用 ggplot 畫 hclust 的結果

用 ggplot 畫 hclust 的結果

drawing hclust result with ggplot

data(mtcars)

Tree  <- hclust(dist(mtcars))
plot(Tree)

library(ggplot2)
library(ggdendro)

hc       <- hclust(dist(mtcars))           # heirarchal clustering
dendr    <- dendro_data(hc, type="rectangle") # convert for ggplot
clust    <- cutree(hc,k=5)                    # find 2 clusters
clust.df <- data.frame(label=names(clust), cluster=factor(clust))
## dendr[["labels"]] has the labels, merge with clust.df based on label column
dendr[["labels"]] <- merge(dendr[["labels"]],clust.df, by="label")
## plot the dendrogram; note use of color=cluster in geom_text(...)
ggplot() +
  geom_segment(data=segment(dendr), aes(x=x, y=y, xend=xend, yend=yend)) +
  geom_text(data=label(dendr), aes(x, y, label=label, hjust=0, color=cluster),
           size=3) +
  coord_flip() + scale_y_reverse(expand=c(0.2, 0)) +
  theme(axis.line.y=element_blank(),
        axis.ticks.y=element_blank(),
        axis.text.y=element_blank(),
        axis.title.y=element_blank(),
        panel.background=element_rect(fill="white"),
        panel.grid=element_blank())

美美噠！

自定義間距：

library(ggplot2)
library(ggdendro)

hc       <- hclust(dist(head(mtcars)))
dendr    <- dendro_data(hc, type="rectangle") # convert for ggplot
clust    <- cutree(hc,k=2)                    # find 2 clusters
clust.df <- data.frame(label=names(clust), cluster=factor(clust))
## dendr[["labels"]] has the labels, merge with clust.df based on label column
dendr[["labels"]] <- merge(dendr[["labels"]],clust.df, by="label")
## plot the dendrogram; note use of color=cluster in geom_text(...)
ggplot() +
  geom_segment(data=segment(dendr), aes(x=x, y=y, xend=xend, yend=yend)) +
  geom_text(data=label(dendr), aes(x, y, label=label, hjust=0, color=cluster),
           size=3) +
  coord_flip() + scale_y_reverse(expand=c(0.2, 0)) +
  theme(axis.line.y=element_blank(),
        axis.ticks.y=element_blank(),
        axis.text.y=element_blank(),
        axis.title.y=element_blank(),
        panel.background=element_rect(fill="white"),
        panel.grid=element_blank())

觀察數據可知， 樹圖數據在dendr$segment裏面， 名字在dendr$label裏面。先給定一個listWidth_tree = c(1,2,5,10,11,20)

hc       <- hclust(dist(head(mtcars)))

dendr    <- dendro_data(hc, type="rectangle") # convert for ggplot
clust    <- cutree(hc,k=2)                    # find 2 clusters
clust.df <- data.frame(label=names(clust), cluster=factor(clust))
## dendr[["labels"]] has the labels, merge with clust.df based on label column
dendr[["labels"]] <- merge(dendr[["labels"]],clust.df, by="label")
## plot the dendrogram; note use of color=cluster in geom_text(...)
ggplot() +
  geom_segment(data=segment(dendr), aes(x=x, y=y, xend=xend, yend=yend)) +
  geom_text(data=label(dendr), aes(x, y, label=label, hjust=0, color=cluster),
           size=3) +
  scale_y_reverse(expand=c(0.2, 0)) +
  theme(axis.line.y=element_blank(),
        axis.ticks.y=element_blank(),
        axis.text.y=element_blank(),
        axis.title.y=element_blank(),
        panel.background=element_rect(fill="white"),
        panel.grid=element_blank())

Width_tree = c(1,2,5,10,11,20)

dendr$labels$x = Width_tree[dendr$labels$x]
dendr$segments = dendr$segments[order(dendr$segments$x),]

## 做個list
List = c()
for(i in c(1:length(Width_tree))){
  List = c(List, which(dendr$segments$x==i))
}

打包一個函數，方便重複畫圖

PLOT <- function(dendr){
  ggplot() +
    geom_segment(data=segment(dendr), aes(x=x, y=y, xend=xend, yend=yend)) +
    geom_text(data=label(dendr), aes(x, y, label=label, hjust=0, color=cluster),
             size=3) +
    scale_y_reverse(expand=c(0.2, 0)) +
    theme(axis.line.y=element_blank(),
          axis.ticks.y=element_blank(),
          axis.text.y=element_blank(),
          axis.title.y=element_blank(),
          panel.background=element_rect(fill="white"),
          panel.grid=element_blank())
}
PLOT2 <- function(dendr){
  ggplot() +
  geom_segment(data=segment(dendr), aes(x=x, y=y, xend=xend, yend=yend)) +
  geom_text(data=label(dendr), aes(x, y, label=label, hjust=0, color=cluster),
           size=3) +
  coord_flip() + scale_y_reverse(expand=c(0.2, 0)) +
  theme(axis.line.y=element_blank(),
        axis.ticks.y=element_blank(),
        axis.text.y=element_blank(),
        axis.title.y=element_blank(),
        panel.background=element_rect(fill="white"),
        panel.grid=element_blank())
}

調整豎線

for( i in c(1:6)){
Dif_tmp = Width_tree[i]- dendr$segments$x[List[i]]

dendr$segments$x[List[i]:nrow(dendr$segments)] = dendr$segments$x[List[i]:nrow(dendr$segments)]+Dif_tmp
dendr$segments$xend[List[i]:nrow(dendr$segments)] = dendr$segments$xend[List[i]:nrow(dendr$segments)]+Dif_tmp
}

PLOT(dendr)

鏈接橫線

##刪除橫線
dendr$segments = dendr$segments[dendr$segments$x == dendr$segments$xend,]

Y_list = dendr$segments$y[duplicated(dendr$segments$y)]

for(i in Y_list){  
tmp = (dendr$segments$x[dendr$segments$y  == i])
dendr$segments = rbind(dendr$segments, data.frame(x=tmp[1],y=i,xend=tmp[2],yend=i))
}

PLOT(dendr)

能用。。。但是好像會有bug。。唉= =

修正

LS_judg<- function(TB){
  if (TB['x'] == TB['xend']){
    R = 'v'
  }else{
    R = 'h'
  }
  return(R)
}

##修正竖线
Seg = dendr$segments

for( i in c(nrow(dendr$segments):1)){
  if(LS_judg(dendr$segments[i,]) == 'h'){
    tmpy = dendr$segments[i,]$y
    tmpTB = Seg[Seg$yend== tmpy,]
      for( ii in c(1:nrow(tmpTB))){
      if(LS_judg(tmpTB[ii,]) == 'v'){
        Num = rownames(tmpTB[1,])
        dendr$segments[match(Num, row.names(dendr$segments)),][c(1,3)] = sum(Seg[i,c('x','xend')])/2
      }
    }
  }
}

## 重画横线：
dendr$segments = dendr$segments[dendr$segments$x == dendr$segments$xend,]

Y_list = dendr$segments$y[duplicated(dendr$segments$y)]

for(i in Y_list){  
tmp = (dendr$segments$x[dendr$segments$y  == i])
dendr$segments = rbind(dendr$segments, data.frame(x=tmp[1],y=i,xend=tmp[2],yend=i))
}

PLOT(dendr)

整合一下：

Width_tree = c(1,2,5,10,11,20)

LS_judg<- function(TB){
  if (TB['x'] == TB['xend']){
    R = 'v'
  }else{
    R = 'h'
  }
  return(R)
}

TreePlot <- function(dendr, Width_tree){
  dendr$labels$x = Width_tree[dendr$labels$x]
  dendr$segments = dendr$segments[order(dendr$segments$x),]
  # 做個list
  List = c()
  for(i in c(1:length(Width_tree))){
    List = c(List, which(dendr$segments$x==i))
  }
  # 調整豎線
  for( i in c(1:length(dendr$labels$label))){
  Dif_tmp = Width_tree[i]- dendr$segments$x[List[i]]
  dendr$segments$x[List[i]:nrow(dendr$segments)] = dendr$segments$x[List[i]:nrow(dendr$segments)]+Dif_tmp
  dendr$segments$xend[List[i]:nrow(dendr$segments)] = dendr$segments$xend[List[i]:nrow(dendr$segments)]+Dif_tmp
  }
  # 刪除添加新的橫線
  dendr$segments = dendr$segments[dendr$segments$x == dendr$segments$xend,]
  Y_list = dendr$segments$y[duplicated(dendr$segments$y)]
  for(i in Y_list){  
  tmp = (dendr$segments$x[dendr$segments$y  == i])
  dendr$segments = rbind(dendr$segments, data.frame(x=tmp[1],y=i,xend=tmp[2],yend=i))
  }
  Seg = dendr$segments
  for( i in c(nrow(dendr$segments):1)){
    if(LS_judg(dendr$segments[i,]) == 'h'){
      tmpy = dendr$segments[i,]$y
      tmpTB = Seg[Seg$yend== tmpy,]
        for( ii in c(1:nrow(tmpTB))){
        if(LS_judg(tmpTB[ii,]) == 'v'){
          Num = rownames(tmpTB[1,])
          dendr$segments[match(Num, row.names(dendr$segments)),][c(1,3)] = sum(Seg[i,c('x','xend')])/2
        }
      }
    }
  }
  # 重画横线：
  dendr$segments = dendr$segments[dendr$segments$x == dendr$segments$xend,]
  Y_list = dendr$segments$y[duplicated(dendr$segments$y)]
  for(i in Y_list){  
  tmp = (dendr$segments$x[dendr$segments$y  == i])
  dendr$segments = rbind(dendr$segments, data.frame(x=tmp[1],y=i,xend=tmp[2],yend=i))
  }
 return(dendr)
}

再來試一下：

1. 正常情況:

library(ggplot2)
library(ggdendro)

hc       <- hclust(dist(mtcars))           # heirarchal clustering
dendr    <- dendro_data(hc, type="rectangle") # convert for ggplot
clust    <- cutree(hc,k=5)                    # find 2 clusters
clust.df <- data.frame(label=names(clust), cluster=factor(clust))
## dendr[["labels"]] has the labels, merge with clust.df based on label column
dendr[["labels"]] <- merge(dendr[["labels"]],clust.df, by="label")
## plot the dendrogram; note use of color=cluster in geom_text(...)
PLOT2(dendr)

轉化後：

Width_tree =c(2, 5, 6, 10, 12, 13, 16, 20, 23, 24, 29, 37, 41, 42, 45, 47, 51, 53, 54, 57, 60, 61, 63, 67, 70, 173, 175, 276, 280, 281, 287, 593)

AA <- TreePlot(dendr,Width_tree)
PLOT2(AA)

原圖	後圖

终于- - 终于终于， 修正好了， 最终版本

else: factoextra+dendextend