Trees and the like...

So I am trying to figure out how to draw phylogenetic trees and add colour and other data to them.

This is a very rich area with lots of R packages and info....

Relevant packages:

APE
Phylo Tools



A key point is that there are various classes of trees:

• dendrogram - https://stat.ethz.ch/R-manual/R-devel/library/stats/html/dendrogram.html
• phylo 

The plotting techniques vary depending on the types of tree

• http://www.sthda.com/english/wiki/beautiful-dendrogram-visualizations-in-r-5-must-known-methods-unsupervised-machine-learning
• http://bioconductor.org/packages/release/bioc/manuals/ggtree/man/ggtree.pdf
• http://stackoverflow.com/questions/18802519/label-and-color-leaf-dendrogram-in-r
• https://rpubs.com/gaston/dendrograms

More about ggtree

• http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/full
• https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeVisualization.html
• http://bioconductor.org/packages/release/bioc/html/ggtree.html
• 
  

More about ape:

• http://ape-package.ird.fr/ape_screenshots.html
• https://www.biostars.org/p/160461/

Pinintrest has lots of images of trees which are inspiring:

• https://www.pinterest.com/davidwinter/tree-of-life/

To make the trees requires a multiple sequence alignment:

• https://bioconductor.org/packages/devel/bioc/vignettes/msa/inst/doc/msa.pdf
• and the package Biostrings: https://bioconductor.org/packages/release/bioc/html/Biostrings.html
• Info here: http://manuals.bioinformatics.ucr.edu/home/ht-seq#TOC-Multiple-Sequence-Alignments-MSAs-

Kinase sequences & visualisation:

• http://kinase.com/kinbase/FastaFiles/Human_kinase_domain.fasta
• http://kinase.com/web/current/human/
• http://science.sciencemag.org/content/298/5600/1912.full.pdf+html

Web interface, I think:

• https://peerj.com/articles/126/
• Kinome Render: a stand-alone and web-accessible tool to annotate the human protein kinome tree

Kinome google image search is interesting too....

Other packages:

• phangorn - https://cran.r-project.org/web/packages/phangorn/vignettes/Trees.pdf