王胖的生信笔记第40期：一些常见的科研做图

大家是不是在科研论文里经常见到这样的图：

就是成对比较的两组，画出两组箱线图的同时，每个成对之间也画出线连接。

怎么画呢？这个STHDA的教程不错，和大家分享。

http://www.sthda.com/english/articles/32-r-graphics-essentials/132-plot-grouped-data-box-plot-bar-plot-and-more/

当然不是一定要用R去画，你擅长用GraphPad也可以。

设置环境

主要是要用到以下几个包。

library(dplyr) 
library(ggplot2)
library(ggpubr)

用的数据集是自带的五万个钻石价格。不过为了方便展示，只用D，E，F两个颜色的数据。（原始教程用的两组，配色是介绍里提到的那样，在这时期比较敏感，我这里就用了法国国旗配色代替https://www.flagcolorcodes.com/france）。

柱状图

df <- diamonds %>%
  filter(color %in% c("D", "E","F")) %>%
  group_by(cut, color) %>%
  summarise(counts = n())

# 堆叠柱状图
ggplot(df, aes(x = cut, y = counts)) +
  geom_bar(
    aes(color = color, fill = color),
    stat = "identity", position = position_stack()
  ) +
  scale_color_manual(values = c("#002395", "#FFFFFF","#ED2939"))+
  scale_fill_manual(values = c("#002395", "#FFFFFF","#ED2939"))
# 分组柱状图
ggplot(df, aes(x = cut, y = counts)) +
  geom_bar(
    aes(color = color, fill = color),
    stat = "identity", position = position_dodge(0.8),
    width = 0.7
  ) +
  scale_color_manual(values = c("#002395", "#FFFFFF","#ED2939"))+
  scale_fill_manual(values = c("#002395", "#FFFFFF","#ED2939"))

还能直接在上面标注出数字。

ggplot(df, aes(x = cut, y = counts)) +
  geom_bar(
    aes(color = color, fill = color),
    stat = "identity", position = position_dodge(0.8),
    width = 0.7
  ) +
  scale_color_manual(values = c("#002395", "#FFFFFF","#ED2939"))+
  scale_fill_manual(values = c("#002395", "#FFFFFF","#ED2939"))+
  ggtitle("分组柱状图")+ geom_text(
  aes(label = counts, group = color), 
  position = position_dodge(0.8),
  vjust = -0.3, size = 3.5
) +theme_dark()

df <- df %>%
  arrange(cut, desc(color)) %>%
  mutate(lab_ypos = cumsum(counts) - .5 * counts)
# 这里的.5就意味着文字在堆叠柱状图的中间
ggplot(df, aes(x = cut, y = counts)) +
  geom_bar(
    aes(color = color, fill = color),
    stat = "identity", position = position_stack()
  ) +
  scale_color_manual(values = c("#002395", "#FFFFFF","#ED2939"))+
  scale_fill_manual(values = c("#002395", "#FFFFFF","#ED2939"))+
  ggtitle("堆叠柱状图")

棒棒糖图

ggplot(df, aes(cut, counts)) +
  geom_linerange(
    aes(x = cut, ymin = 0, ymax = counts, group = color), 
    color = "lightgray", size = 1.5,
    position = position_dodge(0.3)
  )+
  geom_point(
    aes(color = color),
    position = position_dodge(0.3), size = 3
  )+
  scale_color_manual(values = c("#002395", "#FFFFFF","#ED2939"))+
  theme_dark()+
  ggtitle("棒棒糖图")

实际上使用ggdotchart肯恩更需要的参数更少一些，不过这里我就不展开啦

带Error Bar的折线图

换个维生素D对豚鼠牙齿生长的数据

df <- ToothGrowth 
df$dose <- as.factor(df$dose)
df.summary <- df %>%
  group_by(dose) %>%
  summarise(
    sd = sd(len, na.rm = TRUE),
    len = mean(len)
  )

做带Error Bar的图。注意这里使用as.numeric的话，下面的坐标就是按照实际数值来，使用as.factor的话，下面的坐标就是按照组别来。

df.summary$dose <- as.numeric(df.summary$dose)
ggplot(df.summary, aes(dose, len)) +
  geom_line() +
  geom_errorbar( aes(ymin = len-sd, ymax = len+sd),width = 0.2) +
  geom_point(size = 2)+theme_classic()

可以再加上每组的数据散点

df$dose <- as.numeric(df$dose)
ggplot(df, aes(dose, len)) +
  geom_jitter( position = position_jitter(0.2),
               color = "darkgray") + 
  geom_line(aes(group = 1), data = df.summary) +
  geom_errorbar(
    aes(ymin = len-sd, ymax = len+sd),
    data = df.summary, width = 0.2) +
  geom_point(data = df.summary, size = 2)+theme_classic()

做介绍里的成对比较图

ggpaired(ToothGrowth, x = "supp", y = "len",
         color = "supp", line.color = "gray", line.size = 0.4,
         palette = c("#002395","#ED2939"))+
  stat_compare_means(paired = TRUE)