用R语言在图中添加注释信息

萍智医信

于 2023-11-16 23:56:04 发布

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文章标签： r语言健康医疗学习

本文链接：https://blog.csdn.net/WLPWL/article/details/134453232

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添加文字

library(ggplot2)
p <- ggplot(faithful, aes(x = eruptions, y = waiting)) +
  geom_point()

p +
  annotate("text", x = 3, y = 48, label = "Group 1") +
  annotate("text", x = 4.5, y = 66, label = "Group 2")

p <- ggplot(faithful, aes(x = eruptions, y = waiting)) +
  geom_point()
p +
  annotate("text", x = 3, y = 48, label = "Group 1",
           family = "serif", fontface = "italic", colour = "darkred", size = 3) +
  annotate("text", x = 4.5, y = 66, label = "Group 2",
           family = "serif", fontface = "italic", colour = "darkred", size = 3)

要添加单独的文本对象时，请注意不要使用geom_text()。可以使用annotate(geom=“text”)来向绘图中添加单个文本对象，而geom_text()将根据数据创建多个文本对象。

library(ggplot2)
p <- ggplot(faithful, aes(x = eruptions, y = waiting)) +
  geom_point()
p +
  annotate("text", x = 3, y = 48, label = "Group 1", alpha = .1) +
  geom_text(x = 4.5, y = 66, label = "Group 2", alpha = .1)

可以看到Group 2的透明度不是10%。

如果坐标轴是连续的，可以使用特殊值Inf和-Inf将文本注释放在绘图区域的边缘。还可以使用hjust和vjust来调整文本相对于角落的位置——如果将hjust和vjust设置为默认值，则文本将以边缘为中心。

library(ggplot2)
p <- ggplot(faithful, aes(x = eruptions, y = waiting)) +
  geom_point()
p +
  annotate("text", x = -Inf, y = Inf, label = "Upper left", hjust = -.2, vjust = 2) +
  annotate("text", x = mean(range(faithful$eruptions)), y = -Inf, vjust = -0.4,
           label = "Bottom middle")

添加数学公式

通过在annotate(geom = "text")中设置parse = TRUE来生成数学表达式的格式。

library(ggplot2)
p <- ggplot(data.frame(x = c(-3,3)), aes(x = x)) +
  stat_function(fun = dnorm)

p +
  annotate("text", x = 2, y = 0.3, parse = TRUE,
           label = "frac(1, sqrt(2 * pi)) * e ^ {-x^2 / 2}")

若要将正则文本与表达式混合使用，请在双引号中使用单引号来标记纯文本部分。每个由内引号括起来的文本块都被视为数学表达式中的一个变量。在R的数学表达式语法中，不能简单地将一个变量放在另一个变量的旁边，而中间没有其他东西。要显示相邻的两个变量，请在它们之间放置一个*运算符。在图形中显示时，它被视为不可见的乘法符号（对于可见的乘法符号，请使用%*%）：

library(ggplot2)
p <- ggplot(data.frame(x = c(-3,3)), aes(x = x)) +
  stat_function(fun = dnorm)
p +
  annotate("text", x = 0, y = 0.05, parse = TRUE, size = 4,
           label = "'Function:  ' * y==frac(1, sqrt(2*pi)) * e^{-x^2/2}")

添加参考线

对于添加水平线和垂直线，可以使用geom_hline（）和geom_vline（），对于倾斜线，可以使用geom_abline（）。

library(ggplot2)
library(gcookbook)  
hw_plot <- ggplot(heightweight, aes(x = ageYear, y = heightIn, colour = sex)) +
  geom_point()
hw_plot +
  geom_hline(yintercept = 60) +
  geom_vline(xintercept = 14)

hw_plot +
  geom_abline(intercept = 37.4, slope = 1.75)

library(dplyr)
library(ggplot2)
library(gcookbook)  
hw_plot <- ggplot(heightweight, aes(x = ageYear, y = heightIn, colour = sex)) +
  geom_point()
hw_means <- heightweight %>%
  group_by(sex) %>%
  summarise(heightIn = mean(heightIn))

hw_plot +
  geom_hline(
    data = hw_means,
    aes(yintercept = heightIn, colour = sex),
    linetype = "dashed",
    size = 1
  )

如果其中一个轴是离散的而不是连续的，则不能将截距仅指定为字符串——它们仍然必须指定为数字。

pg_plot <- ggplot(PlantGrowth, aes(x = group, y = weight)) +
  geom_point()
pg_plot +
  geom_vline(xintercept = 2)

如果轴为因子，则第一个级别的数值为1，第二个级别的值为2，依此类推。可以手动指定数值截距，也可以使用which(levels(...))计算数值。

pg_plot <- ggplot(PlantGrowth, aes(x = group, y = weight)) +
  geom_point()
pg_plot +
  geom_vline(xintercept = which(levels(PlantGrowth$group) == "ctrl"))

添加线段和箭头

library(ggplot2)
library(gcookbook) 
p <- ggplot(filter(climate, Source == "Berkeley"), aes(x = Year, y = Anomaly10y)) +
  geom_line()
p +
  annotate("segment", x = 1950, xend = 1980, y = -.25, yend = -.25)

library(ggplot2)
library(gcookbook) 
p <- ggplot(filter(climate, Source == "Berkeley"), aes(x = Year, y = Anomaly10y)) +
  geom_line()
# 默认角度为30，箭头线的默认长度为0.2英寸
library(grid)
p +
  annotate("segment", x = 1850, xend = 1820, y = -.8, yend = -.95,
           colour = "blue", size = 2, arrow = arrow())

library(ggplot2)
library(gcookbook) 
p <- ggplot(filter(climate, Source == "Berkeley"), aes(x = Year, y = Anomaly10y)) +
  geom_line()

library(grid)
p +
  annotate("segment", x = 1850, xend = 1820, y = -.8, yend = -.95,
           colour = "blue", size = 2, arrow = arrow()) +
  annotate("segment", x = 1950, xend = 1980, y = -.25, yend = -.25,
           arrow = arrow(ends = "both", angle = 90, length = unit(.2,"cm")))

添加阴影矩形

library(ggplot2)
library(gcookbook) 

p <- ggplot(filter(climate, Source == "Berkeley"), aes(x = Year, y = Anomaly10y)) +
  geom_line()

p +
  annotate("rect", xmin = 1950, xmax = 1980, ymin = -1, ymax = 1,
           alpha = .1,fill = "blue")

高亮显示图中的一部分

pg_mod <- PlantGrowth %>%
  mutate(hl = recode(group, "ctrl" = "no", "trt1" = "no", "trt2" = "yes"))

ggplot(pg_mod, aes(x = group, y = weight, fill = hl)) +
  geom_boxplot() +
  scale_fill_manual(values = c("grey85", "#FFDDCC"), guide = "none")

ggplot(PlantGrowth, aes(x = group, y = weight, fill = group)) +
  geom_boxplot() +
  scale_fill_manual(values = c("red", "blue", "#FFDDCC"), guide = "none")

添加误差线

library(gcookbook) 
library(dplyr)

ce_mod <- cabbage_exp %>%
  filter(Cultivar == "c39")

se：the standard error of the mean

sd：the standard deviation

library(ggplot2)
# width = .2 用来设置误差线末端的宽度
ggplot(ce_mod, aes(x = Date, y = Weight)) +
  geom_col(fill = "white", colour = "black") +
  geom_errorbar(aes(ymin = Weight - se, ymax = Weight + se), width = .2)

ggplot(ce_mod, aes(x = Date, y = Weight)) +
  geom_line(aes(group = 1)) +
  geom_point(size = 4) +
  geom_errorbar(aes(ymin = Weight - se, ymax = Weight + se), width = .2)

ggplot(cabbage_exp, aes(x = Date, y = Weight, fill = Cultivar)) +
  geom_col(position = "dodge") +
  geom_errorbar(aes(ymin = Weight - se, ymax = Weight + se),
                position = position_dodge(0.9), width = .2)

pd <- position_dodge(.3)  

ggplot(cabbage_exp, aes(x = Date, y = Weight, colour = Cultivar, group = Cultivar)) +
  geom_errorbar(
    aes(ymin = Weight - se, ymax = Weight + se),
    width = .2,
    size = 0.25,
    colour = "black",
    position = pd
  ) +
  geom_line(position = pd) +
  geom_point(position = pd, size = 2.5)

各子图（分面）中添加文字

mpg_plot <- ggplot(mpg, aes(x = displ, y = hwy)) +
  geom_point() +
  facet_grid(. ~ drv)

f_labels <- data.frame(drv = c("4", "f", "r"), label = c("4wd", "Front", "Rear"))

mpg_plot +
  geom_text(x = 6, y = 40, aes(label = label), data = f_labels)

mpg_plot +
  annotate("text", x = 6, y = 42, label = "label text")

lm_labels <- function(dat) {
  mod <- lm(hwy ~ displ, data = dat)
  formula <- sprintf("italic(y) == %.2f %+.2f * italic(x)",
                     round(coef(mod)[1], 2), round(coef(mod)[2], 2))
  r <- cor(dat$displ, dat$hwy)
  r2 <- sprintf("italic(R^2) == %.2f", r^2)
  data.frame(formula = formula, r2 = r2, stringsAsFactors = FALSE)
}

library(dplyr)
labels <- mpg %>%
  group_by(drv) %>%
  do(lm_labels(.))

mpg_plot +
  geom_smooth(method = lm, se = FALSE) +
  geom_text(data = labels, aes(label = formula), x = 3, y = 40, parse = TRUE, hjust = 0) +
  geom_text(x = 3, y = 35, aes(label = r2), data = labels, parse = TRUE, hjust = 0)

labels <- mpg %>%
  group_by(drv) %>%
  summarise(r2 = cor(displ, hwy)^2)

labels$r2 <- sprintf("italic(R^2) == %.2f", labels$r2)
labels

mpg_plot +
  geom_smooth(method = lm, se = FALSE) +
  geom_text(x = 3, y = 35, aes(label = r2), data = labels, parse = TRUE, hjust = 0)

参考资料

https://r-graphics.org/

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用R语言在图中添加注释信息

欢迎关注微信公众号（医学生物信息学)，医学生的生信笔记，记录学习过程。
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