superheat | 级的热图绘制解决方案~二聚类和注释图的添加~

1写在前面

前面写了superheat的教程，今天写一下第二波，如何进行聚类以及添加注释图吧。🤩

分分钟提升你的heatmap的颜值哦！~🥰

2用到的包

# devtools::install_github("rlbarter/superheat")
library(superheat)
library(tidyverse)

3示例数据

data("mtcars")

DT::datatable(mtcars)

4行聚类

4.1 生成聚类树

superheat(mtcars,
          scale = T,
          row.dendrogram = T)

4.2 聚类结果可视化

set.seed(123)
superheat(mtcars,
          scale = T,
          n.clusters.rows = 3)

4.3 强制显示行名

默认情况下，在聚类时，相应的标签会分组到聚类名称中（通常为 1、2、3……等）。😘

如果想强制标签为原始变量名称，可以分别指定left.label = 'variable'或Bottom.label = 'variable'。🥳

set.seed(123)
superheat(mtcars,
          scale = T,
          n.clusters.rows = 3,
          left.label = 'variable')

4.4 提取聚类结果

我们来试试提取一下聚类的结果吧。🤩

set.seed(123)
superheatmap <- superheat(mtcars,
                          scale = T,
                          n.clusters.rows = 3,
                          left.label = 'variable',
                          print.plot = F)

superheatmap$membership.rows

4.5 自定义聚类结果

有时候你可能会有自己想要的聚类结果，手动定义一下吧。😘

gears <- paste(mtcars$gear, "gears")

set.seed(123)
superheat(mtcars,
          scale = T,
          membership.rows = gears)

5注释图-Scatterplots

我们可以在热图的旁边添加一些注释图，非常简单，比如yt (‘y top’)或者yr(‘y right’)。🤒

常用的类型有以下几种，我们一起看看吧。😂

5.1 基础绘图

superheat(dplyr::select(mtcars, -mpg), 
          scale = T,
          yr = mtcars$mpg,
          yr.axis.name = "miles per gallon")

5.2 调整大小

superheat(dplyr::select(mtcars, -mpg), 
          scale = T,
          yr = mtcars$mpg,
          yr.axis.name = "miles per gallon",
          yr.point.size = 4)

5.3 调整颜色

point.col <- rep("wheat3", nrow(mtcars))
point.col[5] <- "red"

superheat(dplyr::select(mtcars, -mpg), 
          scale = T,
          yr = mtcars$mpg,
          yr.axis.name = "miles per gallon",
          yr.obs.col = point.col,
          yr.point.size = 4)

5.4 聚类颜色

我们甚至可以直接设置聚类的颜色，参数为yr.cluster.col。🧐

superheat(dplyr::select(mtcars, -mpg, -gear), 
          # scale
          scale = T,
          # 行聚类
          membership.rows = paste(mtcars$gear, "gears"),
          left.label = "variable",
          # mpg scatterplot
          yr = mtcars$mpg,
          yr.axis.name = "miles per gallon",
          yr.cluster.col = c("turquoise4", "plum4", "springgreen4"),
          yr.point.size = 4)

5.5 只显示一个聚类点

mpg.per.cluster <- mtcars %>% 
  group_by(gear) %>% 
  summarize(mpg.avg = mean(mpg)) %>% 
  select(mpg.avg) %>%
  unlist

superheat(dplyr::select(mtcars, -mpg, -gear), 
          scale = T,
          membership.rows = paste(mtcars$gear, "gears"),
          left.label = "variable",
          yr = mpg.per.cluster,
          yr.axis.name = "miles per gallon",
          yr.cluster.col = c("black", "red", "orange"),
          yr.point.size = 4)

6注释图-Scatterplots

6.1 基础绘图

换个Line plot试试。🤪

superheat(dplyr::select(mtcars, -mpg), 
          scale = T,
          yr = mtcars$mpg,
          yr.axis.name = "miles per gallon",
          yr.plot.type = "line",
          order.rows = order(mtcars$mpg))

6.2 调整大小

superheat(dplyr::select(mtcars, -mpg), 
          scale = T,
          yr = mtcars$mpg,
          yr.axis.name = "miles per gallon",
          yr.plot.type = "line",
          yr.line.size = 4,
          order.rows = order(mtcars$mpg))

6.3 调整颜色

superheat(dplyr::select(mtcars, -mpg), 
          scale = T,
          yr = mtcars$mpg,
          yr.axis.name = "miles per gallon",
          yr.plot.type = "line",
          yr.line.size = 4,
          yr.line.col = "springgreen4",
          order.rows = order(mtcars$mpg))

6.4 聚类

superheat(dplyr::select(mtcars, -mpg), 
          scale = T,
          membership.rows = paste(mtcars$gear, "gears"),
          left.label = "variable",
          yr = mtcars$mpg,
          yr.axis.name = "miles per gallon",
          yr.plot.type = "line",
          yr.line.size = 4,
          yr.cluster.col = c("plum4", "paleturquoise4", "salmon3"),
          order.rows = order(mtcars$mpg))

7注释图-Smoothed line

7.1 Loess curve

superheat(dplyr::select(mtcars, -mpg), 
          scale = T,
          yr = mtcars$mpg,
          yr.axis.name = "miles per gallon",
          yr.plot.type = "smooth",
          yr.line.size = 4,
          yr.line.col = "red4",
          order.rows = order(mtcars$cyl))

7.2 Linear regression line

superheat(dplyr::select(mtcars, -mpg), 
          scale = T,
          yr = mtcars$mpg,
          yr.axis.name = "miles per gallon",
          yr.plot.type = "smooth",
          smoothing.method = "lm",
          yr.line.size = 4,
          yr.line.col = "plum4",
          order.rows = order(mtcars$cyl))

7.3 Scatterplot with connecting line plot

superheat(dplyr::select(mtcars, -mpg), 
          scale = T,
          yr = mtcars$mpg,
          yr.axis.name = "miles per gallon",
          yr.plot.type = "scatterline",
          yr.line.col = "tomato3",
          yr.obs.col = rep("orange", nrow(mtcars)),
          yr.point.size = 4,
          order.rows = order(mtcars$cyl))

7.4 Scatterplot with smoothed line

superheat(dplyr::select(mtcars, -mpg), 
          scale = T,
          yr = mtcars$mpg,
          yr.axis.name = "miles per gallon",
          yr.plot.type = "scattersmooth",
          yr.line.col = "tomato3",
          yr.obs.col = rep("orange", nrow(mtcars)),
          order.rows = order(mtcars$cyl))

8注释图-Barplot

8.1 基础绘图

superheat(dplyr::select(mtcars, -mpg), 
          scale = T,
          yr = mtcars$mpg,
          yr.axis.name = "miles per gallon",
          yr.plot.type = "bar")

8.2 调整颜色

superheat(dplyr::select(mtcars, -mpg), 
          scale = T,
          yr = mtcars$mpg,
          yr.axis.name = "miles per gallon",
          yr.plot.type = "bar",
          yr.bar.col = "black",
          yr.obs.col = rep("beige", nrow(mtcars)))

8.3 聚类

mpg.per.cluster <- mtcars %>% 
  group_by(gear) %>% 
  summarize(mpg.avg = mean(mpg)) %>% 
  select(mpg.avg) %>%
  unlist

superheat(dplyr::select(mtcars, -mpg, -gear), 
          scale = T,
          membership.rows = paste(mtcars$gear, "gears"),
          left.label = "variable",
          yr = mpg.per.cluster,
          yr.axis.name = "miles per gallon",
          yr.plot.type = "bar",
          yr.bar.col = "black",
          yr.cluster.col = c("beige", "white", "beige"))

9注释图-Boxplot

9.1 基础绘图

mpg.per.cluster <- mtcars %>% 
  group_by(gear) %>% 
  summarize(mpg.avg = mean(mpg)) %>% 
  select(mpg.avg) %>%
  unlist

superheat(dplyr::select(mtcars, -mpg, -gear), 
          scale = T,
          membership.rows = paste(mtcars$gear, "gears"),
          left.label = "variable",
          yr = mtcars$mpg,
          yr.axis.name = "miles per gallon",
          yr.plot.type = "boxplot")

9.2 调整颜色

mpg.per.cluster <- mtcars %>% 
  group_by(gear) %>% 
  summarize(mpg.avg = mean(mpg)) %>% 
  select(mpg.avg) %>%
  unlist

superheat(dplyr::select(mtcars, -mpg, -gear), 
          scale = T,
          membership.rows = paste(mtcars$gear, "gears"),
          left.label = "variable",
          yr = mtcars$mpg,
          yr.axis.name = "miles per gallon",
          yr.plot.type = "boxplot",
          yr.cluster.col = c("beige", "slategray1", "beige"))

10注释图坐标轴的调整

10.1 调整轴名称

用到yr.axis.name或者yt.axis.name就行啦。🤒

superheat(dplyr::select(mtcars, -mpg), 
          scale = T,
          yr = mtcars$mpg,
          yr.axis.name = "miles per gallon",
          yt = cor(mtcars)[-1,"mpg"],
          yt.plot.type = "bar",
          yt.axis.name = "Correlation\nwith mpg")

10.2 调整坐标轴名称及数字大小

可以分别使用yr.axis.name.size/yt.axis.name.size或yr.axis.size/yt.axis.size来调整。😘

superheat(dplyr::select(mtcars, -mpg), 
          scale = T,
          yr = mtcars$mpg,
          yr.axis.name = "miles per gallon",
          yt = cor(mtcars)[-1,"mpg"],
          yt.plot.type = "bar",
          yt.axis.name = "Correlation\nwith mpg",
          yt.axis.size = 14,
          yt.axis.name.size = 14)

10.3 调整坐标轴Limits

superheat(dplyr::select(mtcars, -mpg), 
          scale = T,
          yr = mtcars$mpg,
          yr.axis.name = "miles per gallon",
          yr.lim = c(0, 60),
          yt = cor(mtcars)[-1,"mpg"],
          yt.plot.type = "bar",
          yt.axis.name = "Correlation\nwith mpg",
          yt.lim = c(-1.5, 1))

10.4 调整坐标轴ticks

superheat(dplyr::select(mtcars, -mpg), 
          scale = T,
          yr = mtcars$mpg,
          yr.axis.name = "miles per gallon",
          yr.lim = c(0, 60),
          yr.breaks = c(10, 40),        
          yt = cor(mtcars)[-1,"mpg"],
          yt.plot.type = "bar",
          yt.axis.name = "Correlation\nwith mpg")

10.5 调整坐标轴ticks的labels

superheat(dplyr::select(mtcars, -mpg), 
          scale = T,
          yr = mtcars$mpg,
          yr.axis.name = "miles per gallon",
          yr.lim = c(0, 60),
          yr.breaks = c(10, 40),
          yr.break.labels = c("low", "high"),
          yt = cor(mtcars)[-1,"mpg"],
          yt.plot.type = "bar",
          yt.axis.name = "Correlation\nwith mpg")

10.6 调整注释图大小

superheat(dplyr::select(mtcars, -mpg), 
          scale = T,
          yr = mtcars$mpg,
          yr.axis.name = "miles per gallon",
          yr.axis.size = 14,
          yr.axis.name.size = 14,
          yr.plot.size = 0.8,
          yt = cor(mtcars)[-1,"mpg"],
          yt.plot.type = "bar",
          yt.axis.name = "Correlation with mpg",
          yt.axis.size = 14,
          yt.axis.name.size = 14,
          yt.plot.size = 0.7)

点个在看吧各位~ ✐.ɴɪᴄᴇ ᴅᴀʏ 〰

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