R中的Forestplot。如何添加箭头、x轴中断和扩展x轴？

Question

我使用下面的 forestplot 包和代码创建了一个森林图。

我想补充三点：

1. 在 x 轴下添加箭头和文本（即，任一方向的箭头解释关联）。

我已经使用不同的包查看了这些帖子。

How to add arrows to forest plot in survminer (ggforest)

How to add arrows to a forest plot?

1. 我还想打破 x 轴，因为我有一个变量具有非常宽的 CI。

2. 我还想将 x 轴的负侧扩展到 -5，以平衡图形（即使大多数数据点都在右侧）。

我正在使用森林情节包。任何想法如何用这个包做到这一点？

table2OR_ex <- structure(list(X = c("Aeroplanes", "Sex (F)", "1", "2", "Cars", "Sex (F)", "1", "2"), 
                 mean = c(NA, 1.35, 7.81, 6.14, NA, 1.17, 0.15, 0.4), 
                 lower = c(NA, 1.13, 5.69, 4.36, NA, 0.74, 0.05, 0.16), 
                 upper = c(NA, 1.61, 11.01, 8.83, NA, 1.88, 0.35, 0.89),
                 p.value = c("", "< 0.001", "< 0.001", "< 0.001", "", "0.509", "< 0.001", "0.034")), 

                 .Names = c("Transport", "mean", "lower", "upper", "p value"), 
                 class = "data.frame", row.names = c(NA, -8L))

tabletext <- cbind(c("Transport","\n",table2OR_ex$Transport), 
               c("Odds ratio","\n",table2OR_ex$mean),
               c("Confidence Interval","\n", 
                 ifelse(is.na(table2OR_ex$lower), "", paste(table2OR_ex$lower, table2OR_ex$upper, 
sep= " - "))))
mat <- rbind(rbind(rep(NA, 3), rbind(rep(NA, 3), as.matrix(table2OR_ex[, 2:4]))))


fn <- local({
i = 0
no_lines <- sum(!is.na(mat[,"mean"])) 
b_clrs = colorRampPalette(colors=c("pink", "blue"))(no_lines)
l_clrs = colorRampPalette(colors=c("blue", "pink"))(no_lines) 
function(..., clr.line, clr.marker){
    i <<- i + 1
    fpDrawDiamondCI(..., clr.line = l_clrs[i], clr.marker = b_clrs[i])
}
})

forestplot(labeltext=tabletext, 
       mat,
       graphwidth=unit (70, "mm"), 
       graph.pos=3, 
       fn.ci_norm = fn,
       clip =c(-.125, max(table2OR_ex$upper, na.rm = TRUE)),
       is.summary=c(TRUE, TRUE, rep(FALSE, 8)),
       txt_gp=fpTxtGp(label=gpar(fontsize=12, cex=1), 
                      ticks=gpar(fontsize=12, cex=1.4),
                      xlab=gpar(fontsize=12,cex = 1),
                      title=gpar(fontsize=12,cex = 1.2)),

       zero=1,
       boxsize=0.4)

Answer 1

这并没有你想要的一切，但它是一个开始。也许其他人可以改进这个答案。

1. 我已经使用 grid.text 在空值的左侧和右侧添加了标签，但它没有箭头。您可能需要调整 grid.text 的 y 值，使标签不会与 x 轴刻度重叠。
2. 我不知道如何在 x 轴上打断，但应该在对数刻度上绘制优势比（请参阅 https://doi.org/10.1002/sim.4780070807），我认为这可以解决问题。
3. 在绘制 OR 时，在 x 轴上设置负值是没有意义的，但是使用对数刻度，您可以通过将下限设置为上限的倒数来使 x 轴对称绑定，这就是我所做的。

library(forestplot)

table2OR_ex <- structure(list(X = c("Aeroplanes", "Sex (F)", "1", "2", "Cars", "Sex (F)", "1", "2"), 
                 mean = c(NA, 1.35, 7.81, 6.14, NA, 1.17, 0.15, 0.4), 
                 lower = c(NA, 1.13, 5.69, 4.36, NA, 0.74, 0.05, 0.16), 
                 upper = c(NA, 1.61, 11.01, 8.83, NA, 1.88, 0.35, 0.89),
                 p.value = c("", "< 0.001", "< 0.001", "< 0.001", "", "0.509", "< 0.001", "0.034")), 

                 .Names = c("Transport", "mean", "lower", "upper", "p value"), 
                 class = "data.frame", row.names = c(NA, -8L))

tabletext <- cbind(c("Transport","\n",table2OR_ex$Transport), 
               c("Odds ratio","\n",table2OR_ex$mean),
               c("Confidence Interval","\n", 
                 ifelse(is.na(table2OR_ex$lower), "", paste(table2OR_ex$lower, table2OR_ex$upper, 
sep= " - "))))
mat <- rbind(rbind(rep(NA, 3), rbind(rep(NA, 3), as.matrix(table2OR_ex[, 2:4]))))


fn <- local({
i = 0
no_lines <- sum(!is.na(mat[,"mean"])) 
b_clrs = colorRampPalette(colors=c("pink", "blue"))(no_lines)
l_clrs = colorRampPalette(colors=c("blue", "pink"))(no_lines) 
function(..., clr.line, clr.marker){
    i <<- i + 1
    fpDrawDiamondCI(..., clr.line = l_clrs[i], clr.marker = b_clrs[i])
}
})

ticks <- c(0.04, 0.2, 1, 5, 25) # ADDITION
attr(ticks, "labels") <- as.character(ticks) # ADDITION
#attr(ticks, "labels") <- c("1/25", "1/5", "1", "5", "25") # ADDITION

forestplot(labeltext=tabletext, 
       mat,
       graphwidth=unit (70, "mm"), 
       graph.pos=3, 
       fn.ci_norm = fn,
       mar = unit(rep(10, times = 4), "mm"), # ADDITION
       xlog=TRUE, # ADDITION
       xticks=ticks, # ADDITION
       clip =c(0.04, 25), # CHANGE
       is.summary=c(TRUE, TRUE, rep(FALSE, 8)),
       txt_gp=fpTxtGp(label=gpar(fontsize=12, cex=1), 
                      ticks=gpar(fontsize=12, cex=1.4),
                      xlab=gpar(fontsize=12,cex = 1),
                      title=gpar(fontsize=12,cex = 1.2)),

       zero=1,
       boxsize=0.4)

# ADDITION
downViewport("forestplot_margins")
downViewport("axis_margin")
downViewport("axis")
grid.text("Favors X", x=0.46, y=-0.25, just=c("right", "center"))
grid.text("Favors Y", x=0.54, y=-0.25, just=c("left", "center"))