Question: venn plot data?
0
gravatar for star
12 days ago by
star140
Netherlands
star140 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 12 days ago by kanika.15160 • written 12 days ago by star140
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 12 days ago by RamRS21k

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 12 days ago by Luiz30

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

ADD REPLYlink written 12 days ago by lieven.sterck4.5k

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 12 days ago by star140

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 12 days ago by star140

Interactiven is able toe draw from 2 to 6 datasets.

ADD REPLYlink written 12 days ago by Luiz30

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

ADD REPLYlink written 12 days ago by star140

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 12 days ago by Tye Kahn10
1
gravatar for kanika.151
12 days ago by
kanika.15160
United States
kanika.15160 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 12 days ago by RamRS21k • written 12 days ago by kanika.15160
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 12 days ago by RamRS21k

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 12 days ago by star140
0
gravatar for kanika.151
12 days ago by
kanika.15160
United States
kanika.15160 wrote:

venn

Highlighting only 4 of them in your venn diagram.

venn("10000, 01000, 00100, 00010")
ADD COMMENTlink modified 12 days ago by RamRS21k • written 12 days ago by kanika.15160

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 12 days ago • written 12 days ago by star140
0
gravatar for Prakash
12 days ago by
Prakash920
India
Prakash920 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 12 days ago • written 12 days ago by Prakash920
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