mcc_col_tree_plot: plotting tree with background sequences labelled

In emvolz-phylodynamics/sarscov2Rutils: Scripts to support preparation and analysis of SARS CoV 2 analyses

Description

Edit of mcc_tree_plot allowing non-region tips to be coloured by continent. requires nexus input tree, most recent sample date and dictionary converting second element of sequence names to continent.

Usage

mcc_col_tree_plot(
  nexfn,
  mostRecentSampleDate,
  country_dictionary,
  internal = "Region",
  style = 1,
  regionDemes = c("Il", "Ih", "E"),
  ofn = "mcc.png"
)

Arguments

nexfn	Path to nexus file containing annotated MCC tree (output of treeannotator2)
mostRecentSampleDate	A character string containign the date of the most recent sample in the form 2020-03-17
country_dictionary	data dictionary to convert country names to world bank continents
internal	A character string giving the name of the region of interest
style	plot style from 1,2 or 3
regionDemes	A character vector of deme names which will be coloured red
ofn	Output file name of figure

Value

A ggtree object which can be customized further

emvolz-phylodynamics/sarscov2Rutils documentation built on Nov. 17, 2020, 9:22 a.m.