Question: venn plot data?
0
gravatar for star
10 months ago by
star210
Netherlands
star210 wrote:

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)
ADD COMMENTlink modified 10 months ago by kanika.15180 • written 10 months ago by star210
1

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.
code_formatting

ADD REPLYlink written 10 months ago by RamRS25k

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

ADD REPLYlink written 10 months ago by Luiz30

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

ADD REPLYlink written 10 months ago by lieven.sterck7.0k

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.

ADD REPLYlink written 10 months ago by star210

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.

ADD REPLYlink written 10 months ago by star210

Interactiven is able toe draw from 2 to 6 datasets.

ADD REPLYlink written 10 months ago by Luiz30

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

ADD REPLYlink written 10 months ago by star210

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.

ADD REPLYlink written 10 months ago by Tye Kahn10
2
gravatar for Prakash
10 months ago by
Prakash1.8k
India
Prakash1.8k wrote:

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 .

ADD COMMENTlink modified 10 months ago • written 10 months ago by Prakash1.8k
1
gravatar for kanika.151
10 months ago by
kanika.15180
Italy
kanika.15180 wrote:

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"));
ADD COMMENTlink modified 10 months ago by RamRS25k • written 10 months ago by kanika.15180
1

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.
code_formatting

ADD REPLYlink written 10 months ago by RamRS25k

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

ADD REPLYlink written 10 months ago by star210
0
gravatar for kanika.151
10 months ago by
kanika.15180
Italy
kanika.15180 wrote:

venn

Highlighting only 4 of them in your venn diagram.

venn("10000, 01000, 00100, 00010")
ADD COMMENTlink modified 10 months ago by RamRS25k • written 10 months ago by kanika.15180

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

ADD REPLYlink modified 10 months ago • written 10 months ago by star210
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