[BioC] Creating a Venn Diagram with 4 sets

[James W. MacDonald]

Hi Whomever,

Three things.

First, VennDiagram isn't a BioC package, so this isn't the correct list 
for this question. You would be better off on R-help, or directly 
contacting the author of that package.

Second, anonymous posts tend to bring out the less civilized nature of 
man. If you choose not to identify yourself, it is less likely you will 
get a response, and if you do get a response it will likely be more 
terse and possibly rude than if you had identified yourself.


Third, the data you show in your matrix are not the same as what you get 
from the list (x) you use in your call to venn.diagram(). How did you 
decide to construct the list (x), and why did you think it would give 
you the same results as in your data structure? When you re-post on 
R-help, you should at least show how you arrived at your data matrix, 
and explain why you think the list you pass to venn.diagram() should 
give identical results.

Best,

Jim



On 4/13/2012 4:02 AM, lcarvalh at btk.fi wrote:
> I am trying to create a Venn diagram for this data, and the Venn diagram needs
> to show the number of occurring cases of each different intersection, for
> example in the diagram section were c1,c2 intersect each other should be the
> value 13.
>
> Data:
>
>        c1 c2 c3 c4 Counts
>   [1,]  0  0  0  0     26
>   [2,]  0  0  0  1     27
>   [3,]  0  0  1  0      4
>   [4,]  0  0  1  1      6
>   [5,]  0  1  0  0      5
>   [6,]  0  1  0  1     12
>   [7,]  0  1  1  0     42
>   [8,]  0  1  1  1     78
>   [9,]  1  0  0  0     18
> [10,]  1  0  0  1     52
> [11,]  1  0  1  0      4
> [12,]  1  0  1  1     63
> [13,]  1  1  0  0     13
> [14,]  1  1  0  1     47
> [15,]  1  1  1  0     88
> [16,]  1  1  1  1    182
>
> I have been trying to use the package VennDiagram, with the function
> venn.diagram. But I am only able to get some of the values correct in the
> diagram. Can anyone give me some help? maybe some other way of making a nice
> looking venn diagram? or help me correcting this code so that I can produce the
> correct venn diagram?
>
> Code:
>
>
> library (VennDiagram)
> library(grid)
>
> venn.diagram(
> 	x = list(
>    	       comp1=c(1:18, 19:31, 32:119, 120:123, 124:186, 187:238, 239:420,
> 421:467),
>
> 		comp4=c(692:695,561:603,472:560,120:123, 187:238, 239:420, 603:681,682:688),
> 		comp2=c(468:472,19:31, 32:119, 239:420, 421:467, 561:602, 603:680, 681:6918),
> 		comp3=c(780:807,716:779,603:680,681:691, 239:420, 421:467, 124:186,
> 187:238)		),
> 	filename = "quadruple_Venn.tiff",
> 	col = "black",
> 	lty = "dotted",
> 	lwd = 4,
> 	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"),
> 	cex = 2.5,
> 	fontfamily = "serif",
> 	fontface = "bold",
> 	cat.col = c("darkblue", "darkgreen", "orange", "darkorchid4"),
> 	cat.cex = 2.5,
> 	cat.fontfamily = "serif"
> 	);
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099