tree_workflow: Make phylogenetic trees colored according to strata

In Neato-Nick/mllR:

Description

Make phylogenetic trees colored according to strata

Usage

tree_workflow(x, formula = NULL, name, scale_quality = "population",
  vcf = NULL, geo_tree = NULL, treeType = "upgma",
  dist = "provesti.dist", input_type = "genclone")

Arguments

x	Preferably a genclone object, genlights sometimes break it. Must have strata
formula	Hierarchical formula to group the populations by in plots.
name	Used to label plot axes and titles.
scale_quality	What to color the tree tips by.
vcf	Original vcfR object, used to calculate statistics on
geo_tree	Optionally supply your own tree instead of running poppr::aboot
treeType	Algorithm to make tree by. Make sure the package to use is loaded.
dist	Algorithm to calculate distance. Make sure the package to use is loaded.
input_type	Specify if a genclone or genlight is inputted

Value

Phylogenetic tree plots

Examples

pca_workflow(ultra_filtered_genlight, 'Nursery', strata_defs)

Neato-Nick/mllR documentation built on May 17, 2019, 6:22 p.m.