Viz

Visualizing Phylogenetic Trees with R and jsPhyloSVG

During the last year I’ve been working on a daily basis with phylogenetic trees, objects that in graph jargon are called Directed Acyclic Graphs. While R does have some cool packages out there to visualize these–including phylocanvas which looks great!–I wanted to tryout jsPhyloSVG, and moreover, to learn how to use htmlwidgets. So, after a week-long process of playing with JavaScript, of which I had no prior knowledge (so thank you W3shools)!

Read viz attributes from GEXF files

So one of the new features that I’ve working on is processing viz attributes. In the CRAN version of rgexf, the function read.gexf only reads in non-visual attributes and the graph structure itself, which is no longer true as of today (at least for the static viz attributes, all the other dynamic features supported by GEXF will come in the future). We start by loading the R packages and reading the “lesmiserables.

Some notes on my first shiny app

Since there are plenty of examples out there telling you how to get started with shiny (like Rstudio’s, or Google), I will focus on telling some of the stuff that I did learned and may not be obvious at first, including some of the mistakes I made. Before start, I just want to stress that I’m writing this after my first shiny app, you’ve been warned! Here it goes: Use the “two-file” method Instead of putting everything, UI and Server, in a single app.

Reboot of rgexf

The rgexf R package has been around a couple of years now, but without much going on on CRAN (my bad!). In this post I’ll show how to use the new version (on development and soon the be shipped to CRAN) together with the netdiffuseR R package to visualize a random diffusion process.