基于标签的重新排序和颜色树状图

Question

我想控制树状图的顺序和颜色。显然，树形图的要点是通过相似性排序，但在分支内我想设置一个有意义的顺序（字母数字）。

library(vegan) 
library(stats) 

x <-data.frame(data = c(1:10)) 
y = data.frame(type = c("A","B","C","A","C","D","A","B","C","B"), site_name = c("A1","B1","C1","A2","C2","D1","A3","B2","C3","B3")) 
row.names(x) = y$site_name 
dis = vegdist(x) 
hc <- hclust(dis) 
dd <- as.dendrogram(hc) 
plot(dd) 

我的数据标签文本，但他们确实有在列举了一组顺序的变量

site_order = c("A1","A2","A3","B1","B2","B3","C1","C2","C3","D1") 

1）我想找到排序根据树状图的解决方案到分行内的site_order。

例如A1，B1，A2，C1，C2，D2，A3，B2，B3，C3

我也希望颜色和形状使用site_type 例如（A =红色圆圈标签，B =蓝色正方形，C =绿色三角形，D =黄色十字）

这可能吗？

Answer 1

这是使用dendextend的rotate函数最好的工作。

library(vegan) 
library(stats) 

x <-data.frame(data = c(1:10)) 
y = data.frame(type = c("A","B","C","A","C","D","A","B","C","B"), site_name = c("A1","B1","C1","A2","C2","D1","A3","B2","C3","B3")) 
row.names(x) = y$site_name 
dis = vegdist(x) 
hc <- hclust(dis) 
dd <- as.dendrogram(hc) 

par(mfrow = c(1,2)) 
plot(dd, main = "orig") 

library(dendextend) 
dd2 <- rotate(dd, sort(labels(dd))) 
plot(dd2, main = "as sorted as possible \n(under the constraints)") 

输出：

您可以了解更多关于dendextend包从the online vignettes。