plotGroves: Scatterplot of groups of trees

In treescape: Statistical Exploration of Landscapes of Phylogenetic 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

x	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
bg	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

Details

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

Value

An adegraphics object (class: ADEgS)

Author(s)

Thibaut Jombart [e-mail]

See Also

findGroves to find any clusters in the tree landscape s.class

Examples

## 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)

treescape documentation built on May 19, 2017, 3:32 p.m.