数据集的子集作为单独的树状图，但在同一图中 [英] Subsets of a dataset as separate dendrograms, but in the same plot

问题描述

我知道我可以按照以下方式绘制树状图

I know I can plot a dendrogram as follows

library(cluster)
d <- mtcars
d[,8:11] <- lapply(d[,8:11], as.factor)

gdist <- daisy(d, metric = c("gower"), stand = FALSE)
dendro <- hclust(gdist, method = "average")
plot(as.dendrogram(dendro))

但是我已经确定了一些组（例如，通过迭代分类方法），作为 d 中的最后一列给出

However I have some groups identified (eg. by an iterative classification method), given as the last column in d

G <- c(1,2,3,3,4,4,5,5,5,5,1,2,1,1,2,4,1,3,4,5,1,7,4,3,3,2,1,1,1,3,5,6)
d$Group <- G

head(d)
                   mpg cyl disp  hp drat    wt  qsec vs am gear carb  Group
Mazda RX4         21.0   6  160 110 3.90 2.620 16.46  0  1    4    4     1
Mazda RX4 Wag     21.0   6  160 110 3.90 2.875 17.02  0  1    4    4     2
Datsun 710        22.8   4  108  93 3.85 2.320 18.61  1  1    4    1     3
Hornet 4 Drive    21.4   6  258 110 3.08 3.215 19.44  1  0    3    1     3
Hornet Sportabout 18.7   8  360 175 3.15 3.440 17.02  0  0    3    2     4
Valiant           18.1   6  225 105 2.76 3.460 20.22  1  0    3    1     4

我试图将所有树状图一起绘制在同一图上，并且比例相同。只有一个成员的组也需要绘制。 （第6组和第7组）

I am trying to plot all the dendrograms together on the same plot with the same scale. The groups with only a single member also needs to be plotted. (group 6 and 7)

我可以为数据子集绘制单独的树状图，除非组中的成员数只有一个时。但我认为这不是正确的方法。

I am able to plot individual dendrograms for subset of the data except when number of members in a group is only one. But I don't think this is the right approach.

layout(matrix(1:9, 3,3,byrow=TRUE))

gdist <- as.matrix(gdist)

N <- max(G)
for (i in 1:N){
  rc_tokeep <- row.names(subset(d, G==i))
  dis <- as.dist(gdist[rc_tokeep, rc_tokeep])
  dend <- hclust(dis, method = "average")
  plot(as.dendrogram(dend))
}

循环为最后两组给出此错误。 （6和7）只有一个成员。

The loop is giving this error for the last two groups. (6 and 7) having only a single member.

Error in hclust(dis, method = "average") : 
  must have n >= 2 objects to cluster

基本上，我不会复制这些类型地块。

Essentially I wan't to reproduce these type of plots. The clusters with single members are also plotted here.

推荐答案

如果要模仿最后几张图，可以执行以下操作：

If you want to mimic the last few graphs, you can do something like this:

N <- max(G)
layout(matrix(c(0,1:N,0),nc=1))

gdist <- as.matrix(gdist)

for (i in 1:N){
    par(mar=c(0,3,0,7))
    rc_tokeep <- row.names(subset(d, G==i))
    if(length(rc_tokeep)>2){ #The idea is to catch the groups with one single element to plot them differently
        dis <- as.dist(gdist[rc_tokeep, rc_tokeep])
        dend <- hclust(dis, method = "average")
        plot(as.dendrogram(dend),horiz=TRUE,
                 xlim=c(.8,0),axes=FALSE) # giving the same xlim will scale all of them, here i used 0.8 to fit your data but you can change it to whatever
        }else{
            plot(NA,xlim=c(.8,0),ylim=c(0,1),axes=F,ann=F)
            segments(0,.5,.1,.5) #I don't know how you intend to compute the length of the branch in a group of 1 element, you might want to change that
            text(0,.5, pos=4,rc_tokeep,xpd=TRUE)
            }
}

以您的示例为例：

如果要添加比例，可以在所有图形中添加网格，并在最后一个图形中添加比例：

If you want to add the scale you can add a grid in all graphs and a scale in the last one:

N <- max(G)
layout(matrix(c(0,1:N,0),nc=1))

gdist <- as.matrix(gdist)

for (i in 1:N){
    par(mar=c(0,3,0,7))
    rc_tokeep <- row.names(subset(d, G==i))
    if(length(rc_tokeep)>2){
        dis <- as.dist(gdist[rc_tokeep, rc_tokeep])
        dend <- hclust(dis, method = "average")
        plot(as.dendrogram(dend),horiz=TRUE,xlim=c(.8,0),xaxt="n",yaxt="n")
        abline(v=seq(0,.8,.1),lty=3) #Here the grid
        }else{
            plot(NA,xlim=c(.8,0),ylim=c(0,1),axes=F,ann=F)
            segments(0,.5,.1,.5)
            text(0,.5, pos=4,rc_tokeep,xpd=TRUE)
            abline(v=seq(0,.8,.1),lty=3) #Here the grid
            }
    }
axis(1,at=seq(0,.8,.1)) #Here the axis

最后，如果您想在结果图，您可以使用 table（d $ Group）获取每个组的成员数，并将其用作每个子图的高度：

And finally if you want to even the spaces between the different branches in the resulting plot, you can use table(d$Group) to get the number of members of each group and use it as a height for each subplot:

N <- max(G)

layout(matrix(c(0,1:7,0),nc=1), height=c(3,table(d$Group),3)) #Plus the height of the empty spaces.

gdist <- as.matrix(gdist)

for (i in 1:N){
    par(mar=c(0,3,0,7))
    rc_tokeep <- row.names(subset(d, G==i))
    if(length(rc_tokeep)>2){
        dis <- as.dist(gdist[rc_tokeep, rc_tokeep])
        dend <- hclust(dis, method = "average")
        plot(as.dendrogram(dend),horiz=TRUE,xlim=c(.8,0),xaxt="n",yaxt="n")
        abline(v=seq(0,.8,.1),lty=3)
        }else{
            plot(NA,xlim=c(.8,0),ylim=c(0,1),axes=F,ann=F)
            segments(0,.5,.1,.5)
            text(0,.5, pos=4,rc_tokeep,xpd=TRUE)
            abline(v=seq(0,.8,.1),lty=3)
            }
    }
axis(1,at=seq(0,.8,.1))

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