venn plot data?

Question

[star]

I like to draw a Venn diagram plot for my dataset but I couldn't do it. I can do it with other packages like Vennerable or VennDiagram, but I do not know how I can make a list of data as INPUT for venn R packages?

Data:

Names = c("A", "B", "C", "D", "E")
Intersect = c(`00000`= 0, `10000` = 1534, `01000` = 600, `00100` = 189978, `00010` = 2000,`00001` = 2750, 
`11000` = 9,`10100` = 1278, `10010` = 109, `10001` = 1,`01100` = 810, `01010` = 28, `01001` = 22, `00110` = 2343, `00101` = 1169, `00011` = 8, `11100` = 9, `11010` = 3, `11001` = 0, 
`10110` = 99, `10101` = 0, `10011` = 0, `01110` = 49, `01101` = 25, `01011` = 0, `00111` = 4, `11110` = 3, `11101` = 0, `11011` = 0, `10111` = 0, `01111` = 0, `11111` = 0)

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

[Luiz]

Personally, i prefer to use online tools such as interactiveen or genevenn in order to build a venn diagram. Do you already tried it?

[lieven.sterck]

another alternative: http://bioinformatics.psb.ugent.be/webtools/Venn/

[star]

would you please let me know how can I use this tool? I have bed files contain genomic coordinates, and when I upload them this tool only give me the total number related to each beb file.

[star]

some times I have more than 5-6 datasets, so the online tools are not useful in that case, and I think the interactiveen tool also use Vennerable packages for drawing.

[Luiz]

Interactiven is able toe draw from 2 to 6 datasets.

[star]

you are right, but it uses Vennerable packages that is not as fancy as venn package is.

[Tye Kahn]

Have you tried the examples from the documentation before using it in your data? If they work, then try to use the same format for your data.

Answer 1

[Prakash]

If you are interested to intersect bed file and show the no. of overlapping and unique regions, I would suggest to use upSet plot for representation, you could use online available tool Bedsect for this purpose .

Answer 2

[kanika.151]

I hope this helps:

https://stackoverflow.com/questions/37239128/how-to-put-comma-in-large-number-of-venndiagram

http://bioinfogp.cnb.csic.es/tools/venny/index2.0.2.html

An example code:

where d is your data-frame

p=draw.triple.venn(
   area1 = nrow(subset(d, d[,1] == 1)), 
   area2 = nrow(subset(d, d[,2] == 1)), 
   area3 = nrow(subset(d, d[,3] == 1)), 
   n12 = nrow(subset(d, d[,1] == 1 & d[,2] == 1)), 
   n23 = nrow(subset(d, d[,2] == 1 & d[,3] == 1)), 
   n13 = nrow(subset(d, d[,1] == 1 & d[,3] == 1)), 
   n123 = nrow(subset(d, d[,1] == 1 & d[,2] == 1 & d[,3] ==1)), 
   category = c(panels[1,2],panels[2,2],panels[3,2]), 
   lty = "blank",
   fill = c("skyblue", "pink1", "mediumorchid"));

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

[star]

Thanks for your reply, but VennDiagram package does it and I have done it. I like to do it with venn R package.

Answer 3

[kanika.151]

Highlighting only 4 of them in your venn diagram.

venn("10000, 01000, 00100, 00010")

[star]

Thanks. but I couldnot you mean! I like to know how can I use my intersect data to draw a plot using venn