【r<-图形】森林图forest plot绘制

【r<-图形】森林图forest plot绘制

作者: 王诗翔 | 来源:发表于2018-09-11 18:28 被阅读2次

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

文章作者王诗翔

上次更新 2018-09-10

许可协议 CC BY-NC-ND 4.0

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