plotGrovesD3: Scatterplot of groups of trees using `scatterD3`

Description

This function displays the scatterplot of the Multidimensional Scaling (MDS) output by treespace, superimposing group information (derived by findGroves) using colors. scatterD3 enables interactive plotting based on d3.js, including zooming, panning and fading effects in the legend.

Usage

plotGrovesD3(
  x,
  groups = NULL,
  xax = 1,
  yax = 2,
  treeNames = NULL,
  symbol_var = NULL,
  xlab = paste0("Axis ", xax),
  ylab = paste0("Axis ", yax),
  ...
)

Value

A scatterD3 plot

Arguments

x: a list returned by findGroves or a MDS with class dudi
groups: a factor defining groups of trees. If x is a list returned by findGroves these will be detected automatically.
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
treeNames: if a list of tree names or labels are given, these will be plotted alongside the points. Their size can be altered using labels_size - see ?scatterD3 for more information.
symbol_var: a factor by which to vary the symbols in the plot
xlab: the label for the 'x' axis. Defaults to use the value of 'xax'
ylab: the label for the 'y' axis. Defaults to use the value of 'yax'
...: further arguments passed to scatterD3

Author

Thibaut Jombart thibautjombart@gmail.com

Examples

Run this code


if (FALSE) {
if(require("adegenet") && require("scatterD3")){
## load data
data(woodmiceTrees)

## run findGroves: treespace+clustering
res <- findGroves(woodmiceTrees, nf=5, nclust=6)

## basic plot
plotGrovesD3(res)

## adding tree labels
plotGrovesD3(res, treeNames=1:201)

## customizing: vary the colour and the symbol by group
plotGrovesD3(res, symbol_var=res$groups)

## example with no group information
plotGrovesD3(res$treespace$pco)
}
}