r - dendextend：color_branches 不适用于某些 hclust 方法

Question

我正在使用 R dendextend 包来绘制由 hclust{stats} 中的每个 hclust 方法生成的 hclust 树对象：“ward.D”、“ward.D2”、“single”、“complete”、“average”（= UPGMA）， “mcquitty”（= WPGMA）、“中值”（= WPGMC）或“质心”（= UPGMC）。

当我使用方法 =“中值”或“质心”时，我注意到 color_branches 的颜色编码失败。

我用随机生成的矩阵对其进行了测试，并为“中值”和“质心”方法复制了错误，这有什么具体原因吗？

请参阅输出图的链接：图 1。hclust 方法 (a) ward.D2, (b) 中位数, (c) 质心

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。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

您可以使用以下方法解决此问题branches_attr_by_clusters（尽管可能会有些棘手，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