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xzpgocxx

铁虫 (初入文坛)

应助: 0 (幼儿园)
金币: 63.5
帖子: 19
在线: 4.7小时
虫号: 2539405
注册: 2013-07-10
专业: 植物遗传学

[求助] RGui

### An extract from Sibley and Ahlquist (1990)
cat("(((Strix_aluco:4.2,Asio_otus:4.2):3.1,",
"Athene_noctua:7.3):6.3,Tyto_alba:13.5);",
file = "ex.tre", sep = "\n"

tree.owls <- read.tree("ex.tre"

plot(tree.owls)
unlink("ex.tre"

# delete the file "ex.tre"

### Show the types of trees.
layout(matrix(1:6, 3, 2))
plot(tree.owls, main = "With branch lengths"

plot(tree.owls, type = "c"

plot(tree.owls, type = "u"

plot(tree.owls, use.edge.length = FALSE, main = "Without branch lengths"

plot(tree.owls, type = "c", use.edge.length = FALSE)
plot(tree.owls, type = "u", use.edge.length = FALSE)
layout(matrix(1))

data(bird.orders)
### using random colours and thickness
plot(bird.orders,
edge.color = sample(colors(), length(bird.orders$edge)/2),
edge.width = sample(1:10, length(bird.orders$edge)/2, replace = TRUE))
title("Random colours and branch thickness"

### rainbow colouring...
X <- c("red", "orange", "yellow", "green", "blue", "purple"

plot(bird.orders,
edge.color = sample(X, length(bird.orders$edge)/2, replace = TRUE),
edge.width = sample(1:10, length(bird.orders$edge)/2, replace = TRUE))
title("Rainbow colouring"

plot(bird.orders, type = "c", use.edge.length = FALSE,
edge.color = sample(X, length(bird.orders$edge)/2, replace = TRUE),
edge.width = rep(5, length(bird.orders$edge)/2))
segments(rep(0, 6), 6.5:1.5, rep(2, 6), 6.5:1.5, lwd = 5, col = X)
text(rep(2.5, 6), 6.5:1.5, paste(X, "..."

, adj = 0)
title("Character mapping..."

plot(bird.orders, "u", font = 1, cex = 0.75)
data(bird.families)
plot(bird.families, "u", lab4ut = "axial", font = 1, cex = 0.5)
plot(bird.families, "r", font = 1, cex = 0.5)
### cladogram with oblique tip labels
plot(bird.orders, "c", FALSE, direction = "u", srt = -40, x.lim = 25.5)
### facing trees with different informations...
tr <- bird.orders
tr$tip.label <- rep("", 23)
layout(matrix(1:2, 1, 2), c(5, 4))
plot(bird.orders, "c", FALSE, adj = 0.5, no.margin = TRUE, label.offset = 0.8,
   edge.color = sample(X, length(bird.orders$edge)/2, replace = TRUE),
   edge.width = rep(5, length(bird.orders$edge)/2))
text(7.5, 23, "Facing trees with\ndifferent informations", font = 2)
plot(tr, "p", direction = "l", no.margin = TRUE,
   edge.width = sample(1:10, length(bird.orders$edge)/2, replace = TRUE))
### Recycling of arguments gives a lot of possibilities
### for tip labels:
plot(bird.orders, tip.col = c(rep("red", 5), rep("blue", 18)),
   font = c(rep(3, 5), rep(2, 17), 1))
plot(bird.orders, tip.col = c("blue", "green"

,
cex = 23:1/23 + .3, font = 1:3)
co <- c(rep("blue", 9), rep("green", 35))
plot(bird.orders, "f", edge.col = co)
plot(bird.orders, edge.col = co)
layout(1)

求解释都什么意思啊，看不懂？不甚感激

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