R 中按组划分的树状图的颜色分支（没有 h 或 k 元素）

Question

I want to color branches of a dendrogram by specific groups that a defined in a dataframe.

library(reshape2)
library(factoextra) # clustering visualization 
library(dendextend)
#iris dataset
#defining colors
colori = rep(NA, length=length(iris$Species))
colori[which(iris$Species=="setosa")] = "red"
colori[which(iris$Species=="versicolor")] = "blue"
colori[which(iris$Species=="virginica")] = "yellow"

iris_dist <- dist(iris[ ,1:4],)
hc1_iris <- hclust(iris_dist,method = "average")
col_dendro_iris <- color_branches(as.dendrogram(hc1_iris),groupLabels =T, clusters = iris$Species,col=colori)

col_dendro_iris_plot <- plot(col_dendro_iris,main = "Dendrogram of normalized BLS\ncolored by manmade groups",labels = NULL,xlab = NULL)

That only colors the branches red. Why? How can I solve that

EDIT: It works when I do this

pca_iris <- PCA(iris[ ,1:4])
colori = rep(NA, length=length(iris$Species))
colori[which(iris$Species=="versicolor")] = "red"
colori[which(iris$Species=="virginica")] = "yellow"
colori[which(iris$Species=="setosa")] = "blue"
# species <- iris$Species
iris_gr <- cbind(iris,colori)
# 
pca_iris <- fviz_pca_ind(pca_iris,
             pointshape = 21,habillage = iris$Species,
             geom.ind = c("point"),geom = c("point"),palette = iris$colori,
             title="PCA of normalized BLS\ncolored by manmade groups")
pca_iris<- pca_iris + theme(legend.position = "upper.right")

Just for future readers. But actually I can´t color the dendrogram in an analog way. I do not have a k or h element for defining clusters. Like in iris, I have predefined clusters I want to color.

Answer 1

You should use the library dendextend . It has the functions for extending dendrogram objects.

Below a simple example.

library(dendextend)
dend_var<-as.dendrogram(hc_var)
dend_colored<-color_branches(dend_var, h=10000, k=7)
plot(dend_colored)

dend_var is aa dendrogram or hclust tree object.

k is used to choose the number of groups.

h is used to choose the height at which to cut tree.