Question

我在尝试使用两个树形图来调整热图时遇到了麻烦。现在它看起来像这样（我使用虚线只是为了显示情节＆＃39;边界）：

我的目标是在plot.margin中不使用任何魔术常量来获得这样的东西（这个特定的图像是使用它们创建的），所以我可以使用一个脚本来获取数百个数据集的树形图热图，而不是只有一个：

（注意顶部的树形图和热图之间的自由空间以及热图的标签和图的下边缘）。

我认为主要问题是我不知道如何正确计算热图的宽度和高度以及轴的空间。文本。

完全可重复的示例代码：

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

n_samples <- 20
n_modules <- 11

my_data <- dget("http://pastebin.com/raw/bKSXY5kP")

base_size <- 9
longest_sample_name <- max(nchar(my_data$names))
heatmap_height <- round((10 / 27.1) * n_samples, digits=3)
heatmap_width <- round((10 / 27.1) * n_modules, digits=3)
title_width <- round((10 / 27.1) * 0.25 * longest_sample_name, digits=3)

heatmap <- 
    ggplot(my_data, aes(Module, Sample)) + 
    geom_tile(aes(fill = value), colour = "black", size=0.5) + 
    scale_fill_gradientn(colours=c("blue", "blue", "white", "red", "red"), space="Lab") + 
    theme_grey(base_size=base_size, base_family = "mono") +
    scale_x_discrete(expand=c(0,0)) + 
    scale_y_discrete(expand=c(0,0)) +
    coord_fixed() +
    theme(
      panel.border = element_rect(linetype = "dashed", colour = "black", fill=NA),    
      plot.margin=unit(c(0, 0, 0, 0), "in"),
      legend.position ="none",
      axis.title = element_blank(),
      axis.text.y = element_text(size=base_size * 1.2, colour="black"), 
      axis.text.x = element_text(size=base_size * 1.2, colour="black"))

x <- matrix(my_data$value, nrow = n_samples, ncol = n_modules + 1)

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

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

theme_dendro <- theme(
  panel.border = element_rect(linetype = "dashed", colour = "black", fill=NA),
  plot.margin=unit(c(0, 0, 0, 0), "in"),
  panel.grid.major = element_blank(),
  panel.grid.minor = element_blank(),
  panel.background = element_blank(),
  axis.title = element_blank(),
  axis.text = element_blank(),
  axis.ticks = element_blank(),
  axis.line = element_blank())

dendro_horizontal <- 
  ggplot(segment(ddata_x)) + 
  geom_segment(aes(x=x, y=y, xend=xend, yend=yend)) + 
  scale_x_discrete(expand=c(0,0)) + 
  scale_y_discrete(expand=c(0,0)) + 
  theme_dendro +
  coord_flip()

dendro_vertical <- 
  ggplot(segment(ddata_y)) + 
  geom_segment(aes(x=x, y=y, xend=xend, yend=yend)) + 
  scale_x_discrete(expand=c(0,0)) + 
  scale_y_discrete(expand=c(0,0)) + 
  theme_dendro

layout_matrix <- rbind(c(NA, 1, NA),
                       c(2,  2, 3))

widths <- c(title_width, heatmap_width, heatmap_width * 2 / 3)
heights <- c(heatmap_height / 2, heatmap_height)

grobs <- arrangeGrob(grobs = list(dendro_vertical, heatmap, dendro_horizontal), 
                     layout_matrix = layout_matrix,
                     widths = widths,
                     heights = heights)

ggsave("heatmap_with_dendro.png", 
       plot = grobs, 
       width = sum(widths),
       height = sum(heights),
       units = "in")

这是我计算grobs＆＃39;大小（＆＃39;魔术＆＃39;数字是从以前的编码员继承的，没有敢触摸它们）：

longest_sample_name <- max(nchar(my_data$names))
heatmap_height <- round((10 / 27.1) * n_samples, digits=3)
heatmap_width <- round((10 / 27.1) * n_modules, digits=3)
title_width <- round((10 / 27.1) * 0.25 * longest_sample_name, digits=3)

我如何创建热图：

heatmap <- 
    ggplot(my_data, aes(Module, Sample)) + 
    geom_tile(aes(fill = value), colour = "black", size=0.5) + 
    scale_fill_gradientn(colours=c("blue", "blue", "white", "red", "red"), space="Lab") + 
    theme_grey(base_size=base_size, base_family = "mono") +
    scale_x_discrete(expand=c(0,0)) + 
    scale_y_discrete(expand=c(0,0)) +
    coord_fixed() +
    theme(
      panel.border = element_rect(linetype = "dashed", colour = "black", fill=NA),    
      plot.margin=unit(c(0, 0, 0, 0), "in"),
      legend.position ="none",
      axis.title = element_blank(),
      axis.text.y = element_text(size=base_size * 1.2, colour="black"), 
      axis.text.x = element_text(size=base_size * 1.2, colour="black"))

和树状图：

x <- matrix(my_data$value, nrow = n_samples, ncol = n_modules + 1)

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

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

theme_dendro <- theme(
  panel.border = element_rect(linetype = "dashed", colour = "black", fill=NA),
  plot.margin=unit(c(0, 0, 0, 0), "in"),
  panel.grid.major = element_blank(),
  panel.grid.minor = element_blank(),
  panel.background = element_blank(),
  axis.title = element_blank(),
  axis.text = element_blank(),
  axis.ticks = element_blank(),
  axis.line = element_blank())

dendro_horizontal <- 
  ggplot(segment(ddata_x)) + 
  geom_segment(aes(x=x, y=y, xend=xend, yend=yend)) + 
  scale_x_discrete(expand=c(0,0)) + 
  scale_y_discrete(expand=c(0,0)) + 
  theme_dendro +
  coord_flip()

dendro_vertical <- 
  ggplot(segment(ddata_y)) + 
  geom_segment(aes(x=x, y=y, xend=xend, yend=yend)) + 
  scale_x_discrete(expand=c(0,0)) + 
  scale_y_discrete(expand=c(0,0)) + 
  theme_dendro

我如何使用gridExtra安排它们：

layout_matrix <- rbind(c(NA, 1, NA),
                       c(2,  2, 3))

widths <- c(title_width, heatmap_width, heatmap_width * 2 / 3)
heights <- c(heatmap_height / 2, heatmap_height)

grobs <- arrangeGrob(grobs = list(dendro_vertical, heatmap, dendro_horizontal), 
                     layout_matrix = layout_matrix,
                     widths = widths,
                     heights = heights)

最终保存图片：

ggsave("heatmap_with_dendro.png", 
       plot = grobs, 
       width = sum(widths),
       height = sum(heights),
       units = "in")

使用树状图拟合热图

0 个答案: