用 ggplot2 再现晶格树状图 [英] Reproducing lattice dendrogram graph with ggplot2

问题描述

可以用ggplot2重现这个格子图吗?

Is this possible to reproduce this lattice plot with ggplot2?

library(latticeExtra)
data(mtcars)
x  <- t(as.matrix(scale(mtcars)))
dd.row <- as.dendrogram(hclust(dist(x)))
row.ord <- order.dendrogram(dd.row)

dd.col <- as.dendrogram(hclust(dist(t(x))))
col.ord <- order.dendrogram(dd.col)

library(lattice)

levelplot(x[row.ord, col.ord],
      aspect = "fill",
      scales = list(x = list(rot = 90)),
      colorkey = list(space = "left"),
      legend =
      list(right =
           list(fun = dendrogramGrob,
                args =
                list(x = dd.col, ord = col.ord,
                     side = "right",
                     size = 10)),
           top =
           list(fun = dendrogramGrob,
                args =
                list(x = dd.row,
                     side = "top",
                     size = 10))))

推荐答案

EDIT

从 2011 年 8 月 8 日起，ggdendro 包可在 CRAN另请注意，树状图提取函数现在称为 dendro_data 而不是 cluster_data

From 8 August 2011 the ggdendro package is available on CRAN Note also that the dendrogram extraction function is now called dendro_data instead of cluster_data

是的，是的.但就目前而言，您将不得不跳过几个环节:

Yes, it is. But for the time being you will have to jump through a few hoops:

1. 安装 ggdendro 包(可从 CRAN 获得).这个包将从几种类型的聚类方法(包括Hclust和dendrogram)中提取聚类信息，其目的是在ggplot中绘图.
2. 使用网格图形创建视口并对齐三个不同的图.

1. Install the ggdendro package (available from CRAN). This package will extract the cluster information from several types of cluster methods (including Hclust and dendrogram) with the express purpose of plotting in ggplot.
2. Use grid graphics to create viewports and align three different plots.

代码:

首先加载库并为 ggplot 设置数据:

First load the libraries and set up the data for ggplot:

library(ggplot2)
library(reshape2)
library(ggdendro)

data(mtcars)
x <- as.matrix(scale(mtcars))
dd.col <- as.dendrogram(hclust(dist(x)))
col.ord <- order.dendrogram(dd.col)

dd.row <- as.dendrogram(hclust(dist(t(x))))
row.ord <- order.dendrogram(dd.row)

xx <- scale(mtcars)[col.ord, row.ord]
xx_names <- attr(xx, "dimnames")
df <- as.data.frame(xx)
colnames(df) <- xx_names[[2]]
df$car <- xx_names[[1]]
df$car <- with(df, factor(car, levels=car, ordered=TRUE))

mdf <- melt(df, id.vars="car")

提取树状图数据并创建绘图

Extract dendrogram data and create the plots

ddata_x <- dendro_data(dd.row)
ddata_y <- dendro_data(dd.col)

### Set up a blank theme
theme_none <- theme(
  panel.grid.major = element_blank(),
  panel.grid.minor = element_blank(),
  panel.background = element_blank(),
  axis.title.x = element_text(colour=NA),
  axis.title.y = element_blank(),
  axis.text.x = element_blank(),
  axis.text.y = element_blank(),
  axis.line = element_blank()
  #axis.ticks.length = element_blank()
)

### Create plot components ###    
# Heatmap
p1 <- ggplot(mdf, aes(x=variable, y=car)) + 
  geom_tile(aes(fill=value)) + scale_fill_gradient2()

# Dendrogram 1
p2 <- ggplot(segment(ddata_x)) + 
  geom_segment(aes(x=x, y=y, xend=xend, yend=yend)) + 
  theme_none + theme(axis.title.x=element_blank())

# Dendrogram 2
p3 <- ggplot(segment(ddata_y)) + 
  geom_segment(aes(x=x, y=y, xend=xend, yend=yend)) + 
  coord_flip() + theme_none

使用网格图形和一些手动对齐来定位页面上的三个图

Use grid graphics and some manual alignment to position the three plots on the page

### Draw graphic ###

grid.newpage()
print(p1, vp=viewport(0.8, 0.8, x=0.4, y=0.4))
print(p2, vp=viewport(0.52, 0.2, x=0.45, y=0.9))
print(p3, vp=viewport(0.2, 0.8, x=0.9, y=0.4))

这篇关于用 ggplot2 再现晶格树状图的文章就介绍到这了，希望我们推荐的答案对大家有所帮助，也希望大家多多支持IT屋！