get.admixture {MoBPS}

Admixture Plot

Description

Function to generate admixture plots

Usage

get.admixture(
  population,
  geno = NULL,
  gen = NULL,
  database = NULL,
  cohorts = NULL,
  d = NULL,
  verbose = TRUE,
  plot = TRUE,
  sort = FALSE,
  sort.cutoff = 0.01
)

Arguments

population

Population list

geno

Manually provided genotype dataset to use instead of gen/database/cohorts

gen

Quick-insert for database (vector of all generations to consider)

database

Groups of individuals to consider

cohorts

Quick-insert for database (vector of names of cohorts to consider)

d

dimensions to consider in admixture plot (default: automatically estimate a reasonable number)

verbose

Set to FALSE to not display any prints

plot

Set to FALSE to not generate an admixture plot

sort

Set to TRUE to sort individuals according to contributes from the first dimension

sort.cutoff

Skip individuals with contributions under this threshold (and use next dimension instead) data(ex_pop) get.admixture(ex_pop, gen=4:6, d=2, sort=TRUE)

Value

Matrix with admixture proportion