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The interactive diatom phylogeny app now online

I just deployed the InteractiveDiatomPhylogeny application on shinyapps.io. Now one can browse the diatom phylogeny without the need of any phylogeny programs or R code. Here is a screen shot:

Screenshot from 2014-09-12 22:11:17

The error messages are what comes out of R, so they are uninformative if you’re not familiar with the workings of some of the functions used. An important case comes up if one is trying to plot a sub-tree based on a genus but the genus is represented by a single species in the phylogeny. Since the code requires two species to extract a clade, this results with the cryptic output:

Error: object "phy" is not of class "phylo"
Error: arguments must have same length

Certainly not helpful. And it comes up for some important genera like Melosira, Thalassiosira and Placoneis. Some of these cases will disappear once I incorporate a bigger tree (most genera will be represented by two or more species). Nonetheless, there are always going to be cases of a genus represented by a single species. So I’ll try to fix these issues over the next few weeks.

To run the app, just point your browser here.


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