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Converting data from shared OTUs (QIIME 1) for UpSetR

Dear, сolleagues. I am trying to make a graph based on shared OTUs (from QIIME).

shared_phylotypes.py -i otu_table.biom -o shared_otus.txt

The upset uses binary matrices as input, how I can convert data to work with this package? For simplicity, only 9 values are shown (I actually have 15 sets.). Example data:

       Set1  Set2   Set3
Set1    11    0      2 
Set2    0     18     0
Set3    2     0      80
upsetr shared otu
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written by SergFly • SergFly

1 answer

I figured out how to solve the problem. You need to take the OTU table at the entrance. Where there are 0 and 1, if there is more than 1 number, then I have placed it manually. But another problem arose. If there are 80 sequences in the sample, then only 60 are displayed on the graph. How so?

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written by SergFly • SergFly

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