s.class2: Plot of factorial maps with representation of point classes...
In lixiangchun/lxctk: Li Xiangchun's tool-kit (lxctk)

Description Usage Arguments Value Author(s) Examples

performs the scatter diagrams with representation of point classes with additional control over lwd of ellipse, axesell and star line, which is modified by Xiangchun Li to address personal requirements.

s.class2(dfxy, fac, wt = rep(1, length(fac)), xax = 1, 
    yax = 2, cstar = 1, cellipse = 1.5, axesell = TRUE, 
    label = levels(fac), clabel = 1, cpoint = 1, pch = 20, 
    col = rep(1, length(levels(fac))), xlim = NULL, ylim = NULL, 
    grid = TRUE, addaxes = TRUE, origin = c(0,0), 
    include.origin = TRUE, sub = "", csub = 1, possub = "bottomleft", 
    cgrid = 1, pixmap = NULL, contour = NULL, area = NULL, add.plot = FALSE,
	ellipse.lwd=2, axesell.lwd=1, star.lwd=0.5, axes=TRUE, xlab='NMDS1', ylab='NMDS2')

`dfxy`	a data frame containing the two columns for the axes
`fac`	a factor partitioning the rows of the data frame in classes
`wt`	a vector of the point weightings of the data frame used for computing the means (star centers) and the ellipses of dispersion
`xax`	the column number of x in `dfxy`
`yax`	the column number of y in `dfxy`
`cstar`	a number between 0 and 1 which defines the length of the star size
`cellipse`	a positive coefficient for the inertia ellipse size
`axesell`	a logical value indicating whether the ellipse axes should be drawn
`label`	a vector of strings of characters for the point labels
`clabel`	if not NULL, a character size for the labels, used with `par("cex")*clabel`
`cpoint`	a character size for plotting the points, used with `par("cex")*cpoint`. If zero, no points are drawn
`pch`	if `cpoint` > 0, an integer specifying the symbol or the single character to be used in plotting points
`col`	a vector of colors used to draw each class in a different color
`xlim`	the ranges to be encompassed by the x, if NULL they are computed
`ylim`	the ranges to be encompassed by the y, if NULL they are computed
`grid`	a logical value indicating whether a grid in the background of the plot should be drawn
`addaxes`	a logical value indicating whether the axes should be plotted
`origin`	the fixed point in the graph space, for example c(0,0) the origin axes
`include.origin`	a logical value indicating whether the point "origin" should be belonged to the graph space
`sub`	a string of characters to be inserted as legend
`csub`	a character size for the legend, used with `par("cex")*csub`
`possub`	a string of characters indicating the sub-title position ("topleft", "topright", "bottomleft", "bottomright")
`cgrid`	a character size, parameter used with par("cex")* `cgrid` to indicate the mesh of the grid
`pixmap`	an object 'pixmap' displayed in the map background
`contour`	a data frame with 4 columns to plot the contour of the map : each row gives a segment (x1,y1,x2,y2)
`area`	a data frame of class 'area' to plot a set of surface units in contour
`add.plot`	if TRUE uses the current graphics window
`ellipse.lwd`	ellipse lwd.
`axesell.lwd`	axesell lwd.
`star.lwd`	star lwd.
`axes`	if FALSE, axes are not added.
`xlab,ylab`	xlab and ylab.

The matched call.

Daniel Chessel, modified by Xiangchun Li

library(randomForest)
rf=randomForest(iris[,-5], proximity=TRUE)
rf.mds <- stats:::cmdscale(1 - rf$proximity, eig = TRUE, k = 2)
s.class2(rf.mds$points, iris$Species, ellipse.lwd=3, axesell.lwd=0.5, star.lwd=0.5)