kplot.sepan: Multiple Graphs for Separated Analyses in a K-tables In ade4: Analysis of Ecological Data : Exploratory and Euclidean Methods in Environmental Sciences

Description

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

Usage

 ``` 1 2 3 4 5 6 7 8 9 10``` ```## 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.

Daniel Chessel

Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30``` ```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) } ```

ade4 documentation built on May 31, 2017, 4:06 a.m.