3. Generation of Phylosift trees with gene table - maxlcummins/APEC-MGEN-2018 GitHub Wiki

To generate a Phylosift with a table showing gene presence and absence a Phylosift tree was generated as shown in part two of this wiki.

Note that the reference genomes were not included in the generation of this Phylosift tree as these reference sequences were not genotyped by the use of ARIBA.

The R package ggtree played an important role in the generation of this figure, so thanks to Guangchuang Yu for his work on the package.

The script utilised is accessible here

All supporting data is avaiable in the data folder of this github repository.

The package and R versions used are shown below via R's built in 'sessionInfo()' command:

R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.4

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] magrittr_1.5    readr_1.1.1     phytools_0.6-44 maps_3.3.0      ape_5.1         ggtree_1.8.2   
[7] treeio_1.0.2    ggplot2_2.2.1   dplyr_0.7.5