在r中为带有彩色叶子的树状图创建图例

Question

我在树状图中给叶子着色如下

require(graphics)

dm <- hclust(dist(USArrests[1:5,]), "ave")

df<-data.frame("State"=c("Alabama","Alaska","Arizona","Arkansas","California"),   "Location"=c("South","North","West","South","West"))


color.sites<-function(dm){
    dend<-as.dendrogram(dm)
    plot(dend)

    cols <- attributes(dend)
    df$ColorGroups <- factor(df$Location)

    #Set colour pallette
    Location.Pal <- rainbow(nlevels(df$ColorGroups), s=0.9,v=0.9,start=0.1,end=0.9,alpha=1)

    colorleaves <- function (n) {
    # only apply to "leaves" in other words the labels
    if(is.leaf(n)) { 
        i <- which(df$State == attr(n,"label"))
        col.lab  <- Location.Pal[[unclass(df$ColorGroups[[i]])]]
        a <- attributes(n)
        attr(n, "nodePar") <- c(a$nodePar, list(lab.col = col.lab))
    }
    n
}

xx <- dendrapply(dend, colorleaves)

plot(xx, cex=3, cex.main=2, cex.lab=5, cex.axis=1, mar=c(3,3,3,3), main="Title")
}

color.sites(dm)

我想:1)添加一个解释颜色的图例(即橙色=北方)2)使叶子标签更大更大胆(cex.lab似乎不起作用)3)创建一个具有鲜明对比的调色板当树状图中有许多叶子和颜色时,颜色(彩虹,热量,颜色等)似乎都混合在一起.

任何意见是极大的赞赏 !

Answer 1

如果您已经知道如何使用和调整ggplot2图形,另一种解决方案是使用@Andrie ggdendro包

library(ggplot2)
library(ggdendro)

dm <- hclust(dist(USArrests[1:5,]), "ave")

df <- data.frame(State = c("Alabama","Alaska","Arizona","Arkansas","California"),
                 Location = c("South","North","West","South","West"))


hcdata<- dendro_data(dm, type="rectangle")

hcdata$labels <- merge(x = hcdata$labels, y = df,  by.x = "label", by.y = "State")


ggplot() +
 geom_segment(data=segment(hcdata), aes(x=x, y=y, xend=xend, yend=yend)) +
 geom_text(data = label(hcdata), aes(x=x, y=y, label=label, colour = Location, hjust=0), size=3) +
 geom_point(data = label(hcdata), aes(x=x, y=y), size=3, shape = 21) +
 coord_flip() +
 scale_y_reverse(expand=c(0.2, 0)) +
 scale_colour_brewer(palette = "Dark2") + 
 theme_dendro() 

Answer 2

1. 使用legend()

   cols <- c("orange","forestgreen")
   legend("topright", legend = c("North","South"),
          fill = cols, border = cols, bty = "n")
   

2. 我不相信你可以，无需黑客攻击，stats:::plot.dendrogram()因为标签是用绘制的text()并且图形参数不会传递给该函数。中的相关代码stats:::plot.dendrogram()为：

   if (!is.null(et <- attr(x, "edgetext"))) {
       my <- mean(hgt, yTop)
       if (horiz) 
           text(my, x0, et)
       else text(x0, my, et)
   }
   

   将整个函数源复制到编辑器中并对其进行编辑以执行您想要的操作，然后将其分配给您自己的函数对象并使用它。如果由于找不到函数而失败（它们可能未从命名空间导出，请找出它是哪个命名空间，在有问题的函数前面加上ns:::相关ns命名空间的位置。

3. 尝试使用RColorBrewer包作为选择分类调色板的一个选项。