In zkamvar/ggcompoplot: Plot Posterior Assignment Values From a 'DAPC' Analysis

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-",
  fig.width = 9,
  fig.height = 10,
  cache = TRUE
)

ggcompoplot

The goal of ggcompoplot is to create compoplots that can be manipulated using the grammar of graphics. This code originally appeared in https://zenodo.org/record/13007.

Installation

To install, download devtools, and copy and past this into your R console:

devtools::install_github("zkamvar/ggcompoplot")

Example

Compoplot from DAPC Analysis (from adegenet)

library('adegenet')
library('ggcompoplot')
library('ggplot2')

data(microbov)
strata(microbov) <- data.frame(other(microbov))

dapc1 <- dapc(microbov, n.pca=20, n.da=15)

compoplot(dapc1, lab="") # Adegenet compoplot

Using ggcompoplot

To use ggcompoplot, all you need is the results of your DAPC analysis and your genind/genlight object:

# Setting a named palette of colors
(rainbov <- setNames(rainbow(nPop(microbov)), popNames(microbov)))

ggcompoplot(dapc1, microbov, pal = rainbov) + theme(axis.text.x = element_blank())

# 3 columns
ggcompoplot(dapc1, microbov, cols = 3, pal = rainbov) + theme(axis.text.x = element_blank())

# Different color palette
ggcompoplot(dapc1, microbov, cols = 3, pal = funky) + theme(axis.text.x = element_blank())

# Per Country
setPop(microbov) <- ~coun
ggcompoplot(dapc1, microbov, pal = rainbov) + theme(axis.text.x = element_blank())