dendextend：color_branches在某些hclust方法中不起作用

Question

我正在使用R dendextend包來繪制每個hclust方法從hclust {stats}生成的hclust樹對象的圖：“ ward.D”，“ ward.D2”，“ single”，“ complete”，“ average”（= UPGMA）， “ mcquitty”（= WPGMA），“ median”（= WPGMC）或“ centroid”（= UPGMC）。

我注意到當我使用method =“ median”或“ centroid”時color_branches的顏色編碼失敗。

我使用隨機生成的矩陣對其進行了測試，並且“中位數”和“質心”方法的誤差得以復制，這是否有特定原因？

請查看輸出圖的鏈接： fig1。 hclust方法（a）病房D2，（b）中位數，（c）質心

library(dendextend)
set.seed(1)
df <- as.data.frame(replicate(10, rnorm(20)))
df.names <- rep(c("black", "red", "blue", "green", "cyan"), 2)
df.col <- rep(c("black", "red", "blue", "green", "cyan"), 2)
colnames(df) <- df.names
df.dist <- dist(t(df), method = "euclidean")

# plotting works for "ward.D", "ward.D2", "single", "complete", "average", "mcquitty"
dend <- as.dendrogram(hclust(df.dist, method = "ward.D2"), labels = df.names)
labels_colors(dend) <- df.col[order.dendrogram(dend)]
dend.colorBranch <- color_branches(dend, k = length(df.names), col = df.col[order.dendrogram(dend)])
dend.colorBranch %>% set("branches_lwd", 3) %>% plot(horiz = TRUE)

# color_branches fails for "median" or "centroid"
dend <- as.dendrogram(hclust(df.dist, method = "median"), labels = df.names)
labels_colors(dend) <- df.col[order.dendrogram(dend)]
dend.colorBranch <- color_branches(dend, k = length(df.names), col = df.col[order.dendrogram(dend)])
dend.colorBranch %>% set("branches_lwd", 3) %>% plot(horiz = TRUE)

dend <- as.dendrogram(hclust(df.dist, method = "centroid"), labels = df.names)
labels_colors(dend) <- df.col[order.dendrogram(dend)]
dend.colorBranch <- color_branches(dend, k = length(df.names), col = df.col[order.dendrogram(dend)])
dend.colorBranch %>% set("branches_lwd", 3) %>% plot(horiz = TRUE)

我正在使用dendextend_1.4.0。 會話信息如下：

sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.3

謝謝。

Answer 1

您可以使用branches_attr_by_clusters解決此問題（盡管可能會有些棘手，請參見下面的示例）：

library(dendextend)
set.seed(1)
df <- as.data.frame(replicate(10, rnorm(20)))
df.names <- rep(c("black", "red", "blue", "green", "cyan"), 2)
df.col <- rep(c("black", "red", "blue", "green", "cyan"), 2)
colnames(df) <- df.names
df.dist <- dist(t(df), method = "euclidean")

# plotting works for "ward.D", "ward.D2", "single", "complete", "average", "mcquitty"
dend <- as.dendrogram(hclust(df.dist, method = "ward.D2"), labels = df.names)
labels_colors(dend) <- df.col[order.dendrogram(dend)]
dend.colorBranch <- color_branches(dend, k = length(df.names), col = df.col[order.dendrogram(dend)])
dend.colorBranch %>% set("branches_lwd", 3) %>% plot(horiz = TRUE)

# color_branches fails for "median" or "centroid"
dend <- as.dendrogram(hclust(df.dist, method = "median"), labels = df.names)
aa <- df.col[order.dendrogram(dend)]
labels_colors(dend) <- aa
dend.colorBranch <- color_branches(dend, k = length(df.names), col = df.col[order.dendrogram(dend)])
dend.colorBranch %>% set("branches_lwd", 3) %>% plot(horiz = TRUE)

aa <- factor(aa, levels = unique(aa))
dend %>% branches_attr_by_clusters(aa, value = levels(aa)) %>% plot