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RGui
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### 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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