s.match.class: Scatterplot of two sets of coordinates and a partionning into...

In ade4: Analysis of Ecological Data : Exploratory and Euclidean Methods in Environmental Sciences

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)

Stephane Dray [e-mail]

See Also

s.class, s.match

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)
}

Example output

ade4 documentation built on May 2, 2019, 5:50 p.m.