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tree plots do not work #2024

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@danton267

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@danton267

library(plotly)
library(ggplot2)
library(igraph)
library(ggimage)
library(ggtree)
 url <- paste0("https://raw.githubusercontent.com/TreeViz/",
             "metastyle/master/design/viz_targets_exercise/")

 x <- read.tree(paste0(url, "tree_boots.nwk"))
 info <- read.csv(paste0(url, "tip_data.csv"))


p <- ggtree(x) %<+% info + xlim(-.1, 4)
p2 <- p + geom_tiplab(offset = .6, hjust = .5) +
    geom_tippoint(aes(shape = trophic_habit, color = trophic_habit, size = mass_in_kg)) + 
    theme(legend.position = "right") + scale_size_continuous(range = c(3, 10))

d2 <- read.csv(paste0(url, "inode_data.csv"))
p2 %<+% d2 + geom_label(aes(label = vernacularName.y, fill = posterior)) + 
    scale_fill_gradientn(colors = RColorBrewer::brewer.pal(3, "YlGnBu"))

ggplotly(p2)

The result is not captured properly. More examples which are not working: https://yulab-smu.top/treedata-book/chapter7.html

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