vanni_et_al-figures

Code for the figures included in the manuscript Light into the darkness: Unifying the known and unknown coding sequence space in microbiome analyses

To recreate the figures follow the instructions below:

This has been tested on R 3.6.3

Clone the repo with:

git clone https://github.com/functional-dark-side/vanni_et_al-figures.git
cd vanni_et_al-figures

Then get the data we used from here. The data is stored in SQlite dbs, one DB for each figure.

curl -JLO https://ndownloader.figshare.com/files/24109856
tar xvfz vanni_et_al-data.tar.gz

Then let's install the packages we used to plot the figures. First start R to get renv installed:

R

If you open the project file vanni_et_al-figures.Rproj in Rstudio it will perform the same steps.

If everything went well, renv will be installed and you will get a message like:

* Installing renv 0.11.0 ... Done!
Successfully installed and loaded renv 0.11.0.
* Project '/vol/cloud/SANDBOX/vanni_et_al-figures' loaded. [renv 0.11.0]

And restore the environment:

renv::restore()
q()

Now you can recreate the basic figures with:

./scripts/Figure1.R

Figures will be saved in figures/

Or you can play with the code and recreate the figures in your favorite IDE.

In the folder figures-manuscipt you can find the final figures used in the manuscript after some beautifying.