venn diagramm - richness doesn't correspond to input file

mothur bugs
1

Hi,

I generated a venn diagram of my shared file with a workaround once suggested by westcott:

merge.groups(shared=cg.good.unique.good.filter.unique.precluster.pick.pick.an.unique_list.0.03.subsample.shared, design=design_cg.txt)
venn(shared=current, groups=rhen-inv)

However, the total richness of both groups as announced in the .svg file doesn’t correspond to the number of OTUs I have in that shared file.
In the .svg it says “The total richness for all groups is 3125” but my shared file has 4304 OTUs.

Is it a bug or am I missing something?

Thank’s a lot!

C.

2

Does your shared file have more than the rhen and inv groups in it?

3

No it doesn’t.

It actually gives the same result when I do

venn(shared=current)

4

Could you send your shared and log file to mothur.bugs@gmail.com?

5

From your shared file you have 3125 OTUs.

label Group numOtus Otu00001 Otu00002 …
0.03 inv 3125 24185 2570 …
0.03 rhen 3125 7405 4712 …

6

That’s true but the original shared file which I use in the merge.groups command has 4303 OTUs.
And as I replied to PSchloss I don’t have other groups than inv and rhen in my shared file so I expect to have all OTUs in the end.

Does it make sense if I send you my original shared file and my design file?

Thanks!

7

Yes, can you send me the original files so I can run the merge.files and venn command?

8

To complete this, there was indeed a bug which is now corrected in the updated version, 1.37.1

Thanks again to Sarah for her patience and her quick help!
You guys from mothur are awesome! :slight_smile: