# Graphical display of phylogeny and traits This function represents traits onto the tips of a phylogeny. Plotted objects must be valid phylo4d objects (implemented by the `phylobase` package). Current version allows plotting of a tree and one or more quantitative traits (possibly containing missing data, represented by an 'x'). ```r table.phylo4d( x, treetype = c("phylogram", "cladogram"), symbol = c("circles", "squares", "colors"), repVar = 1:ncol(tdata(x, type = "tip")), 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 = tipLabels(x), var.label = colnames(tdata(x, type = "tip")), cex.symbol = 1, cex.label = 1, cex.legend = 1, pch = 20, col = heat.colors(100), coord.legend = NULL, ... ) ``` ## Arguments - `x`: a phylo4d object - `treetype`: the type of tree to be plotted ("phylogram" or "cladogram") - `symbol`: the type of symbol used to represent data ("circles", "squares", or "colors") - `repVar`: the numerical index of variables to be plotted - `center`: a logical stating whether variables should be centred (TRUE, default) or not (FALSE) - `scale`: a logical stating whether variables should be scaled (TRUE, default) or not (FALSE) - `legend`: a logical stating whether a legend should be added to the plot (TRUE) or not (FALSE, default) - `grid`: a logical stating whether a grid should be added to the plot (TRUE, default) or not (FALSE) - `box`: a logical stating whether a box should be added around the plot (TRUE, default) or not (FALSE) - `show.tip.label`: a logical stating whether tip labels should be printed (TRUE, default) or not (FALSE) - `show.node.label`: a logical stating whether node labels should be printed (TRUE, default) or not (FALSE) - `show.var.label`: a logical stating whether labels of variables should be printed (TRUE, default) or not (FALSE) - `ratio.tree`: the proportion of width of the figure occupied by the tree - `font`: an integer specifying the type of font for the labels: 1 (plain text), 2 (bold), 3 (italic, default), or 4 (bold italic). - `tip.label`: a character vector giving the tip labels - `var.label`: a character vector giving the labels of variables - `cex.symbol`: a numeric giving the factor scaling the symbols - `cex.label`: a numeric giving the factor scaling all labels - `cex.legend`: a numeric giving the factor scaling the legend - `pch`: is `symbol` is set to 'colors', a number indicating the type of point to be plotted (see ?points) - `col`: is `symbol` is set to 'colors', a vector of colors to be used to represent the data - `coord.legend`: an optional list with two components 'x' and 'y' indicating the lower-left position of the legend. Can be set to `locator(1) to position the legend interactively.` - ``...``: further arguments to be passed to plot methods from `ape`. See `plot.phylo`. ## Returns No return value, function produces only a plot. ## Details The plot of phylogenies is performed by a call to `plot.phylo` from the `ape` package. Hence, many of the arguments of `plot.phylo` can be passed to `table.phylo4d`, through the `...` argument, but their names must be complete. For large trees, consider using `bullseye`. The function `table.phylo4d` is based on former plot method for phylo4d objects from the `phylobase` package. It replaces the deprecated `ade4` functions `symbols.phylog` and `table.phylog`. ## Examples ```r 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) # build a phylo4d object table.phylo4d(obj) # default scatterplot table.phylo4d(obj,cex.leg=.6, use.edge.length=FALSE) # customized table.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 table.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 table.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 table.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") } ``` ## See Also The phylo4d class for storing `phylogeny+data`. For large trees, consider using `bullseye`. `plot.phylo` from the `ape` package. An alternative (deprecated) representation is available from `dotchart.phylog`. ## Author(s) Thibaut Jombart tjombart@imperial.ac.uk

table.phylo4d function