ade4: s.match.class – R documentation

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s.match.class

Scatterplot of two sets of coordinates and a partionning into classes

Description

Performs a graphical representation of two sets of coordinates (different colors and symbols) and a partitionning into classes

Usage

s.match.class(df1xy, df2xy, fac, wt = rep(1/nrow(df1xy), nrow(df1xy)),
xax = 1, yax = 2, pch1 = 16, pch2 = 15, col1 = rep("lightgrey",
nlevels(fac)), col2 = rep("darkgrey", nlevels(fac)), cpoint = 1, label =
levels(fac), clabel = 1, cstar = 1, cellipse = 0, axesell = TRUE, xlim =
NULL, ylim = NULL, grid = TRUE, addaxes = TRUE, cgrid = 1,
include.origin = TRUE, origin = c(0, 0), sub = "", csub = 1.25, possub =
"bottomleft", pixmap = NULL, contour = NULL, area = NULL, add.plot = FALSE)

Arguments

`df1xy`	a dataframe with the first system of coordinates
`df2xy`	a dataframe with the secocnd system of coordinates
`fac`	a factor partitioning the rows of the data frame in classes
`wt`	a vector of weights
`xax`	a number indicating which column should be plotted on the x-axis
`yax`	a number indicating which column should be plotted on the x-axis
`pch1`	if `cpoint` > 0, an integer specifying the symbol or the single character to be used for plotting points
`pch2`	if `cpoint` > 0, an integer specifying the symbol or the single character to be used for plotting points
`col1`	a color for symbols
`col2`	a color for symbols
`cpoint`	a character size for plotting the points, used with `par("cex")*cpoint`. If zero, no points are drawn
`label`	a vector of strings of characters for the couple labels
`clabel`	if not NULL, a character size for the labels, used with `par("cex")*clabel`
`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
`xlim`	the ranges to be encompassed by the x axis, if NULL they are computed
`ylim`	the ranges to be encompassed by the y axis, 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
`cgrid`	a character size, parameter used with par("cex")* `cgrid` to indicate the mesh of the grid
`include.origin`	a logical value indicating whether the point "origin" should belong to the graph space
`origin`	a fixed point in the graph space, for example c(0,0) for the origin of axes
`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")
`pixmap`	a `pixmap` object
`contour`	a dataframe with 4 columns to plot the contour of the map : each row gives a segment (x1,y1,x2,y2)
`area`	a dataframe of class 'area' to plot an areal map
`add.plot`	if TRUE, add the plot to the current graphic device

Value

The matched call.

Author(s)

Stéphane Dray stephane.dray@univ-lyon1.fr

Examples

xy <- data.frame(matrix(rnorm(100), 50, 2))
xy[, 1] <- xy[, 1] + rep(seq(0, 12, by = 3), rep(10, 5))
xy[, 2] <- xy[, 2] + rep(seq(0, 12, by = 3), rep(10, 5))
fac <- gl(5, 10)
xy2 <- xy + matrix(rnorm(100), 50, 2) + 1

if(adegraphicsLoaded()) {
  mat <- rbind(xy, xy2)
  minmat <- apply(mat, 2, min)
  maxmat <- apply(mat, 2, max)
  lag <- 0.1 * abs(minmat - maxmat)
  xli <- c(minmat[1] - lag[1], maxmat[1] + lag[1])
  yli <- c(minmat[2] - lag[2], maxmat[2] + lag[2])
  
  g1 <- s.class(xy, fac, ellipseSize = 0, col = rep("grey45", nlevels(fac)), xlim = xli, 
    ylim = yli, plabels.cex = 0, plot = FALSE)
  g2 <- s.class(xy2, fac, ellipseSize = 0, col = rep("grey75", nlevels(fac)), xlim = xli, 
    ylim = yli, plabels.cex = 0, plot = FALSE)
  g3 <- s.match(g1@stats$means, g2@stats$means, xlim = xli, ylim = yli, plines.lwd = 2, 
    psub.text = "xy -> xy2", plot = FALSE)
  
  g4 <- do.call("superpose", list(g1, g2))
  g4@Call <- call("superpose", g1@Call, g2@Call)
  g4 <- do.call("superpose", list(g4, g3))
  g4@Call <- call("superpose", g4@Call, g3@Call)
  g4
  
} else {
  s.match.class(xy, xy2, fac)
}

ade4

Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

v1.7-16

GPL (>= 2)

Authors

Stéphane Dray <stephane.dray@univ-lyon1.fr>, Anne-Béatrice Dufour <anne-beatrice.dufour@univ-lyon1.fr>, and Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>, with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sébastien Ollier, Daniel Borcard, Pierre Legendre, Stéphanie Bougeard and Aurélie Siberchicot. Based on earlier work by Daniel Chessel.

Initial release