plotGroves: Scatterplot of groups of trees

Description

This function displays the scatterplot of the Multidimensional Scaling (MDS) output by treescape, superimposing group information (derived by findGroves) using colors.

Usage

plotGroves(x, groups = NULL, xax = 1, yax = 2, type = c("chull", "ellipse"), col.pal = funky, bg = "white", lab.show = FALSE, lab.col = "black", lab.cex = 1, lab.optim = TRUE, point.cex = 1, scree.pal = NULL, scree.size = 0.2, scree.posi = c(0.02, 0.02), ...)

Arguments

a list returned by findGroves or a MDS with class dudi

groups

a factor defining groups of trees

xax

a number indicating which principal component to be used as 'x' axis

yax

a number indicating which principal component to be used as 'y' axis

type

a character string indicating which type of graph to use

col.pal

a color palette to be used for the groups

the background color

lab.show

a logical indicating whether labels should be displayed

lab.col

a color for the labels

lab.cex

the size of the labels

lab.optim

a logical indicating whether label positions should be optimized to avoid overlap; better display but time-consuming for large datasets

point.cex

the size of the points

scree.pal

a color palette for the screeplot

scree.size

a size factor for the screeplot, between 0 and 1

scree.posi

either a character string or xy coordinates indicating the position of the screeplot.

...

further arguments passed to s.class

Value

An adegraphics object (class: ADEgS)

Details

This function relies on s.class from the adegraphics package.

Examples

Run this code


## Not run: 
# if(require("adegenet") && require("adegraphics")){
# ## load data
# data(woodmiceTrees)
# 
# ## run findGroves: treescape+clustering
# res <- findGroves(woodmiceTrees, nf=5, nclust=6)
# 
# ## basic plot
# plotGroves(res)
# 
# ## adding labels
# plotGroves(res, lab.show=TRUE)
# 
# ## customizing
# plotGroves(res, lab.show=TRUE,
# bg="black", lab.col="white", scree.size=.35)
# 
# ## customizing
# plotGroves(res, type="ellipse", lab.show=TRUE,
# lab.optim=FALSE, scree.size=.35)
# 
# ## example with no group information
# plotGroves(res$treescape$pco)
# 
# ## adding labels
# plotGroves(res$treescape$pco, lab.show=TRUE, lab.cex=2)
# 
# }
# ## End(Not run)