-## plot.phylo.R (2009-09-23)
+## plot.phylo.R (2009-09-30)
## Plot Phylogenies
} else {
xx <- .nodeDepthEdgelength(Ntip, Nnode, z$edge, Nedge, z$edge.length)
}
- }
- if (type == "fan") {
+ } else switch(type, "fan" = {
## if the tips are not in the same order in tip.label
## and in edge[, 2], we must reorder the angles: we
## use `xx' to store temporarily the angles
}
xx <- r*cos(theta)
yy <- r*sin(theta)
-
- }
- if (type == "unrooted") {
+ }, "unrooted" = {
nb.sp <- .nodeDepth(Ntip, Nnode, z$edge, Nedge)
XY <- if (use.edge.length)
unrooted.xy(Ntip, Nnode, z$edge, z$edge.length, nb.sp)
## rescale so that we have only positive values
xx <- XY$M[, 1] - min(XY$M[, 1])
yy <- XY$M[, 2] - min(XY$M[, 2])
- }
- if (type == "radial") {
+ }, "radial" = {
X <- .nodeDepth(Ntip, Nnode, z$edge, Nedge)
X[X == 1] <- 0
## radius:
Y <- .nodeHeight(Ntip, Nnode, z$edge, Nedge, yy)
xx <- X * cos(Y)
yy <- X * sin(Y)
- }
+ })
if (phyloORclado) {
if (!horizontal) {
tmp <- yy
if (direction == "leftwards") xx <- x.lim[2] - xx #max(xx[ROOT] + tmp)
# else max(xx[1:Ntip] + tmp)
} else x.lim <- c(1, Ntip)
- }
- if (type == "fan") {
+ } else switch(type, "fan" = {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
x.lim <- c(min(xx) - offset, max(xx) + offset)
} else x.lim <- c(min(xx), max(xx))
- }
- if (type == "unrooted") {
+ }, "unrooted" = {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
x.lim <- c(0 - offset, max(xx) + offset)
} else x.lim <- c(0, max(xx))
- }
- if (type == "radial") {
+ }, "radial" = {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.03 * cex)
x.lim <- c(-1 - offset, 1 + offset)
} else x.lim <- c(-1, 1)
- }
+ })
} else if (length(x.lim) == 1) {
x.lim <- c(0, x.lim)
if (phyloORclado && !horizontal) x.lim[1] <- 1
y.lim[2] <- tmp
if (direction == "downwards") yy <- y.lim[2] - yy
}
- }
- if (type == "fan") {
+ } else switch(type, "fan" = {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
y.lim <- c(min(yy) - offset, max(yy) + offset)
} else y.lim <- c(min(yy), max(yy))
- }
- if (type == "unrooted") {
+ }, "unrooted" = {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.018 * max(yy) * cex)
y.lim <- c(0 - offset, max(yy) + offset)
} else y.lim <- c(0, max(yy))
- }
- if (type == "radial") {
+ }, "radial" = {
if (show.tip.label) {
offset <- max(nchar(x$tip.label) * 0.03 * cex)
y.lim <- c(-1 - offset, 1 + offset)
} else y.lim <- c(-1, 1)
- }
+ })
} else if (length(y.lim) == 1) {
y.lim <- c(0, y.lim)
if (phyloORclado && horizontal) y.lim[1] <- 1
if (direction == "leftwards") x.lim[2] <- x.lim[2] + x$root.edge
if (direction == "downwards") y.lim[2] <- y.lim[2] + x$root.edge
}
- ## fix by Klaus Schliep (2008-03-28):
- asp <- if (type %in% c("fan", "radial")) 1 else NA
+ asp <- if (type %in% c("fan", "radial")) 1 else NA # fix by Klaus Schliep (2008-03-28)
plot(0, type = "n", xlim = x.lim, ylim = y.lim, ann = FALSE, axes = FALSE, asp = asp, ...)
if (is.null(adj))
adj <- if (phyloORclado && direction == "leftwards") 1 else 0
}
## ... et un trait horizontal partant de chaque tip et chaque noeud
## vers la racine
-### sq <- c(1:Ntip, nodes[-1])
-### y0h <- yy[sq]
-### x1h <- xx[sq]
-### ## match() is very useful here becoz each element in edge[, 2] is
-### ## unique (not sure this is so useful in edge[, 1]; needs to be checked)
-### ## `pos' gives for each element in `sq' its index in edge[, 2]
-### pos <- match(sq, edge[, 2])
-### x0h <- xx[edge[pos, 1]]
x0h <- xx[edge[, 1]]
x1h <- xx[edge[, 2]]
y0h <- yy[edge[, 2]]
-### donc plus besoin de 'pos' ni 'sq'
nc <- length(edge.color)
nw <- length(edge.width)
}
}
-### ## function dispatching the features to the vertical edges
-### foo <- function(edge.feat, default) {
-### e <- unique(edge.feat)
-### if (length(e) == 1) return(rep(e, Nnode))
-### else {
-### feat.v <- rep(default, Nnode)
-### for (i in 1:Nnode) {
-### br <- NodeInEdge1[[i]]
-### if (length(br) > 2) {
-### x <- unique(edge.feat[br])
-### if (length(x) == 1) feat.v[i] <- x
-### } else {
-### if (edge.feat[br[1]] == edge.feat[br[2]])
-### feat.v[i] <- edge.feat[br[1]]
-### else {
-### feat.v[i] <- edge.feat[br[2]]
-### ## add a new line:
-### y0v <<- c(y0v, y0v[i])
-### y1v <<- c(y1v, yy[i + Ntip])
-### x0v <<- c(x0v, x0v[i])
-### feat.v <- c(feat.v, edge.feat[br[1]])
-### ## shorten the line:
-### y0v[i] <<- yy[i + Ntip]
-### }
-### }
-### }
-### }
-### feat.v
-### }
-### color.v <- foo(edge.color, "black")
-### width.v <- foo(edge.width, 1)
-### lty.v <- foo(edge.lty, 1)
-
-### ## we need to reorder:
-### edge.width <- edge.width[pos]
-### edge.color <- edge.color[pos]
-### edge.lty <- edge.lty[pos]
-
if (horizontal) {
segments(x0h, y0h, x1h, y0h, col = edge.color, lwd = edge.width, lty = edge.lty) # draws horizontal lines
segments(x0v, y0v, x0v, y1v, col = color.v, lwd = width.v, lty = lty.v) # draws vertical lines
projects / ape.git / blobdiff