Shiny Graphing

Theta and neutrality test statistic graphing

Note: you need the following packages installed in R to use this:

• Shiny:

    \> install.packages("shiny")
  

• genomeIntervals

    \> source("http://bioconductor.org/biocLite.R");
  
    \> biocLite("genomeIntervals")
  

Note: this application is not meant to be used on clusters, only local computers.

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angsd-wrapper contains a shiny application for graphing thetas and neutrality test statistics. This allows interactive plotting of data generated from angsd in the web browser:

To use this, you first need a copy of your theta results. If you are using a windowed analysis, you need the *.thetas.gz.pestPG file. If you used a cluster or other remote computer for the analysis, you will need to transfer the file from that computer to your local one. scp works well for this. Once you have the file, you can start the shiny application doing the following:

$ cd scripts/
$ R
> library(shiny) # if it's not installed, use install.packages("shiny") first, then run this line
> runApp("shiny")

A web browser should open and it should look similar to the screenshot above. Initially, it will load the default data included with the package. You can load your data by using the file chooser. If you run into any issues, please submit an Issue on Github.

This application can also graph gene annotations along with theta. You can use the maize chromosome 10 annotation (downloaded from Ensembl) included in the repository as a test file. First, upload the file, then toggle the GFF annotation. Only genes are graphed now, but more features can be added by request.

Genes are plotted as blue with an alpha value. This allows you to see where gene annotations overlap. Please make sure you use the correct annotation for your reference genome.