Scatterplot of groups of trees

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

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

Value

An adegraphics object (class: ADEgS)

Details

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

See also

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

Author

Thibaut Jombart thibautjombart@gmail.com

Examples

if (FALSE) {
if(require("adegenet") && require("adegraphics")){
## load data
data(woodmiceTrees)

## run findGroves: treespace+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$treespace$pco)

## adding labels
plotGroves(res$treespace$pco, lab.show=TRUE, lab.cex=2)

}
}