[Adephylo-commits] r5 - in pkg: . man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Nov 20 15:56:37 CET 2008
Author: jombart
Date: 2008-11-20 15:56:37 +0100 (Thu, 20 Nov 2008)
New Revision: 5
Added:
pkg/man/s.phylo4d.Rd
Modified:
pkg/TODO
Log:
Add doc for s.phylo4d. Appended TODO.
Modified: pkg/TODO
===================================================================
--- pkg/TODO 2008-11-20 13:30:43 UTC (rev 4)
+++ pkg/TODO 2008-11-20 14:56:37 UTC (rev 5)
@@ -35,11 +35,13 @@
# NEW IMPLEMENTATIONS:
=====================
-* plot methods from phylobase ('old' version)
-* proximities like Abouheif, etc.
+* plot methods from phylobase ('old' version) -- done (TJ)
+* proximities between OTUs like Abouheif, etc.
+* distances between OTUs (like sum of branch lengths)
+* dummy vectors indicating class of related OTUs (like in orthogram)
* orthogram
* ppca
-* put some sample datasets from ade4
+* put some datasets from ade4
@@ -52,7 +54,7 @@
# LOW PRIORITY / MINOR ISSUES
===========================
===========================
-*
+* draw a rectangle around legend in s.phylo4d
# LONG TERM
Added: pkg/man/s.phylo4d.Rd
===================================================================
--- pkg/man/s.phylo4d.Rd (rev 0)
+++ pkg/man/s.phylo4d.Rd 2008-11-20 14:56:37 UTC (rev 5)
@@ -0,0 +1,111 @@
+\name{s.phylo4d}
+\alias{s.phylo4d}
+\title{scatterplot for a phylogeny and traits}
+\description{
+ This function displays scatterplots of traits provided for the tips of
+ a phylogeny. Plotted objects must be valid \linkS4class{phylo4d}
+ objects (implemented by the \code{phylobase} package). Current version
+ allows plotting of a tree and one or more quantitative traits
+ (possibly containing missing data, represented by an 'x').\cr
+
+ The plot of phylogenies is performed by a call to \code{\link[pkg:ape]{plot.phylo}}
+ from the \code{ape} package. Hence, many of the arguments of
+ \code{\link[pkg:ape]{plot.phylo}} can be passed to \code{s.phylo4d},
+ through the \dots argument, but their names must be complete.
+}
+\usage{
+s.phylo4d(x, treetype=c("phylogram","cladogram"), symbol=c("circles", "squares"),
+ center=TRUE, scale=TRUE, legend=TRUE, grid=TRUE, box=TRUE,
+ show.tip.label=TRUE, show.node.label=TRUE, show.var.label=TRUE,
+ ratio.tree=1/3, font=3,
+ tip.label=x at tip.label, var.label=colnames(x at tip.data),
+ cex.symbol=1, cex.label=1, cex.legend=1, coord.legend=NULL, \dots)
+}
+\arguments{
+ \item{x}{a \linkS4class{phylo4d} object}
+ \item{treetype}{the type of tree to be plotted ("phylogram" or "cladogram")}
+ \item{symbol}{the type of symbol used to represent data ("circles" or "squares")}
+ \item{center}{a logical stating whether variables should be centred
+ (TRUE, default) or not (FALSE)}
+ \item{scale}{a logical stating whether variables should be scaled
+ (TRUE, default) or not (FALSE)}
+ \item{legend}{a logical stating whether a legend should be added to
+ the plot (TRUE) or not (FALSE, default)}
+ \item{grid}{a logical stating whether a grid should be added to the plot
+ (TRUE, default) or not (FALSE)}
+ \item{box}{a logical stating whether a box should be added around the plot
+ (TRUE, default) or not (FALSE)}
+ \item{show.tip.label}{a logical stating whether tip labels should be
+ printed (TRUE, default) or not (FALSE)}
+ \item{show.node.label}{a logical stating whether node labels should be
+ printed (TRUE, default) or not (FALSE)}
+ \item{show.var.label}{a logical stating whether labels of variables should be
+ printed (TRUE, default) or not (FALSE)}
+ \item{ratio.tree}{the proportion of width of the figure occupied by the tree}
+ \item{font}{an integer specifying the type of font for the labels: 1
+ (plain text), 2 (bold), 3 (italic, default), or 4 (bold italic).}
+ \item{tip.label}{a character vector giving the tip labels}
+ \item{var.label}{a character vector giving the labels of variables}
+ \item{cex.symbol}{a numeric giving the factor scaling the symbols}
+ \item{cex.label}{a numeric giving the factor scaling all labels}
+ \item{cex.legend}{a numeric giving the factor scaling the legend}
+ \item{coord.legend}{an optional list with two components 'x' and 'y'
+ indicating the lower-left position of the legend. Can be set to
+ \code{locator(1) to position the legend interactively.}}
+ \item{\dots}{further arguments to be passed to plot methods from
+ \code{ape}. See \code{?\link[pkg:ape]{plot.phylo}}.}
+}
+\seealso{The \linkS4class{phylo4d} class for storing \code{phylogeny+data}.\cr
+
+ \code{\link[pkg:ape]{plot.phylo}} from the \code{ape} package.\cr
+
+ An alternative (deprecated) representation is available from
+ \code{\link[pkg:ade4]{dotchart.phylog}}.
+}
+\details{
+ The function \code{s.phylo4d} is based on former plot method for
+ \linkS4class{phylo4d} objects from the \code{phylobase} package.
+ It replaces the deprecated \code{ade4} functions
+ \code{\link[pkg:ade4]{symbols.phylog}} and
+ \code{\link[pkg:ade4]{table.phylog}}.
+}
+\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr}}
+\examples{
+if(require(ape) & require(phylobase) & require(ade4)){
+
+## simulated data
+tr <- rtree(20)
+dat <- data.frame(a = rnorm(20), b = scale(1:20), c=runif(20,-2,2) )
+dat[3:6, 2] <- NA # introduce some NAs
+obj <- phylo4d(tr, dat, use.tip=FALSE) # build a phylo4d object
+s.phylo4d(obj) # default scatterplot
+s.phylo4d(obj,cex.leg=.6, use.edge.length=FALSE) # customized
+s.phylo4d(obj,treetype="clad", show.node=FALSE, cex.leg=.6,
+use.edge.length=FALSE, edge.color="blue", edge.width=3) # more customized
+
+
+## teleost fishes data
+data(mjrochet)
+temp <- read.tree(text=mjrochet$tre) # make a tree
+mjr <- phylo4d(x=temp,tip.data=mjrochet$tab) # male a phylo4d object
+s.phylo4d(mjr,cex.lab=.5,show.node=FALSE,symb="square")
+
+
+## lizards data
+data(lizards)
+liz.tr <- read.tree(tex=lizards$hprA) # make a tree
+liz <- phylo4d(liz.tr, lizards$traits) # make a phylo4d object
+s.phylo4d(liz)
+
+
+## plotting principal components
+liz.pca1 <- dudi.pca(lizards$traits, scannf=FALSE, nf=2) # PCA of traits
+myPC <- phylo4d(liz.tr, liz.pca1$li) # store PC in a phylo4d object
+varlab <- paste("Principal \ncomponent", 1:2) # make labels for PCs
+s.phylo4d(myPC, ratio=.8, var.lab=varlab) # plot the PCs
+add.scatter.eig(liz.pca1$eig,2,1,2,posi="topleft", inset=c(0,.15))
+title("Phylogeny and the principal components")
+}
+}
+\keyword{hplot}
+\keyword{multivariate}
\ No newline at end of file
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