森林图forest plot绘制—科研工具箱-叨客学习资料网

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森林图常见于元分析，但其使用绝不仅如此，比如我现在想要研究的对象有诸多HR结果，我想要汇总为一张图，森林图就是个非常好的选择。ggpubr包提供的森林图是针对变量分析绘图，我也尝试使用了metafor包的forest画图函数，但太灵活了，我除了感觉文档画的不错，但实际使用却很难得到想要的结果。

谷歌了一下，找到了forestplot这个包，下面根据文档学习一波。

安装：

install.packages(\"forestplot\")

文本

森林图可以与文本连接起来并自定义。

文本表

下面是一个使用文本表的例子：

library(forestplot)
#> 载入需要的程辑包：grid
#> 载入需要的程辑包：magrittr
#> 载入需要的程辑包：checkmate
# Cochrane data from the \'rmeta\'-package
cochrane_from_rmeta <- 
  structure(list(
    mean  = c(NA, NA, 0.578, 0.165, 0.246, 0.700, 0.348, 0.139, 1.017, NA, 0.531), 
    lower = c(NA, NA, 0.372, 0.018, 0.072, 0.333, 0.083, 0.016, 0.365, NA, 0.386),
    upper = c(NA, NA, 0.898, 1.517, 0.833, 1.474, 1.455, 1.209, 2.831, NA, 0.731)),
    .Names = c(\"mean\", \"lower\", \"upper\"), 
    row.names = c(NA, -11L), 
    class = \"data.frame\")

tabletext<-cbind(
  c(\"\", \"Study\", \"Auckland\", \"Block\", 
    \"Doran\", \"Gamsu\", \"Morrison\", \"Papageorgiou\", 
    \"Tauesch\", NA, \"Summary\"),
  c(\"Deaths\", \"(steroid)\", \"36\", \"1\", 
    \"4\", \"14\", \"3\", \"1\", 
    \"8\", NA, NA),
  c(\"Deaths\", \"(placebo)\", \"60\", \"5\", 
    \"11\", \"20\", \"7\", \"7\", 
    \"10\", NA, NA),
  c(\"\", \"OR\", \"0.58\", \"0.16\", 
    \"0.25\", \"0.70\", \"0.35\", \"0.14\", 
    \"1.02\", NA, \"0.53\"))

forestplot(tabletext, 
           cochrane_from_rmeta,new_page = TRUE,
           is.summary=c(TRUE,TRUE,rep(FALSE,8),TRUE),
           clip=c(0.1,2.5), 
           xlog=TRUE, 
           col=fpColors(box=\"royalblue\",line=\"darkblue\", summary=\"royalblue\"))

汇总线

在上面基础进行增改：

forestplot(tabletext, 
           hrzl_lines = gpar(col=\"#444444\"),
           cochrane_from_rmeta,new_page = TRUE,
           is.summary=c(TRUE,TRUE,rep(FALSE,8),TRUE),
           clip=c(0.1,2.5), 
           xlog=TRUE,
           col=fpColors(box=\"royalblue\",line=\"darkblue\", summary=\"royalblue\"))

我们可以修改线条类型和它所影响的范围：

forestplot(tabletext, 
           hrzl_lines = list(\"3\" = gpar(lty=2), 
                             \"11\" = gpar(lwd=1, columns=1:4, col = \"#000044\")),
           cochrane_from_rmeta,new_page = TRUE,
           is.summary=c(TRUE,TRUE,rep(FALSE,8),TRUE),
           clip=c(0.1,2.5), 
           xlog=TRUE,
           col=fpColors(box=\"royalblue\",line=\"darkblue\", summary=\"royalblue\", hrz_lines = \"#444444\"))

为端点增加垂线：

forestplot(tabletext, 
           hrzl_lines = list(\"3\" = gpar(lty=2), 
                             \"11\" = gpar(lwd=1, columns=1:4, col = \"#000044\")),
           cochrane_from_rmeta,new_page = TRUE,
           is.summary=c(TRUE,TRUE,rep(FALSE,8),TRUE),
           clip=c(0.1,2.5), 
           xlog=TRUE,
           col=fpColors(box=\"royalblue\",line=\"darkblue\", summary=\"royalblue\", hrz_lines = \"#444444\"),
           vertices = TRUE)

调整图元素的位置

forestplot(tabletext, 
           graph.pos = 4,
           hrzl_lines = list(\"3\" = gpar(lty=2), 
                             \"11\" = gpar(lwd=1, columns=c(1:3,5), col = \"#000044\"),
                             \"12\" = gpar(lwd=1, lty=2, columns=c(1:3,5), col = \"#000044\")),
           cochrane_from_rmeta,new_page = TRUE,
           is.summary=c(TRUE,TRUE,rep(FALSE,8),TRUE),
           clip=c(0.1,2.5), 
           xlog=TRUE,
           col=fpColors(box=\"royalblue\",line=\"darkblue\", summary=\"royalblue\", hrz_lines = \"#444444\"))

使用表达式

data(HRQoL)
clrs <- fpColors(box=\"royalblue\",line=\"darkblue\", summary=\"royalblue\")
tabletext <- 
  list(c(NA, rownames(HRQoL$Sweden)),
       append(list(expression(beta)), sprintf(\"%.2f\", HRQoL$Sweden[,\"coef\"])))
forestplot(tabletext, 
           rbind(rep(NA, 3), 
                 HRQoL$Sweden),
           col=clrs,
           xlab=\"EQ-5D index\")

更改字体

tabletext <- cbind(rownames(HRQoL$Sweden),
                   sprintf(\"%.2f\", HRQoL$Sweden[,\"coef\"]))
forestplot(tabletext, 
           txt_gp = fpTxtGp(label = gpar(fontfamily = \"HersheyScript\")),
           rbind(HRQoL$Sweden),
           col=clrs,
           xlab=\"EQ-5D index\")

还可以更改风格：

forestplot(tabletext, 
           txt_gp = fpTxtGp(label = list(gpar(fontfamily = \"HersheyScript\"),
                                         gpar(fontfamily = \"\",
                                              col = \"#660000\")),
                            ticks = gpar(fontfamily = \"\", cex=1),
                            xlab  = gpar(fontfamily = \"HersheySerif\", cex = 1.5)),
           rbind(HRQoL$Sweden),
           col=clrs,
           xlab=\"EQ-5D index\")

置信区间

简单的，给超出范围的区间加箭头（clip）：

forestplot(tabletext, 
           rbind(HRQoL$Sweden),
           clip =c(-.1, Inf),
           col=clrs,
           xlab=\"EQ-5D index\")

多个置信区间范围

这在对比时非常有用：

tabletext <- tabletext[,1]
forestplot(tabletext, 
           mean = cbind(HRQoL$Sweden[, \"coef\"], HRQoL$Denmark[, \"coef\"]),
           lower = cbind(HRQoL$Sweden[, \"lower\"], HRQoL$Denmark[, \"lower\"]),
           upper = cbind(HRQoL$Sweden[, \"upper\"], HRQoL$Denmark[, \"upper\"]),
           clip =c(-.1, 0.075),
           col=fpColors(box=c(\"blue\", \"darkred\")),
           xlab=\"EQ-5D index\")

评估显示器

可以用方块、圆圈等：

forestplot(tabletext, 
            fn.ci_norm = c(fpDrawNormalCI, fpDrawCircleCI),
            boxsize = .25, # We set the box size to better visualize the type
            line.margin = .1, # We need to add this to avoid crowding
            mean = cbind(HRQoL$Sweden[, \"coef\"], HRQoL$Denmark[, \"coef\"]),
            lower = cbind(HRQoL$Sweden[, \"lower\"], HRQoL$Denmark[, \"lower\"]),
            upper = cbind(HRQoL$Sweden[, \"upper\"], HRQoL$Denmark[, \"upper\"]),
            clip =c(-.125, 0.075),
            col=fpColors(box=c(\"blue\", \"darkred\")),
            xlab=\"EQ-5D index\")

选择线型

forestplot(tabletext, 
            fn.ci_norm = c(fpDrawNormalCI, fpDrawCircleCI),
            boxsize = .25, # We set the box size to better visualize the type
            line.margin = .1, # We need to add this to avoid crowding
            mean = cbind(HRQoL$Sweden[, \"coef\"], HRQoL$Denmark[, \"coef\"]),
            lower = cbind(HRQoL$Sweden[, \"lower\"], HRQoL$Denmark[, \"lower\"]),
            upper = cbind(HRQoL$Sweden[, \"upper\"], HRQoL$Denmark[, \"upper\"]),
            clip =c(-.125, 0.075),
            lty.ci = c(1, 2),
            col=fpColors(box=c(\"blue\", \"darkred\")),
            xlab=\"EQ-5D index\")

图例

添加一个基本图例：

forestplot(tabletext, 
           legend = c(\"Sweden\", \"Denmark\"),
           fn.ci_norm = c(fpDrawNormalCI, fpDrawCircleCI),
           boxsize = .25, # We set the box size to better visualize the type
           line.margin = .1, # We need to add this to avoid crowding
           mean = cbind(HRQoL$Sweden[, \"coef\"], HRQoL$Denmark[, \"coef\"]),
           lower = cbind(HRQoL$Sweden[, \"lower\"], HRQoL$Denmark[, \"lower\"]),
           upper = cbind(HRQoL$Sweden[, \"upper\"], HRQoL$Denmark[, \"upper\"]),
           clip =c(-.125, 0.075),
           col=fpColors(box=c(\"blue\", \"darkred\")),
           xlab=\"EQ-5D index\")

通过设定参数可以进一步自定义：

forestplot(tabletext, 
           legend_args = fpLegend(pos = list(x=.85, y=0.25), 
                                  gp=gpar(col=\"#CCCCCC\", fill=\"#F9F9F9\")),
           legend = c(\"Sweden\", \"Denmark\"),
           fn.ci_norm = c(fpDrawNormalCI, fpDrawCircleCI),
           boxsize = .25, # We set the box size to better visualize the type
           line.margin = .1, # We need to add this to avoid crowding
           mean = cbind(HRQoL$Sweden[, \"coef\"], HRQoL$Denmark[, \"coef\"]),
           lower = cbind(HRQoL$Sweden[, \"lower\"], HRQoL$Denmark[, \"lower\"]),
           upper = cbind(HRQoL$Sweden[, \"upper\"], HRQoL$Denmark[, \"upper\"]),
           clip =c(-.125, 0.075),
           col=fpColors(box=c(\"blue\", \"darkred\")),
           xlab=\"EQ-5D index\")

刻度和网格

我们可以手动设定想要的刻度

forestplot(tabletext, 
           legend = c(\"Sweden\", \"Denmark\"),
           fn.ci_norm = c(fpDrawNormalCI, fpDrawCircleCI),
           boxsize = .25, # We set the box size to better visualize the type
           line.margin = .1, # We need to add this to avoid crowding
           mean = cbind(HRQoL$Sweden[, \"coef\"], HRQoL$Denmark[, \"coef\"]),
           lower = cbind(HRQoL$Sweden[, \"lower\"], HRQoL$Denmark[, \"lower\"]),
           upper = cbind(HRQoL$Sweden[, \"upper\"], HRQoL$Denmark[, \"upper\"]),
           clip =c(-.125, 0.075),
           col=fpColors(box=c(\"blue\", \"darkred\")),
           xticks = c(-.1, -0.05, 0, .05),
           xlab=\"EQ-5D index\")

我们可以给想要的刻度加标签：

xticks <- seq(from = -.1, to = .05, by = 0.025)
xtlab <- rep(c(TRUE, FALSE), length.out = length(xticks))
attr(xticks, \"labels\") <- xtlab
forestplot(tabletext, 
           legend = c(\"Sweden\", \"Denmark\"),
           fn.ci_norm = c(fpDrawNormalCI, fpDrawCircleCI),
           boxsize = .25, # We set the box size to better visualize the type
           line.margin = .1, # We need to add this to avoid crowding
           mean = cbind(HRQoL$Sweden[, \"coef\"], HRQoL$Denmark[, \"coef\"]),
           lower = cbind(HRQoL$Sweden[, \"lower\"], HRQoL$Denmark[, \"lower\"]),
           upper = cbind(HRQoL$Sweden[, \"upper\"], HRQoL$Denmark[, \"upper\"]),
           clip =c(-.125, 0.075),
           col=fpColors(box=c(\"blue\", \"darkred\")),
           xticks = xticks,
           xlab=\"EQ-5D index\")

如果图形太高我们可能还需要增加辅助线以显示对应的刻度：

forestplot(tabletext, 
           legend = c(\"Sweden\", \"Denmark\"),
           fn.ci_norm = c(fpDrawNormalCI, fpDrawCircleCI),
           boxsize = .25, # We set the box size to better visualize the type
           line.margin = .1, # We need to add this to avoid crowding
           mean = cbind(HRQoL$Sweden[, \"coef\"], HRQoL$Denmark[, \"coef\"]),
           lower = cbind(HRQoL$Sweden[, \"lower\"], HRQoL$Denmark[, \"lower\"]),
           upper = cbind(HRQoL$Sweden[, \"upper\"], HRQoL$Denmark[, \"upper\"]),
           clip =c(-.125, 0.075),
           col=fpColors(box=c(\"blue\", \"darkred\")),
           grid = TRUE,
           xticks = c(-.1, -0.05, 0, .05),
           xlab=\"EQ-5D index\")

最后我们可以自定义想要的网格：

forestplot(tabletext, 
           legend = c(\"Sweden\", \"Denmark\"),
           fn.ci_norm = c(fpDrawNormalCI, fpDrawCircleCI),
           boxsize = .25, # We set the box size to better visualize the type
           line.margin = .1, # We need to add this to avoid crowding
           mean = cbind(HRQoL$Sweden[, \"coef\"], HRQoL$Denmark[, \"coef\"]),
           lower = cbind(HRQoL$Sweden[, \"lower\"], HRQoL$Denmark[, \"lower\"]),
           upper = cbind(HRQoL$Sweden[, \"upper\"], HRQoL$Denmark[, \"upper\"]),
           clip =c(-.125, 0.075),
           col=fpColors(box=c(\"blue\", \"darkred\")),
           grid = structure(c(-.1, -.05, .05), 
                            gp = gpar(lty = 2, col = \"#CCCCFF\")), 
           xlab=\"EQ-5D index\")

下面两种structure的书写方式是一致的：

grid_arg <- c(-.1, -.05, .05) 
attr(grid_arg, \"gp\") <- gpar(lty = 2, col = \"#CCCCFF\")

identical(grid_arg, 
          structure(c(-.1, -.05, .05), 
                    gp = gpar(lty = 2, col = \"#CCCCFF\")))
#> [1] TRUE

转载自：【r<-图形】森林图forest plot绘制 – 简书

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