R语言绘制森林图详细教程-forestplot

本期主要介绍如何使用forestplot包绘制森林图，常用于meta分析的可视化
根据我的教程书写体验来看forestplot包还很不好用，基于gpar包来设置样式，使用体验极不好，不过写都写了，发一点东西
根据实际体验来看还是forestploter包绘制森林图更好看，代码更合理，样式也更好看，之后会介绍
这期不建议看，这个包也不建议用，连教程文档很多都跑不动

12.1 R包介绍

forestplot包是R语言中用于绘制森林图的包，其主要功能是将数据整理成适合绘制森林图的格式，并提供了丰富的绘图选项，使得用户可以轻松地绘制出各种类型的森林图。

https://cran.r-project.org/web//packages/forestplot/vignettes/forestplot.html

12.2 R包安装

install.packages("forestplot")

12.3 R包教程

12.3.1 载入包

library(forestplot)
library(dplyr)

12.3.2 导入数据

mean: OR区间的平均值
lower/upper：置信区间上下限
study：标签

data <- tibble::tibble(
  mean = c(0.578, 0.165, 0.246, 0.700, 0.348, 0.139, 1.017),
  lower = c(0.372, 0.018, 0.072, 0.333, 0.083, 0.016, 0.365),
  upper = c(0.898, 1.517, 0.833, 1.474, 1.455, 1.209, 2.831),
  study = c(
    "Auckland", "Block", "Doran", "Gamsu",
    "Morrison", "Papageorgiou", "Tauesch"
  ),
  deaths_steroid = c("36", "1", "4", "14", "3", "1", "8"),
  deaths_placebo = c("60", "5", "11", "20", "7", "7", "10"),
  OR = c("0.58", "0.16", "0.25", "0.70", "0.35", "0.14", "1.02")
)

12.3.3 基础绘图

可以看出forestplot包绘制森林图主体为forestplot函数，后续增加fp_xxx函数来完善内容

fp_set_style：设置样式
fp_add_header：添加表头
fp_append_row：额外添加行

data |>
  forestplot(
    labeltext = c(study, deaths_steroid, deaths_placebo, OR),
    clip = c(0.1, 2.5),
    xlog = TRUE
  ) |>
  fp_set_style(
    box = "royalblue",
    line = "darkblue",
    summary = "royalblue"
  ) |>
  fp_add_header(
    study = c("", "Study"),
    deaths_steroid = c("Deaths", "(steroid)"),
    deaths_placebo = c("Deaths", "(placebo)"),
    OR = c("", "OR")
  ) |>
  fp_append_row(
    mean = 0.531,
    lower = 0.386,
    upper = 0.731,
    study = "Summary",
    OR = "0.53",
    is.summary = TRUE
  ) |>
  fp_set_zebra_style("#EFEFEF")

12.4 样式美化

12.4.1 修改样式

使用fp_set_style来修改各内容的样式
使用fp_add_lines来添加线条
更多参数大家需要多看help文档

主要参考的是设置是gpar包样式

data |>
  forestplot(
    labeltext = c(study, deaths_steroid, deaths_placebo, OR),
    clip = c(0.1, 2.5),
    xlog = TRUE
  ) |>
  fp_add_lines() |>
  fp_set_style(
    box = "royalblue",
    line = "darkblue",
    summary = "royalblue",
    align = "lrrr",
    hrz_lines = "#999999"
  ) |>
  fp_add_header(
    study = c("", "Study"),
    deaths_steroid = c("Deaths", "(steroid)") |>
      fp_align_center(),
    deaths_placebo = c("Deaths", "(placebo)") |>
      fp_align_center(),
    OR = c("", fp_align_center("OR"))
  ) |>
  fp_append_row(
    mean = 0.531,
    lower = 0.386,
    upper = 0.731,
    study = "Summary",
    OR = "0.53",
    is.summary = TRUE
  )

12.4.2 对线条自定义

使用fp_add_lines来添加辅助线，lty是线形，lwd是线宽，col是颜色

f_n代表对第几列添加线条，columns设置线条有多宽

data |>
  forestplot(
    labeltext = c(study, deaths_steroid, deaths_placebo, OR),
    clip = c(0.1, 2.5),
    vertices = TRUE,
    xlog = TRUE
  ) |>
  fp_add_lines(
    h_3 = gpar(lty = 2),
    h_11 = gpar(lwd = 1, columns = 1:4, col = "#000044")
  ) |>
  fp_set_style(
    box = "royalblue",
    line = "darkblue",
    summary = "royalblue",
    align = "lrrr",
    hrz_lines = "#999999"
  ) |>
  fp_add_header(
    study = c("", "Study"),
    deaths_steroid = c("Deaths", "(steroid)") |>
      fp_align_center(),
    deaths_placebo = c("Deaths", "(placebo)") |>
      fp_align_center(),
    OR = c("", fp_align_center("OR"))
  ) |>
  fp_append_row(
    mean = 0.531,
    lower = 0.386,
    upper = 0.731,
    study = "Summary",
    OR = "0.53",
    is.summary = TRUE
  )

12.4.3 减小固定box（就是平均值的那个盒子）大小

强制boxsize的大小，使用函数forestplot的参数boxsize,但是设置之后大小也不会随着OR增大而增大

data |>
  forestplot(
    labeltext = c(study, deaths_steroid, deaths_placebo, OR),
    clip = c(0.1, 2.5),
    vertices = TRUE,
    boxsize = 0.2,
    xlog = TRUE
  ) |>
  fp_add_lines(
    h_3 = gpar(lty = 2),
    h_11 = gpar(lwd = 1, columns = 1:4, col = "#000044")
  ) |>
  fp_set_style(
    box = "royalblue",
    line = "darkblue",
    summary = "royalblue",
    align = "lrrr",
    hrz_lines = "#999999"
  ) |>
  fp_add_header(
    study = c("", "Study"),
    deaths_steroid = c("Deaths", "(steroid)") |>
      fp_align_center(),
    deaths_placebo = c("Deaths", "(placebo)") |>
      fp_align_center(),
    OR = c("", fp_align_center("OR"))
  ) |>
  fp_append_row(
    mean = 0.531,
    lower = 0.386,
    upper = 0.731,
    study = "Summary",
    OR = "0.53",
    is.summary = TRUE
  )

12.4.4 分组OR

垃圾包，已经跑不了分组了，应该是groupby更新后没适配上。浪费我一个小时

data(dfHRQoL)

dfHRQoL  |> group_by(group)|>
  forestplot(
    labeltext = c(labeltext),
    boxsize = 0.1,
    lineheight = "lines",
    xlab = "EQ-5D index"
  ) |>
  fp_add_lines("steelblue") |>
  fp_add_header("Variable") 

  |>
  fp_set_style(
    box = c("blue", "darkred") |>
      lapply(function(x) gpar(fill = x, col = "#555555")),
    default = gpar(vertices = TRUE)
  )