dendextend: color_branches对某些hclust方法不起作用

Question

我正在使用R dendextend包绘制由每个hclust方法从hclust {stats}生成hclust树对象："ward.D“、"ward.D2”、"single“、"complete”、"average“(= UPGMA)、"mcquitty”(= WPGMA)、"median“(= WPGMC)或"centroid”(= UPGMC)。

我注意到当我使用color_branches = "median“或"centroid”时，方法的颜色编码失败。

我用随机生成的矩阵测试了它，“中间数”和“质心”方法的误差是重复的，这是有特定原因的吗？

请参阅输出图的链接：fig1. hclust methods (a) ward.D2, (b) median, (c) centroid

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。会话信息如下：

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

谢谢。

Answer 1

你可以使用branches_attr_by_clusters解决这个问题(尽管它可能有点棘手，请参见下面的示例)：

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

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