| phydataplot {ape} | R Documentation |
phydataplot plots data on a tree in a way that adapts to the
type of tree. ring does the same for circular trees.
Both functions match the data with the labels of the tree.
phydataplot(x, phy, style = "bars", offset = 1, scaling = 1,
continuous = FALSE, width = NULL, legend = "below",
funcol = rainbow, ...)
ring(x, phy, style = "ring", offset = 1, ...)
x |
a vector, a factor, a matrix, or a data frame. |
phy |
the tree (which must be already plotted). |
style |
a character string specifying the type of graphics; can be abbreviated (see details). |
offset |
the space between the tips of the tree and the plot. |
scaling |
the scaling factor to apply to the data. |
continuous |
(used if style="mosaic") a logical specifying
whether to treat the values in |
width |
(used if style = "mosaic") the width of the cells; by default, all the available space is used. |
legend |
(used if style = "mosaic") the place where to draw the legend; if not the default, the legend is drawn besides the mosaic. |
funcol |
(used if style = "mosaic") the function used to generate the colours (see details and examples). |
... |
further arguments passed to the graphical functions. |
The possible values for style are “bars”, “segments”,
“image”, “arrows”, “boxplot”, “dotchart”, or “mosaic” for
phydataplot, and “ring”, “segments”, or “arrows” for
ring.
style = "image" works only with square matrices (e.g.,
similarities). If you want to plot a DNA alignment in the same way
than image.DNAbin, try style = "mosaic".
style = "mosaic" can plot any kind of matrices, possibly after
discretizing its values (using continuous). The default colour
palette is taken from the function rainbow.
If you want to use specified colours, a function simply returning the
vector of colours must be used (see examples).
For the moment, only rightwards trees are supported (does not apply to circular trees).
Emmanuel Paradis
plot.phylo, nodelabels,
fancyarrows
## demonstrates matching with names:
tr <- rcoal(n <- 10)
x <- 1:n
names(x) <- tr$tip.label
plot(tr, x.lim = 11)
phydataplot(x, tr)
## shuffle x but matching names with tip labels reorders them:
phydataplot(sample(x), tr, "s", lwd = 3, lty = 3)
## adapts to the tree:
plot(tr, "f", x.l = c(-11, 11), y.l = c(-11, 11))
phydataplot(x, tr, "s")
## leave more space with x.lim to show a barplot and a dotchart:
plot(tr, x.lim = 22)
phydataplot(x, tr, col = "yellow")
phydataplot(x, tr, "d", offset = 13)
ts <- rcoal(N <- 100)
X <- rTraitCont(ts) # names are set
dd <- dist(X)
op <- par(mar = rep(0, 4))
plot(ts, x.lim = 10, cex = 0.4, font = 1)
phydataplot(as.matrix(dd), ts, "i", offset = 0.2)
par(xpd = TRUE, mar = op$mar)
co <- c("blue", "red"); l <- c(-2, 2)
X <- X + abs(min(X)) # move scale so X >= 0
plot(ts, "f", show.tip.label = FALSE, x.lim = l, y.lim = l, open.angle = 30)
phydataplot(X, ts, "s", col = co, offset = 0.05)
ring(X, ts, "ring", col = co, offset = max(X) + 0.1) # the same info as a ring
## as many rings as you want...
co <- c("blue", "yellow")
plot(ts, "r", show.tip.label = FALSE, x.l = c(-1, 1), y.l = c(-1, 1))
for (o in seq(0, 0.4, 0.2)) {
co <- rev(co)
ring(0.2, ts, "r", col = rep(co, each = 5), offset = o)
}
lim <- c(-5, 5)
co <- rgb(0, 0.4, 1, alpha = 0.1)
y <- seq(0.01, 1, 0.01)
plot(ts, "f", x.lim = lim, y.lim = lim, show.tip.label = FALSE)
ring(y, ts, offset = 0, col = co, lwd = 0.1)
for (i in 1:3) {
y <- y + 1
ring(y, ts, offset = 0, col = co, lwd = 0.1)
}
## rings can be in the background
plot(ts, "r", plot = FALSE)
ring(1, ts, "r", col = rainbow(100), offset = -1)
par(new = TRUE)
plot(ts, "r", font = 1, edge.color = "white")
## might be more useful:
co <- c("lightblue", "yellow")
plot(ts, "r", plot = FALSE)
ring(0.1, ts, "r", col = sample(co, size = N, rep = TRUE), offset = -.1)
par(new = TRUE)
plot(ts, "r", font = 1)
## if x is matrix:
tx <- rcoal(m <- 20)
X <- runif(m, 0, 0.5); Y <- runif(m, 0, 0.5)
X <- cbind(X, Y, 1 - X - Y)
rownames(X) <- tx$tip.label
plot(tx, x.lim = 6)
co <- rgb(diag(3))
phydataplot(X, tx, col = co)
## a variation:
plot(tx, show.tip.label = FALSE, x.lim = 5)
phydataplot(X, tx, col = co, offset = 0.05, border = NA)
plot(tx, "f", show.tip.label = FALSE, open.angle = 180)
ring(X, tx, col = co, offset = 0.05)
Z <- matrix(rnorm(m * 5), m)
rownames(Z) <- rownames(X)
plot(tx, x.lim = 5)
phydataplot(Z, tx, "bo", scaling = .5, offset = 0.5,
boxfill = c("gold", "skyblue"))
## plot an alignment with a NJ tree:
data(woodmouse)
trw <- nj(dist.dna(woodmouse))
plot(trw, x.lim = 0.1, align.tip = TRUE, font = 1)
phydataplot(woodmouse[, 1:50], trw, "m", 0.02, border = NA)
## use type = "mosaic" on a 30x5 matrix:
tr <- rtree(n <- 30)
p <- 5
x <- matrix(sample(3, size = n*p, replace = TRUE), n, p)
dimnames(x) <- list(paste0("t", 1:n), LETTERS[1:p])
plot(tr, x.lim = 35, align.tip = TRUE, adj = 1)
phydataplot(x, tr, "m", 2)
## change the aspect:
plot(tr, x.lim = 35, align.tip = TRUE, adj = 1)
phydataplot(x, tr, "m", 2, width = 2, border = "white", lwd = 3, legend = "side")
## user-defined colour:
f <- function(n) c("yellow", "blue", "red")
phydataplot(x, tr, "m", 18, width = 2, border = "white", lwd = 3,
legend = "side", funcol = f)
## use continuous = TRUE with two different scales:
x[] <- 1:(n*p)
plot(tr, x.lim = 35, align.tip = TRUE, adj = 1)
phydataplot(x, tr, "m", 2, width = 1.5, continuous = TRUE, legend = "side",
funcol = colorRampPalette(c("white", "darkgreen")))
phydataplot(x, tr, "m", 18, width = 1.5, continuous = 5, legend = "side",
funcol = topo.colors)