:::: MENU ::::
Browsing posts in: Diatoms

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.

Learning Shiny

In the last couple of days after returning from the Joint Aquatic Sciences Meeting in Portland, I started learning Shiny. Shiny is a great R package for converting R code into interactive web pages. I’ve known about it for a while, but I hadn’t given it a go until now for various reasons not least finishing graduate school. The learning curve was a bit steep for me. My R skills are not exactly stellar to begin with and integrating the R code with a whole set of new functions specific to Shiny was a bit of a mess at first. After a day and a half of trial and error I managed to put together a working Shiny app. It is now available on my GitHub repository under the name Interactive Diatom Phylogeny.
Continue Reading