This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How do I look for shared OTUs in an abundance matrix?

Dear all,

Let's assume I have an abundance matrix that looks like this:

             SampleA SampleB SampleC
OTU1         5               6              0
OTU2         3               1              2
OTU3         1               0              1
OTU4         0               0              2

If I have a large abundance matrix, what software or scripts will you recommend constructing a Venn diagram that can look for shared OTUs, or OTUs that are unique to each sample? The software / script should also produce an output that denotes the number of unique and shared OTUs.

Thank you!

r venn diagram
• 3,857 views • link
updated by zx8754 zx8754 • written by Ming • Ming

For more than three sets, Euler diagrams quickly become unreadable. You may want to explore alternatives such as UpSetR.

• 0 views • link
written by Jean-Karim Heriche Jean-Karim Heriche

1 answer

Transpose the dataframe/matrix so that OTUs are the sets, then convert into logical, then plot:

# example data
df1 <- read.table(text = "SampleA SampleB SampleC
OTU1         5               6              0
OTU2         3               1              2
OTU3         1               0              1
OTU4         0               0              2", header = TRUE, stringsAsFactors = FALSE)


library(gplots)

venn(t(df1 > 0))
• 0 views • link
written by zx8754 zx8754

Note that the venn() function from gplots is limited to a small number of sets

• 0 views • link
written by Jean-Karim Heriche Jean-Karim Heriche

True, not sure what OP wants, OTUs as sets or samples as sets, in their example both less than 5 sets. So 4 set Venn should be OK. Agreed, UpSet is more suitable when sets are more than 4.

• 0 views • link
written by zx8754 zx8754

Log in to answer this question.

More posts like this