tree_workflow: Make phylogenetic trees colored according to strata

In Neato-Nick/mllR:

Make phylogenetic trees colored according to strata

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. Do not wrap in quotes... I think.
name	Used to label plot axes and titles.
scale_quality	What to color the tree tips by. Use 'population' to color by any "formula" you set. Other options are: 'missing', 'median_depth', 'mean_depth', 'heterozygosity', and 'allele_depth'
vcf	Original vcfR object, used to calculate statistics on. Be sure it's the same exact individuals and variants as the data in 'x'.
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 plot

Examples

tree_workflow(ultra_filtered_genlight, ~Nursery, "Nursery of origin", "population", ultra_filtered_vcf)

Neato-Nick/mllR documentation built on Aug. 30, 2024, 7:22 a.m.