       0       0
> [4,]     0       0       0       0       1
> [5,]     1       0       0       0       0
> [6,]     1       0       0       0       0
> [7,]     1       0       0       0       0
> [8,]     1       0       0       1       0
> [9,]     1       0       0       0       0
> [10,]    1       0       0       0       0
> [11,]    1       0       0       0       0
> [12,]    0       0       0       0       1
> [13,]    1       0       0       0       0
> [14,]    0       0       1       0       0
> [15,]    1       0       0       0       0
> [16,]    0       0       1       0       0
> [17,]    1       0       0       0       0
> [18,]    0       0       0       1       0
> [19,]    1       0       0       1       0
> [20,]    0       0       1       0       0
> [21,]    0       1       0       0       0
> [22,]    1       0       0       0       0
> [23,]    0       0       1       0       0
> [24,]    1       0       1       1       1
> [25,]    0       1       0       0       0
> [26,]    1       0       0       0       0
> [27,]    1       0       0       0       0
> [28,]    0       0       0       1       0
> [29,]    0       0       0       1       0
> [30,]    1       0       0       0       0
> [31,]    1       0       0       0       0
> [32,]    0       0       0       1       0
> [33,]    0       0       0       1       0
> [34,]    0       1       0       0       0
> [35,]    1       0       0       0       0
> [36,]    0       0       0       1       0
> [37,]    0       0       1       1       0
> [38,]    1       0       0       1       0
> [39,]    0       0       0       1       0
> [40,]    0       0       0       1       0
> [41,]    0       1       0       0       0
> [42,]    1       0       0       0       0
> [43,]    0       0       0       1       0
> [44,]    0       0       1       0       0
> [45,]    1       0       0       0       0
> [46,]    1       0       0       0       0
> [47,]    0       0       0       1       0
> [48,]    1       0       0       0       0
> [49,]    0       0       0       1       0
> [50,]    0       0       1       0       0
> [51,]    0       0       0       1       0
> [52,]    1       0       0       0       0
> [53,]    0       0       0       1       0
> [54,]    1       0       0       0       0
> [55,]    0       1       0       0       0

davidr@rhotrading.com

2005-Jun-09 14:53 UTC

head link

[R] How to plot more than 3 sets in Venn Diagrams?

Here is a link to see what's possible. 
http://www.combinatorics.org/Surveys/ds5/VennSymmEJC.html

Venn did 4 sets with ellipses (see wikipedia.)

(There was an article in the last year (I think) in one of my math
journals that presented someone who made these complex Venn diagrams as
artwork and sold, but I can't remember the person's name right now.)

HTH
David L. Reiner

-----Original Message-----
From: r-help-bounces at stat.math.ethz.ch
[mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Tan Hui Hui Jenny
Sent: Wednesday, June 08, 2005 7:16 PM
To: r-help at stat.math.ethz.ch
Subject: [R] How to plot more than 3 sets in Venn Diagrams?

I'm trying to plot Venn diagrams with more than 3 sets (5 actually) in
order to describe graphically the genetic variation between populations.
 
I tried the limma library but realised it can only plot 3 sets.
 
Is there any solution? Of course I could plot the chart manually but
it'll take too long (have other datasets)..... One of my dataset is
given below. 
 
THanks for any advice. 
 
j
 
	AA	 CH	 EA	 IN	 MY	
[1,]	 0	 0	 0	 1	 0	
[2,]	 1	 0	 0	 0	 0	
[3,]	 1	 0	 0	 0	 0	
[4,]	 0	 0	 0	 0	 1	
[5,]	 1	 0	 0	 0	 0	
[6,]	 1	 0	 0	 0	 0	
[7,]	 1	 0	 0	 0	 0	
[8,]	 1	 0	 0	 1	 0	
[9,]	 1	 0	 0	 0	 0	
[10,]	 1	 0	 0	 0	 0	
[11,]	 1	 0	 0	 0	 0	
[12,]	 0	 0	 0	 0	 1	
[13,]	 1	 0	 0	 0	 0	
[14,]	 0	 0	 1	 0	 0	
[15,]	 1	 0	 0	 0	 0	
[16,]	 0	 0	 1	 0	 0	
[17,]	 1	 0	 0	 0	 0	
[18,]	 0	 0	 0	 1	 0	
[19,]	 1	 0	 0	 1	 0	
[20,]	 0	 0	 1	 0	 0	
[21,]	 0	 1	 0	 0	 0	
[22,]	 1	 0	 0	 0	 0	
[23,]	 0	 0	 1	 0	 0	
[24,]	 1	 0	 1	 1	 1	
[25,]	 0	 1	 0	 0	 0	
[26,]	 1	 0	 0	 0	 0	
[27,]	 1	 0	 0	 0	 0	
[28,]	 0	 0	 0	 1	 0	
[29,]	 0	 0	 0	 1	 0	
[30,]	 1	 0	 0	 0	 0	
[31,]	 1	 0	 0	 0	 0	
[32,]	 0	 0	 0	 1	 0	
[33,]	 0	 0	 0	 1	 0	
[34,]	 0	 1	 0	 0	 0	
[35,]	 1	 0	 0	 0	 0	
[36,]	 0	 0	 0	 1	 0	
[37,]	 0	 0	 1	 1	 0	
[38,]	 1	 0	 0	 1	 0	
[39,]	 0	 0	 0	 1	 0	
[40,]	 0	 0	 0	 1	 0	
[41,]	 0	 1	 0	 0	 0	
[42,]	 1	 0	 0	 0	 0	
[43,]	 0	 0	 0	 1	 0	
[44,]	 0	 0	 1	 0	 0	
[45,]	 1	 0	 0	 0	 0	
[46,]	 1	 0	 0	 0	 0	
[47,]	 0	 0	 0	 1	 0	
[48,]	 1	 0	 0	 0	 0	
[49,]	 0	 0	 0	 1	 0	
[50,]	 0	 0	 1	 0	 0	
[51,]	 0	 0	 0	 1	 0	
[52,]	 1	 0	 0	 0	 0	
[53,]	 0	 0	 0	 1	 0	
[54,]	 1	 0	 0	 0	 0	
[55,]	 0	 1	 0	 0	 0

______________________________________________
R-help at stat.math.ethz.ch mailing list
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PLEASE do read the posting guide!
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Charles Geyer

2005-Jun-10 16:08 UTC

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[R] How to plot more than 3 sets in Venn Diagrams?

> Message: 23
> Date: Thu, 9 Jun 2005 09:53:02 -0500
> From: <davidr at rhotrading.com>
> Subject: RE: [R] How to plot more than 3 sets in Venn Diagrams?
> To: "Tan Hui Hui Jenny" <medp9193 at nus.edu.sg>,
> 	<r-help at stat.math.ethz.ch>
> Message-ID:
> 	<12AE52872B5C5348BE5CF47C707FF53A5FB672 at rhosvr02.rhotrading.com>
> Content-Type: text/plain;	charset="us-ascii"
> 
> Here is a link to see what's possible. 
> http://www.combinatorics.org/Surveys/ds5/VennSymmEJC.html
> 
> Venn did 4 sets with ellipses (see wikipedia.)
> 
> (There was an article in the last year (I think) in one of my math
> journals that presented someone who made these complex Venn diagrams as
> artwork and sold, but I can't remember the person's name right
now.)
The book is

    Cogwheels of the Mind : The Story of Venn Diagrams
    by A. W. F. Edwards (foreword by Ian Stewart)
    Hardcover: 136 pages
    Publisher: The Johns Hopkins University Press (April 26, 2004)
    ISBN: 0801874343

It is a really beautiful book.  There are also some journal articles
on the subject by Edwards and by Branko Grunbaum
(http://www.math.washington.edu/~grunbaum/BG228.pdf)

Edwards is my intellectual grandfather (thesis advisor's thesis advisor),
and it is a pleasure to recommend this book.  (A bit irrelevant to R,
I know, but still ...)

Jim Lemon

2005-Jun-10 22:55 UTC

head link

[R] How to plot more than 3 sets in Venn Diagrams?

Tan Hui Hui Jenny wrote:> I'm trying to plot Venn diagrams with more than 3 sets (5 actually) in
order to describe graphically the genetic variation between populations.
>  
> I tried the limma library but realised it can only plot 3 sets.
>  
> Is there any solution? Of course I could plot the chart manually but
it'll take too long (have other datasets)..... One of my dataset is given
below.
>  Hi Jenny,

Best I could do is four sets. The code is a bit rough but consistent 
with the vennDiagram function in the limma package.

Jim
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