如何在 survminer (ggforest) 中向森林图添加箭头
How to add arrows to forest plot in survminer (ggforest)
我想知道是否有办法在森林图的 x 轴上添加两个箭头，类似于此示例中显示的内容：How to add arrows to a forest plot?（此代码不适用于 ggforest）
示例代码如下：
library(survival)
library(survminer)
model <- coxph(Surv(time, status) ~ sex + rx + adhere,
data = colon )
ggforest(model)
colon <- within(colon, {
sex <- factor(sex, labels = c("female", "male"))
differ <- factor(differ, labels = c("well", "moderate", "poor"))
extent <- factor(extent, labels = c("submuc.", "muscle", "serosa", "contig."))
})
bigmodel <-
coxph(Surv(time, status) ~ sex + rx + adhere + differ + extent + node4,
data = colon )
ggforest(bigmodel)
我想要 x 轴下方的两个箭头指向任一方向，并带有 "increased risk" 和 "decreased risk" 的注释。
survminer 包中的 ggforest 函数使用 ggplot() 创建绘图，但之后将该绘图转换为 grob 对象。如果您想参考 1 处垂直线的位置适当定位箭头，则必须在 转换之前这样做。
我修改了函数以允许这样做。使用示例如下：
ggforest(bigmodel)
ggforest2(bigmodel) # behaves like normal ggforest
# basic usage: specify left & right labels
ggforest2(bigmodel, arrow = TRUE, arrow.labels = c("increased risk", "decreased risk"))
# change arrow colour & appearance
ggforest2(bigmodel, arrow = TRUE, arrow.labels = c("increased risk", "decreased risk"),
arrow.colour = "blue",
arrow.specification = arrow(angle = 20, length = unit(0.1, "inches")))
# different arrow colours
ggforest2(bigmodel, arrow = TRUE, arrow.labels = c("increased risk", "decreased risk"),
arrow.colour = c("firebrick", "forestgreen"))
ggforest2()的代码：
ggforest2 <- function (model, data = NULL, main = "Hazard ratio",
cpositions = c(0.02, 0.22, 0.4),
fontsize = 0.7, refLabel = "reference", noDigits = 2,
# new parameters with some default values; function's behaviour
# does not differ from ggforest() unless arrow = TRUE
arrow = FALSE, arrow.labels = c("left", "right"),
arrow.specification = arrow(), arrow.colour = "black") {
# this part is unchanged
conf.high <- conf.low <- estimate <- NULL
stopifnot(class(model) == "coxph")
data <- survminer:::.get_data(model, data = data)
terms <- attr(model$terms, "dataClasses")[-1]
terms <- terms[intersect(names(terms),
gsub(rownames(anova(model))[-1], pattern = "`", replacement = ""))]
allTerms <- lapply(seq_along(terms), function(i) {
var <- names(terms)[i]
if (terms[i] == "factor") {
adf <- as.data.frame(table(data[, var]))
cbind(var = var, adf, pos = 1:nrow(adf))
}
else {
data.frame(var = var, Var1 = "", Freq = nrow(data), pos = 1)
}
})
allTermsDF <- do.call(rbind, allTerms)
colnames(allTermsDF) <- c("var", "level", "N", "pos")
inds <- apply(allTermsDF[, 1:2], 1, paste0, collapse = "")
coef <- as.data.frame(broom::tidy(model))
gmodel <- broom::glance(model)
rownames(coef) <- gsub(coef$term, pattern = "`", replacement = "")
toShow <- cbind(allTermsDF, coef[inds, ])[, c("var", "level", "N", "p.value", "estimate",
"conf.low", "conf.high", "pos")]
toShowExp <- toShow[, 5:7]
toShowExp[is.na(toShowExp)] <- 0
toShowExp <- format(exp(toShowExp), digits = noDigits)
toShowExpClean <- data.frame(toShow, pvalue = signif(toShow[, 4], noDigits + 1), toShowExp)
toShowExpClean$stars <- paste0(round(toShowExpClean$p.value, noDigits + 1), " ",
ifelse(toShowExpClean$p.value < 0.05, "*", ""),
ifelse(toShowExpClean$p.value < 0.01, "*", ""),
ifelse(toShowExpClean$p.value < 0.001, "*", ""))
toShowExpClean$ci <- paste0("(", toShowExpClean[, "conf.low.1"],
" - ", toShowExpClean[, "conf.high.1"], ")")
toShowExpClean$estimate.1[is.na(toShowExpClean$estimate)] = refLabel
toShowExpClean$stars[which(toShowExpClean$p.value < 0.001)] = "<0.001 ***"
toShowExpClean$stars[is.na(toShowExpClean$estimate)] = ""
toShowExpClean$ci[is.na(toShowExpClean$estimate)] = ""
toShowExpClean$estimate[is.na(toShowExpClean$estimate)] = 0
toShowExpClean$var = as.character(toShowExpClean$var)
toShowExpClean$var[duplicated(toShowExpClean$var)] = ""
toShowExpClean$N <- paste0("(N=", toShowExpClean$N, ")")
toShowExpClean <- toShowExpClean[nrow(toShowExpClean):1, ]
rangeb <- range(toShowExpClean$conf.low, toShowExpClean$conf.high,
na.rm = TRUE)
breaks <- axisTicks(rangeb/2, log = TRUE, nint = 7)
rangeplot <- rangeb
rangeplot[1] <- rangeplot[1] - diff(rangeb)
rangeplot[2] <- rangeplot[2] + 0.15 * diff(rangeb)
width <- diff(rangeplot)
y_variable <- rangeplot[1] + cpositions[1] * width
y_nlevel <- rangeplot[1] + cpositions[2] * width
y_cistring <- rangeplot[1] + cpositions[3] * width
y_stars <- rangeb[2]
x_annotate <- seq_len(nrow(toShowExpClean))
annot_size_mm <- fontsize * as.numeric(grid::convertX(unit(theme_get()$text$size, "pt"), "mm"))
# modified code from here onwards
p <- ggplot(toShowExpClean, aes(seq_along(var), exp(estimate))) +
geom_rect(aes(xmin = seq_along(var) - 0.5,
xmax = seq_along(var) + 0.5,
ymin = exp(rangeplot[1]),
ymax = exp(rangeplot[2]),
fill = ordered(seq_along(var)%%2 + 1))) +
geom_point(pch = 15, size = 4) +
geom_errorbar(aes(ymin = exp(conf.low), ymax = exp(conf.high)),
width = 0.15) +
geom_hline(yintercept = 1, linetype = 3) +
annotate(geom = "text", x = x_annotate, y = exp(y_variable),
label = toShowExpClean$var, fontface = "bold", hjust = 0,
size = annot_size_mm) +
annotate(geom = "text", x = x_annotate, y = exp(y_nlevel),
hjust = 0, label = toShowExpClean$level,
vjust = -0.1, size = annot_size_mm) +
annotate(geom = "text", x = x_annotate, y = exp(y_nlevel),
label = toShowExpClean$N,
fontface = "italic", hjust = 0,
vjust = ifelse(toShowExpClean$level == "", 0.5, 1.1),
size = annot_size_mm) +
annotate(geom = "text", x = x_annotate, y = exp(y_cistring),
label = toShowExpClean$estimate.1,
size = annot_size_mm,
vjust = ifelse(toShowExpClean$estimate.1 == "reference", 0.5, -0.1)) +
annotate(geom = "text", x = x_annotate, y = exp(y_cistring),
label = toShowExpClean$ci,
size = annot_size_mm, vjust = 1.1, fontface = "italic") +
annotate(geom = "text", x = x_annotate, y = exp(y_stars),
label = toShowExpClean$stars, size = annot_size_mm,
hjust = -0.2, fontface = "italic") +
annotate(geom = "text", x = 0.5, y = exp(y_variable),
label = paste0("# Events: ",
gmodel$nevent, "; Global p-value (Log-Rank): ",
format.pval(gmodel$p.value.log, eps = ".001"), " \nAIC: ",
round(gmodel$AIC, 2), "; Concordance Index: ",
round(gmodel$concordance, 2)),
size = annot_size_mm, hjust = 0, vjust = 1.2,
fontface = "italic") +
scale_y_log10(labels = sprintf("%g", breaks),
expand = c(0.02, 0.02), breaks = breaks) +
scale_fill_manual(values = c("#FFFFFF33", "#00000033"), guide = "none") +
labs(title = main, x = "", y = "") +
coord_flip(ylim = exp(rangeplot),
xlim = c(0.5, nrow(toShowExpClean) + 0.5),
clip = "off") +
theme_light() +
theme(panel.grid.minor = element_blank(),
panel.grid.major.y = element_blank(),
legend.position = "none",
panel.border = element_blank(),
axis.title.y = element_blank(),
axis.text.y = element_blank(),
axis.ticks.y = element_blank(),
plot.title = element_text(hjust = 0.5))
if(arrow){
# define arrow positions based on range of coefficient values, &
# exact y-axis range after flipping coordinates, taking into account
# any expansion due to annotated labels above
range.arrow.outer <- exp(min(abs(rangeb)) * c(-1, 1))
range.arrow.inner <- exp(min(abs(rangeb)) * c(-1, 1) / 2)
arrow.y <- ggplot_build(p)$layout$panel_params[[1]]$y.range[1] -
0.05 * diff(ggplot_build(p)$layout$panel_params[[1]]$y.range)
p <- p +
annotate("segment",
x = arrow.y, xend = arrow.y,
y = range.arrow.inner,
yend = range.arrow.outer,
arrow = arrow.specification, color = arrow.colour) +
annotate("text",
x = arrow.y, y = range.arrow.inner,
label = arrow.labels,
hjust = 0.5, vjust = -0.5, size = annot_size_mm,
color = arrow.colour) +
theme(plot.margin = margin(5.5, 5.5, 20, 5.5, "pt"))
}
# this part is unchanged
gt <- ggplot_gtable(ggplot_build(p))
gt$layout$clip[gt$layout$name == "panel"] <- "off"
ggpubr::as_ggplot(gt)
}
我想知道是否有办法在森林图的 x 轴上添加两个箭头，类似于此示例中显示的内容：How to add arrows to a forest plot?（此代码不适用于 ggforest）
示例代码如下：
library(survival)
library(survminer)
model <- coxph(Surv(time, status) ~ sex + rx + adhere,
data = colon )
ggforest(model)
colon <- within(colon, {
sex <- factor(sex, labels = c("female", "male"))
differ <- factor(differ, labels = c("well", "moderate", "poor"))
extent <- factor(extent, labels = c("submuc.", "muscle", "serosa", "contig."))
})
bigmodel <-
coxph(Surv(time, status) ~ sex + rx + adhere + differ + extent + node4,
data = colon )
ggforest(bigmodel)
我想要 x 轴下方的两个箭头指向任一方向，并带有 "increased risk" 和 "decreased risk" 的注释。
survminer 包中的 ggforest 函数使用 ggplot() 创建绘图，但之后将该绘图转换为 grob 对象。如果您想参考 1 处垂直线的位置适当定位箭头，则必须在 转换之前这样做。
我修改了函数以允许这样做。使用示例如下：
ggforest(bigmodel)
ggforest2(bigmodel) # behaves like normal ggforest
# basic usage: specify left & right labels
ggforest2(bigmodel, arrow = TRUE, arrow.labels = c("increased risk", "decreased risk"))
# change arrow colour & appearance
ggforest2(bigmodel, arrow = TRUE, arrow.labels = c("increased risk", "decreased risk"),
arrow.colour = "blue",
arrow.specification = arrow(angle = 20, length = unit(0.1, "inches")))
# different arrow colours
ggforest2(bigmodel, arrow = TRUE, arrow.labels = c("increased risk", "decreased risk"),
arrow.colour = c("firebrick", "forestgreen"))
ggforest2()的代码：
ggforest2 <- function (model, data = NULL, main = "Hazard ratio",
cpositions = c(0.02, 0.22, 0.4),
fontsize = 0.7, refLabel = "reference", noDigits = 2,
# new parameters with some default values; function's behaviour
# does not differ from ggforest() unless arrow = TRUE
arrow = FALSE, arrow.labels = c("left", "right"),
arrow.specification = arrow(), arrow.colour = "black") {
# this part is unchanged
conf.high <- conf.low <- estimate <- NULL
stopifnot(class(model) == "coxph")
data <- survminer:::.get_data(model, data = data)
terms <- attr(model$terms, "dataClasses")[-1]
terms <- terms[intersect(names(terms),
gsub(rownames(anova(model))[-1], pattern = "`", replacement = ""))]
allTerms <- lapply(seq_along(terms), function(i) {
var <- names(terms)[i]
if (terms[i] == "factor") {
adf <- as.data.frame(table(data[, var]))
cbind(var = var, adf, pos = 1:nrow(adf))
}
else {
data.frame(var = var, Var1 = "", Freq = nrow(data), pos = 1)
}
})
allTermsDF <- do.call(rbind, allTerms)
colnames(allTermsDF) <- c("var", "level", "N", "pos")
inds <- apply(allTermsDF[, 1:2], 1, paste0, collapse = "")
coef <- as.data.frame(broom::tidy(model))
gmodel <- broom::glance(model)
rownames(coef) <- gsub(coef$term, pattern = "`", replacement = "")
toShow <- cbind(allTermsDF, coef[inds, ])[, c("var", "level", "N", "p.value", "estimate",
"conf.low", "conf.high", "pos")]
toShowExp <- toShow[, 5:7]
toShowExp[is.na(toShowExp)] <- 0
toShowExp <- format(exp(toShowExp), digits = noDigits)
toShowExpClean <- data.frame(toShow, pvalue = signif(toShow[, 4], noDigits + 1), toShowExp)
toShowExpClean$stars <- paste0(round(toShowExpClean$p.value, noDigits + 1), " ",
ifelse(toShowExpClean$p.value < 0.05, "*", ""),
ifelse(toShowExpClean$p.value < 0.01, "*", ""),
ifelse(toShowExpClean$p.value < 0.001, "*", ""))
toShowExpClean$ci <- paste0("(", toShowExpClean[, "conf.low.1"],
" - ", toShowExpClean[, "conf.high.1"], ")")
toShowExpClean$estimate.1[is.na(toShowExpClean$estimate)] = refLabel
toShowExpClean$stars[which(toShowExpClean$p.value < 0.001)] = "<0.001 ***"
toShowExpClean$stars[is.na(toShowExpClean$estimate)] = ""
toShowExpClean$ci[is.na(toShowExpClean$estimate)] = ""
toShowExpClean$estimate[is.na(toShowExpClean$estimate)] = 0
toShowExpClean$var = as.character(toShowExpClean$var)
toShowExpClean$var[duplicated(toShowExpClean$var)] = ""
toShowExpClean$N <- paste0("(N=", toShowExpClean$N, ")")
toShowExpClean <- toShowExpClean[nrow(toShowExpClean):1, ]
rangeb <- range(toShowExpClean$conf.low, toShowExpClean$conf.high,
na.rm = TRUE)
breaks <- axisTicks(rangeb/2, log = TRUE, nint = 7)
rangeplot <- rangeb
rangeplot[1] <- rangeplot[1] - diff(rangeb)
rangeplot[2] <- rangeplot[2] + 0.15 * diff(rangeb)
width <- diff(rangeplot)
y_variable <- rangeplot[1] + cpositions[1] * width
y_nlevel <- rangeplot[1] + cpositions[2] * width
y_cistring <- rangeplot[1] + cpositions[3] * width
y_stars <- rangeb[2]
x_annotate <- seq_len(nrow(toShowExpClean))
annot_size_mm <- fontsize * as.numeric(grid::convertX(unit(theme_get()$text$size, "pt"), "mm"))
# modified code from here onwards
p <- ggplot(toShowExpClean, aes(seq_along(var), exp(estimate))) +
geom_rect(aes(xmin = seq_along(var) - 0.5,
xmax = seq_along(var) + 0.5,
ymin = exp(rangeplot[1]),
ymax = exp(rangeplot[2]),
fill = ordered(seq_along(var)%%2 + 1))) +
geom_point(pch = 15, size = 4) +
geom_errorbar(aes(ymin = exp(conf.low), ymax = exp(conf.high)),
width = 0.15) +
geom_hline(yintercept = 1, linetype = 3) +
annotate(geom = "text", x = x_annotate, y = exp(y_variable),
label = toShowExpClean$var, fontface = "bold", hjust = 0,
size = annot_size_mm) +
annotate(geom = "text", x = x_annotate, y = exp(y_nlevel),
hjust = 0, label = toShowExpClean$level,
vjust = -0.1, size = annot_size_mm) +
annotate(geom = "text", x = x_annotate, y = exp(y_nlevel),
label = toShowExpClean$N,
fontface = "italic", hjust = 0,
vjust = ifelse(toShowExpClean$level == "", 0.5, 1.1),
size = annot_size_mm) +
annotate(geom = "text", x = x_annotate, y = exp(y_cistring),
label = toShowExpClean$estimate.1,
size = annot_size_mm,
vjust = ifelse(toShowExpClean$estimate.1 == "reference", 0.5, -0.1)) +
annotate(geom = "text", x = x_annotate, y = exp(y_cistring),
label = toShowExpClean$ci,
size = annot_size_mm, vjust = 1.1, fontface = "italic") +
annotate(geom = "text", x = x_annotate, y = exp(y_stars),
label = toShowExpClean$stars, size = annot_size_mm,
hjust = -0.2, fontface = "italic") +
annotate(geom = "text", x = 0.5, y = exp(y_variable),
label = paste0("# Events: ",
gmodel$nevent, "; Global p-value (Log-Rank): ",
format.pval(gmodel$p.value.log, eps = ".001"), " \nAIC: ",
round(gmodel$AIC, 2), "; Concordance Index: ",
round(gmodel$concordance, 2)),
size = annot_size_mm, hjust = 0, vjust = 1.2,
fontface = "italic") +
scale_y_log10(labels = sprintf("%g", breaks),
expand = c(0.02, 0.02), breaks = breaks) +
scale_fill_manual(values = c("#FFFFFF33", "#00000033"), guide = "none") +
labs(title = main, x = "", y = "") +
coord_flip(ylim = exp(rangeplot),
xlim = c(0.5, nrow(toShowExpClean) + 0.5),
clip = "off") +
theme_light() +
theme(panel.grid.minor = element_blank(),
panel.grid.major.y = element_blank(),
legend.position = "none",
panel.border = element_blank(),
axis.title.y = element_blank(),
axis.text.y = element_blank(),
axis.ticks.y = element_blank(),
plot.title = element_text(hjust = 0.5))
if(arrow){
# define arrow positions based on range of coefficient values, &
# exact y-axis range after flipping coordinates, taking into account
# any expansion due to annotated labels above
range.arrow.outer <- exp(min(abs(rangeb)) * c(-1, 1))
range.arrow.inner <- exp(min(abs(rangeb)) * c(-1, 1) / 2)
arrow.y <- ggplot_build(p)$layout$panel_params[[1]]$y.range[1] -
0.05 * diff(ggplot_build(p)$layout$panel_params[[1]]$y.range)
p <- p +
annotate("segment",
x = arrow.y, xend = arrow.y,
y = range.arrow.inner,
yend = range.arrow.outer,
arrow = arrow.specification, color = arrow.colour) +
annotate("text",
x = arrow.y, y = range.arrow.inner,
label = arrow.labels,
hjust = 0.5, vjust = -0.5, size = annot_size_mm,
color = arrow.colour) +
theme(plot.margin = margin(5.5, 5.5, 20, 5.5, "pt"))
}
# this part is unchanged
gt <- ggplot_gtable(ggplot_build(p))
gt$layout$clip[gt$layout$name == "panel"] <- "off"
ggpubr::as_ggplot(gt)
}