kplot.sepan {ade4} | R Documentation |
performs high level plots for Separed Analyses in a K-tables,
using an object of class sepan
.
## 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"), ...)
object |
an object of class |
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 |
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 |
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.
Daniel Chessel
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) }