dendextend 包中 rect.dendrogram 的奇怪行为

Question

我尝试使用

iris

数据集显示截止高度对聚类数量的影响，并使用

rect.dendrogram

可视化生成的聚类。

if (!require("dendextend")) {install.packages("dendextend")} else {library("dendextend")}

data("iris", package = "datasets")

Data <- list()

Data$Lab <- as.character(iris[,5])
Data$dat <- prcomp(iris[,-5])$x[,1:2]

Data$dist <- dist(Data$dat, method = "euclidean")
Data$hist <- hclust(Data$dist, method = "complete")

# plot dendrogram

hcd <- as.dendrogram(Data$hist)

cluster.height <- 6

par(pty = "m",
    mar = c(1,2,1.5,1),
    mgp = c(1,0,0),
    tck = 0.01,
    cex.axis = 0.75,
    font.main = 1)
plot(sort(hcd), 
     ylab = "Height",
     leaflab = "none")
rect.dendrogram(sort(hcd),
                h = cluster.height,
                border = "black",
                xpd = NA,
                lower_rect = -0.1,
                upper_rect = 0)
abline(h = cluster.height,
       lty = 3)
dev.off()

使用高高度值时，会出现两个矩形。

该函数搜索由截止创建的簇。 问题是有没有办法只获取较大的矩形？ 是否有我忽略的参数/选项，或者是

rect.dendrogram

函数中的错误？

Answer 1

在我看来确实像是某种错误。您可以使用该功能的相关部分。

> rect_dnd <- \(tree, which, h, ybadj=0, ytadj=0, ...) {
+   cl <- cutree(tree, h=h)
+   clt <- table(cl)[unique(cl[tree$order])]
+   m <- c(0, cumsum(clt))
+   k <- min(which(rev(tree$height) < h))
+   rect(xleft=m[which] + 0.66,
+        ybottom=mean(rev(tree$height)[(k - 1):k]) + ytadj,
+        xright=m[which + 1] + 0.33,
+        ytop=par()$usr[3] + ybadj, ...)
+ }
> 
> cluster.height <- 6
> 
> par(pty="m", mar=c(1, 2, 1.5, 1), mgp=c(1, 0, 0), tck=0.01, cex.axis=0.75, 
+     font.main=1)
> plot(hcd, ylab="Height", leaflab="none")
> rect_dnd(Data$hist, which=1, h=cluster.height, ytadj=-.1, border='red')
> abline(h=cluster.height, lty=3)

---

数据：

> Data <- list(Lab=as.character(iris[, 5]), dat=prcomp(iris[, -5])$x[, 1:2])
> Data$dist <- dist(Data$dat, method="euclidean")
> Data$hist <- hclust(Data$dist, method="complete")
> hcd <- as.dendrogram(Data$hist)