我在使用树状图绘制系统发育分析方面非常陌生,而且我被我的代码卡住了。到目前为止,我已经设法绘制了一个系统发育树。我在 pdf 中得到了一张漂亮的图片
使用下面的代码,但它没有标题、图例和映射信息。我想做的是将映射文件添加到绘图上,使其看起来像这样。映射文件是一个 excel 文件,具有三列(有机体名称、其门和序列本身)。我想要完成的是使用门列(同时保持有机体名称不变)对图进行颜色编码的叶子的尖端,有一个图例和一个标题。谢谢你的帮助。
library(dendextend)
library(circlize)
library(factoextra)
pdf("IP6K_tree_factoextra_fan.pdf", width = 55, height = 60)
fviz_dend(
dend1,
k = 10,
h = NULL,
k_colors = c("blue", "green3", "maroon", "magenta", "purple", "red", "orange", "brown", "black", "#00AFBB"),
palette = NULL,
show_labels = TRUE,
color_labels_by_k = TRUE,
label_cols = NULL,
labels_track_height = NULL,
repel = FALSE,
lwd = 3,
type = "circular",
phylo_layout = "layout.auto",
rect = TRUE,
rect_border = "gray",
rect_lty = 2,
rect_fill = TRUE,
horiz = FALSE,
cex = 2,
main = "IP6K Kinase in Eukaryotic organisms",
ggtheme = theme_classic()
)
dev.off()
leaves.colours <- c("#A73030", "#CD534CFF", "#DF536B", "#CD0BBC","#0073C2FF","#003C67FF",
"#7AA6DCFF", "#4A6990FF", "#2297E6", "#0073C299", "#7AA6DC99",
"#003C6799", "#28E2ES", "#4A699099", "#F5C710", "#8F7700FF",
"#EFC00099", "#61D04F", "steelblue", "black")
leaves.nodes <- c("Chordata", "Arthropoda", "Ascomycota", "Basidiomycota", "Mollusca",
"Euglenozoa", "Oomycota", "Microsporidia", "Cnidaria", "Amoebozoa",
"Echinodermata", "Metamonada", "Apicomplexa", "Rhodophyta",
"Chlorophyta", "Platyhelminthes", "Nematoda", "Tracheophytes",
"Zygomycota", "Mucoromycota")
```
[1]: https://i.stack.imgur.com/2Zz2w.jpg
[2]: https://i.stack.imgur.com/6sCxt.png
[3]: https://i.stack.imgur.com/Ya2BC.jpg