Re: [R-sig-phylo] edge color in phylomorphospace3d
Thankyou very much to all for your effort in improving the function!
all the best
paoo
Da: Liam J. Revell
Inviato: martedì 10 giugno 2014 15.13
A: Jonas Eberle; Paolo Piras; r-sig-phylo@r-project.org
Oggetto: Re: edge color in phylomorphospace3d
Thanks Jonas.
I had just added this to phytools. Not yet on CRAN but more details
(including how to use it) can be seen here:
http://blog.phytools.org/2014/06/coloring-edges-in-phylomorphospace3d.html.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 6/10/2014 3:26 AM, Jonas Eberle wrote:
> 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
Re: [R-sig-phylo] edge color in phylomorphospace3d
Thanks Jonas.
I had just added this to phytools. Not yet on CRAN but more details
(including how to use it) can be seen here:
http://blog.phytools.org/2014/06/coloring-edges-in-phylomorphospace3d.html.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 6/10/2014 3:26 AM, Jonas Eberle wrote:
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)
}
}
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Re: [R-sig-phylo] edge color in phylomorphospace3d
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)
}
}
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