Plot Posterior Assignment Values From a 'DAPC' Analysis
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
R
man
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
README-ggcompoplot-1.png
README-ggcompoplot-2.png
README-ggcompoplot-3.png
README-ggcompoplot-4.png
README-setup_adegenet-1.png
README.Rmd
README.md
ggcompoplot.Rproj

README.md

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)))
#>          Borgou            Zebu       Lagunaire           NDama 
#>     "#FF0000FF"     "#FF6600FF"     "#FFCC00FF"     "#CCFF00FF" 
#>           Somba          Aubrac        Bazadais BlondeAquitaine 
#>     "#66FF00FF"     "#00FF00FF"     "#00FF66FF"     "#00FFCCFF" 
#>    BretPieNoire       Charolais          Gascon        Limousin 
#>     "#00CCFFFF"     "#0066FFFF"     "#0000FFFF"     "#6600FFFF" 
#>      MaineAnjou     Montbeliard          Salers 
#>     "#CC00FFFF"     "#FF00CCFF"     "#FF0066FF"

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())