kplot.sepan {ade4} | R Documentation

## Multiple Graphs for Separated Analyses in a K-tables

### Description

performs high level plots for Separed Analyses in a K-tables, using an object of class `sepan`.

### Usage

    ## S3 method for class 'sepan'
    kplot(object, xax = 1, yax = 2, which.tab = 1:length(object$blo),
        mfrow = NULL, permute.row.col = FALSE, clab.row = 1,
        clab.col = 1.25, traject.row = FALSE, csub = 2,
        possub = "bottomright", show.eigen.value = TRUE,...)

    kplotsepan.coa(object, xax = 1, yax = 2, which.tab = 1:length(object$blo),
        mfrow = NULL, permute.row.col = FALSE, clab.row = 1,
        clab.col = 1.25, csub = 2, possub = "bottomright",
        show.eigen.value = TRUE, poseig = c("bottom", "top"), ...)

### Arguments

`object` | an object of class `sepan`
`xax, yax` | the numbers of the x-axis and the y-axis
`which.tab` | a numeric vector containing the numbers of the tables to analyse
`mfrow` | parameter for the array of figures to be drawn, otherwise use n2mfrow
`permute.row.col` | if TRUE the rows are represented by arrows and the columns by points, if FALSE it is the opposite
`clab.row` | a character size for the row labels
`clab.col` | a character size for the column labels
`traject.row` | a logical value indicating whether the trajectories between rows should be drawn in a natural order
`csub` | a character size for the sub-titles, used with `par("cex")*csub`
`possub` | a string of characters indicating the sub-title position ("topleft", "topright", "bottomleft", "bottomright")
`show.eigen.value` | a logical value indicating whether the eigenvalues bar plot should be drawn
`poseig` | if "top" the eigenvalues bar plot is upside, if "bottom", it is downside
`...` | further arguments passed to or from other methods

### Details

`kplot.sepan` superimposes the points for the rows and the arrows for the columns using an adapted rescaling such as the `scatter.dudi`.
`kplotsepan.coa` superimposes the row coordinates and the column coordinates with the same scale.

### Author(s)

Daniel Chessel

### Examples

    data(escopage)
    w1 <- data.frame(scale(escopage$tab))
    w1 <- ktab.data.frame(w1, escopage$blo, tabnames = escopage$tab.names)
    sep1 <- sepan(w1)
    if(adegraphicsLoaded()) {
      kplot(sep1, posieig = "none")
    } else {
      kplot(sep1, show = FALSE)
    }

    data(friday87)
    w2 <- data.frame(scale(friday87$fau, scal = FALSE))
    w2 <- ktab.data.frame(w2, friday87$fau.blo, tabnames = friday87$tab.names)
    if(adegraphicsLoaded()) {
      kplot(sepan(w2), row.plabel.cex = 1.25, col.plab.cex = 0)
    } else {
      kplot(sepan(w2), clab.r = 1.25, clab.c = 0)
    }

    data(microsatt)
    w3 <- dudi.coa(data.frame(t(microsatt$tab)), scann = FALSE)
    loci.fac <- factor(rep(microsatt$loci.names, microsatt$loci.eff))
    wit <- wca(w3, loci.fac, scann = FALSE)
    microsatt.ktab <- ktab.within(wit)
    if(adegraphicsLoaded()) {
      kplotsepan.coa(sepan(microsatt.ktab), posieig = "none", col.plab.cex = 0, row.plab.cex = 1.5)
    } else {
      kplotsepan.coa(sepan(microsatt.ktab), show = FALSE, clab.c = 0,
        mfrow = c(3,3), clab.r = 1.5)
    }

[Package ade4 version 1.7-13 Index]