More about trees but not finished yet....

More understanding about phylogenetic trees.

Learned how to rotate trees with

plot.phylo(ksTree, "u", 
           use.edge.length = FALSE,
           tip.color = tipcol,
           cex = 0.5,
           rotate.tree = -90)

Still need to do lots of things but making progress albeit it slowly!
# this rotate.tree is good.
# BUT some swapping of clades will have to be done too.
# some manual organisation of this will be done with the full version
# to find clade numbers for the full tree.
# then will colour and label.....

# then extract my 'favourites' and add them back.
# once basic tree is done and I'm happy with it then other things can be done...



# TO DO
# Draw full tree.
# add node numbers to identify the 8 key 'clades' and nodes for them...
# add colours for clade (somehow...)
# add clade labels
# add rotate clades to have correct for Science paper...

# need the TK at the top (rotate further) for Cell Signaling Diagram
# also need background and more sytlised lines - how???


MAYBE LOSING TRACK OF MY SCRIPT
SOME SIMPLIFYING NECESSARY!!!!



http://www.sthda.com/english/wiki/beautiful-dendrogram-visualizations-in-r-5-must-known-methods-unsupervised-machine-learning

http://127.0.0.1:15993/library/phytools/html/cladelabels.html

https://sites.google.com/site/phylogeneticworkshop2/labs/plotting-phylogenies

# this is good!!!
https://ecomorph.wordpress.com/2014/10/09/phylogenetic-trees-in-r-4/

https://holtlab.net/2015/10/03/plotting-trees-data/

http://127.0.0.1:15993/library/phytools/html/plotSimmap.html

http://blog.phytools.org/search?q=clade

http://stackoverflow.com/questions/34089242/phylogenetic-tree-tip-color

https://cran.r-project.org/web/views/Phylogenetics.html

https://www.biostars.org/p/81241/

http://127.0.0.1:15993/library/ape/html/nodelabels.html

http://127.0.0.1:15993/library/phytools/html/plotTree.html

http://www.phytools.org/eqg/Lecture_5.1/Revell.ancestral-state-reconstruction.pdf

https://www.r-phylo.org/wiki/HowTo/DataTreeManipulation

https://climateecology.wordpress.com/2012/07/22/r-for-ecologists-phylogenies-in-r/#comments