Dear Paolo, I modified the phylomorphospace3d code some time ago to be able to plot colored branches (see below). You can use pointcol and edgecol to color the plot. These can be simple color specifications (such as "black") or vectors of colors that have the length of your number of tips or edges, respectively.
Thank you Liam for this piece of code! It's really usefull for me! I hope I didn't spoil your code too much :) Jonas ColoredPhylomorphospace3d <- function (tree, X, A = NULL, label = TRUE, pointcol="black", edgecol="black", control = list(), method = c("dynamic", "static"), ...) { method <- method[1] if (class(tree) != "phylo") stop("tree object must be of class 'phylo.'") # controls festlegen con = list(spin = TRUE, axes = TRUE, box = TRUE, simple.axes = FALSE, lwd = 1, ftype = "reg") con[(namc <- names(control))] <- control if (con$simple.axes) con$box <- con$axes <- FALSE con$ftype <- which(c("off", "reg", "b", "i", "bi") == con$ftype) - 1 if (is.null(A)) A <- apply(X, 2, function(x, tree) fastAnc(tree, x), tree = tree) else A <- A[as.character(1:tree$Nnode + length(tree$tip)), ] x <- y <- z <- matrix(NA, nrow(tree$edge), 2) X <- X[tree$tip.label, ] for (i in 1:length(tree$tip)) { x[tree$edge[, 2] == i, 2] <- X[i, 1] y[tree$edge[, 2] == i, 2] <- X[i, 2] z[tree$edge[, 2] == i, 2] <- X[i, 3] } for (i in length(tree$tip) + 1:tree$Nnode) { x[tree$edge[, 1] == i, 1] <- x[tree$edge[, 2] == i, 2] <- A[as.character(i), 1] y[tree$edge[, 1] == i, 1] <- y[tree$edge[, 2] == i, 2] <- A[as.character(i), 2] z[tree$edge[, 1] == i, 1] <- z[tree$edge[, 2] == i, 2] <- A[as.character(i), 3] } if (is.null(colnames(X))) colnames(X) <- c("x", "y", "z") if (method == "dynamic") { params <- get("r3dDefaults") plot3d(rbind(X, A), xlab = colnames(X)[1], ylab = colnames(X)[2], zlab = colnames(X)[3], axes = con$axes, box = con$box, params = params) spheres3d(X, radius = 0.02 * mean(apply(X, 2, max) - apply(X, 2, min)), col=pointcol) for (i in 1:nrow(tree$edge)) segments3d(x[i, ], y[i, ], z[i, ], lwd = con$lwd, col=edgecol[i]) ms <- colMeans(X) rs <- apply(rbind(X, A), 2, range) if (con$simple.axes) { lines3d(x = rs[, 1], y = c(rs[1, 2], rs[1, 2]), z = c(rs[1, 3], rs[1, 3])) lines3d(x = c(rs[1, 1], rs[1, 1]), y = rs[, 2], z = c(rs[1, 3], rs[1, 3])) lines3d(x = c(rs[1, 1], rs[1, 1]), y = c(rs[1, 2], rs[1, 2]), z = rs[, 3]) } rs <- rs[2, ] - rs[1, ] for (i in 1:length(tree$tip)) { adj <- 0.03 * rs * (2 * (X[i, ] > ms) - 1) if (con$ftype) text3d(X[i, ] + adj, texts = tree$tip.label[i], font = con$ftype) } if (con$spin) { xx <- spin3d(axis = c(0, 0, 1), rpm = 10) play3d(xx, duration = 5) invisible(xx) } else invisible(NULL) } else if (method == "static") { if (hasArg(angle)) angle <- list(...)$angle else angle <- 30 if (hasArg(xlim)) xlim <- list(...)$xlim else xlim <- NULL if (hasArg(ylim)) ylim <- list(...)$ylim else ylim <- NULL if (hasArg(zlim)) zlim <- list(...)$zlim else zlim = NULL xx <- scatterplot3d(X, xlab = colnames(X)[1], zlab = colnames(X)[3], pch = 19, angle = angle, ylab = colnames(X)[2], asp = 1, cex.symbols = 1.3, xlim = xlim, ylim = ylim, zlim = zlim) aa <- xx$xyz.convert(A) points(aa$x, aa$y, pch = 19, cex = 0.8) for (i in 1:nrow(tree$edge)) { aa <- xx$xyz.convert(x[i, ], y[i, ], z[i, ]) lines(aa$x, aa$y, lwd = 2) } for (i in 1:length(tree$tip.label)) { aa <- xx$xyz.convert(x[which(tree$edge[, 2] == i), 2], y[which(tree$edge[, 2] == i), 2], z[which(tree$edge[, 2] == i), 2]) text(tree$tip.label[i], x = aa$x, y = aa$y, pos = 2) } invisible(xx) } } [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/