ade4: add.scatter – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

add.scatter

Add graphics to an existing plot

Description

add.scatter is a function which defines a new plot area within an existing plot and displays an additional graphic inside this area. The additional graphic is determined by a function which is the first argument taken by add.scatter. It can be used in various ways, for instance to add a screeplot to an ordination scatterplot (add.scatter.eig).
The function add.scatter.eig uses the following colors: black (represented axes), grey(axes retained in the analysis) and white (others).

Usage

add.scatter(func,posi = c("bottomleft","bottomright","topleft","topright"),
ratio = 0.2, inset = 0.01, bg.col = 'white')
add.scatter.eig(w, nf = NULL, xax, yax, posi = "bottomleft", ratio =
.25, inset = 0.01, sub = "Eigenvalues", csub = 2 * ratio)

Arguments

`func`	an - evaluated - function producing a graphic
`posi`	a character vector (only its first element being considered) giving the position of the added graph. Possible values are "bottomleft" (="bottom"),"bottomright","topleft" (="top"),"topright", and "none" (no plot).
`ratio`	the size of the added graph in proportion of the current plot region
`inset`	the inset from which the graph is drawn, in proportion of the whole plot region. Can be a vector of length 2, giving the inset in x and y. If atomic, same inset is used in x and y
`bg.col`	the color of the background of the added graph
`w`	numeric vector of eigenvalues
`nf`	the number of retained factors, NULL if not provided
`xax`	first represented axis
`yax`	second represented axis
`sub`	title of the screeplot
`csub`	size of the screeplot title

Details

add.scatter uses par("plt") to redefine the new plot region. As stated in par documentation, this produces to (sometimes surprising) interactions with other parameters such as "mar". In particular, such interactions are likely to reset the plot region by default which would cause the additional graphic to take the whole plot region. To avoid such inconvenient, add par([other options], plt=par("plt")) when using par in your graphical function (argument func).

Value

The matched call (invisible).

Author(s)

Thibaut Jombart t.jombart@imperial.ac.uk

Examples

data(microsatt)
  w <- dudi.coa(data.frame(t(microsatt$tab)), scann = FALSE, nf = 3)
    
  if(adegraphicsLoaded()) {
    a1 <- rnorm(100)
    b1 <- s1d.barchart(sort(a1), p1d.horizontal = FALSE, plot = FALSE)
    h1 <- s1d.hist(a1, pgrid.draw = FALSE, porigin.draw = FALSE, pbackground.col = "grey", 
      plot = FALSE, ppoly.col = "white", ppoly.alpha = 1)
    g1 <- insert(h1, b1, posi = "topleft", plot = FALSE)
  
    a2 <- rnorm(100)
    b2 <- s1d.barchart(sort(a2), p1d.horizontal = FALSE, plot = FALSE)
    h2 <- s1d.hist(a2, pgrid.draw = FALSE, porigin.draw = FALSE, pbackground.col = "grey", 
      plot = FALSE, ppoly.col = "white", ppoly.alpha = 1)
    g2 <- insert(h2, b2, posi = "topleft", inset = c(0.25, 0.01), plot = FALSE)
  
    a3 <- rnorm(100)
    b3 <- s1d.barchart(sort(a3), p1d.horizontal = FALSE, plot = FALSE)
    h3 <- s1d.hist(a3, pgrid.draw = FALSE, porigin.draw = FALSE, pbackground.col = "grey", 
      plot = FALSE, ppoly.col = "white", ppoly.alpha = 1)
    g3 <- insert(h3, b3, posi = "bottomleft", inset = 0.4, ratio = 0.2, plot = FALSE)
  
    a4 <- rnorm(100)
    b4 <- s1d.barchart(sort(a4), p1d.horizontal = FALSE, plot = FALSE)
    h4 <- s1d.hist(a4, pgrid.draw = FALSE, porigin.draw = FALSE, pbackground.col = "grey", 
      plot = FALSE, ppoly.col = "white", ppoly.alpha = 1)
    g4 <- insert(h3, b3, posi = "bottomright", ratio = 0.3, plot = FALSE)
    
    G1 <- ADEgS(list(g1, g2, g3, g4), layout = c(2, 2), plot = TRUE)
    
    g5 <- s.label(w$co, plot = FALSE)
    g6 <- plotEig(w$eig, w$nf, psub = list(text = "Eigenvalues"), 
      pbackground = list(box = TRUE), plot = FALSE)
    G2 <- insert(g6, g5, posi = "bottomright", ratio = 0.25)

  } else {
    par(mfrow=c(2,2))
    f1 <- function(a){
      opar=par("mar","xaxt","yaxt","plt")
      on.exit(par(opar))
      par(mar=rep(.1,4),xaxt="n",yaxt="n",plt=par("plt"))
    
      hist(a,xlab="",ylab="",main="",col="white",proba=TRUE)
      lines(seq(-4,4,le=50),dnorm(seq(-4,4,le=50)),col="red")
    }
    
    a <- rnorm(100)
    barplot(sort(a))
    add.scatter(f1(a),posi="topleft",bg.col="grey")
    
    a <- rnorm(100)
    barplot(sort(a))
    add.scatter(f1(a),posi="topleft",bg.col="grey",inset=c(.25,.01))
    
    a <- rnorm(100)
    barplot(sort(a))
    add.scatter(f1(a),posi="topleft",bg.col="grey",inset=.25,ratio=.1)
    
    a <- rnorm(100)
    barplot(sort(a))
    add.scatter(f1(a),posi="bottomright",bg.col="grey",ratio=.3)
    par(mfrow=c(1,1))
    
    s.label(w$co)
    add.scatter.eig(w$eig,w$nf,posi="bottomright",1,2)
  }

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