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joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
http://joey711.github.io/phyloseq/
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Morisita-horn distance, axis more than 100%? #394

Open Aliceall opened 9 years ago

Aliceall commented 9 years ago

Hi joey711, I apologize in advance because I am not very experienced. I wanted to ordinate my samples with Morisita-horn method in an ordination plot using raw read counts (I was asked to do that). I used the function ordinate(data,"PCoA", "horn") on my phyloseq class (imported from qiime, biom otu table, map and tree) and then I plotted the ordination. One of the axis is more than 100% (119) and the other is 2%. It happened in 2 plots out of three and it does not look normal to me, which would be the reason?
It happens also using the function distance() and then ordinate(). I could not find anywhere an explanation. However, I tried with qiime, on the same otu table and map and the plots come out ok. Thank you very much!

joey711 commented 9 years ago

Can you provide a reproducible example? You can use one of the built-in datasets (e.g. GlobalPatterns) to make it easier. It would be especially helpful to see the three different plots to which you are referring.

Thanks for your feedback and interest in phlyoseq!

joey