带有表格 ggplot 编码的森林图答案

【问题标题】：Forest plot with table ggplot coding带有表格 ggplot 编码的森林图
【发布时间】：2020-06-07 14:08:22
【问题描述】：

我正在尝试将一张桌子与我的森林地块并排放置，但这样做时遇到了很多麻烦。

我可以使用以下代码制作森林图：

###dataframe
###dataframe
library(ggplot2)
library(tidyr)
library(grid)
library(gridExtra)
library(forcats)


forestdf <- structure(list(labels = structure(1:36, .Label = c("Age*", "Sex – male vs. female", 
                                                               "Body-mass index*,1 ", "Systolic blood pressure*", "Race - vs. white", 
                                                               "Asian", "Black", "Townsend deprivation index", "Social habit", 
                                                               "Smoking - vs. never", "Previous", "Current", "Alcohol use - vs. never", 
                                                               "Once or twice a week", "Three or four times a week", "Daily or almost daily", 
                                                               "Comorbidity", "Cancer", "Diabetes", "Chronic obstructive pulmonary disease2", 
                                                               "Asthma", "Ischemic heart disease3", "Hypothyroidism", "Hypercholesterolemia", 
                                                               "Allergic rhinitis", "Depression", "Serology", "White blood cell count", 
                                                               "Red blood cell count", "Hemoglobin concentration", "Mean corpuscular volume", 
                                                               "Mean corpuscular hemoglobin concentration", "Platelet count", 
                                                               "Lymphocyte count", "Monocyte count", "Neutrophil count"), class = "factor"), 
                           rr = c(1.18, 1.45, 1.76, 0.98, NA, 2.16, 2.65, 1.09, NA, 
                                  NA, 1.35, 1.15, NA, 0.73, 0.63, 0.63, NA, 1.23, 1.34, 1.51, 
                                  1.12, 1.46, 0.96, 1.1, 1.18, 1.38, NA, 1.03, 0.87, 0.93, 
                                  1, 0.94, 1, 1.03, 1.17, 1.06), rrhigh = c(1.08, 1.28, 1.57, 
                                                                            0.95, NA, 1.63, 2.03, 1.07, NA, NA, 1.18, 0.94, NA, 0.58, 
                                                                            0.49, 0.5, NA, 0.99, 1.08, 1.09, 0.93, 1.15, 0.71, 0.92, 
                                                                            0.91, 1.1, NA, 1.02, 0.73, 0.87, 0.99, 0.88, 1, 1.01, 1.03, 
                                                                            1.01), rrlow = c(1.28, 1.64, 1.97, 1.02, NA, 2.86, 3.44, 
                                                                                             1.11, NA, NA, 1.55, 1.42, NA, 0.9, 0.79, 0.81, NA, 1.53, 
                                                                                             1.66, 2.09, 1.34, 1.85, 1.3, 1.31, 1.52, 1.74, NA, 1.04, 
                                                                                             1.03, 0.98, 1.01, 1.01, 1, 1.05, 1.32, 1.1)), class = "data.frame", row.names = c(NA, 
                                                                                                                                                                               -36L))


forestdf$labels <- factor(forestdf$labels,levels = forestdf$labels)
levels(forestdf$labels)                                                                                                                                                                                                                                                                                                                                                                                   1.52, 1.74, NA, 1.04, 1.03, 0.98, 1.01, 1.01, 1, 1.05, 1.32, 
#forestplot
p <- ggplot(forestdf, aes(x=rr, y=labels, xmin=rrlow, xmax=rrhigh))+
  geom_pointrange(shape=22, fill="black")+
  geom_vline(xintercept = 1, linetype=3)+
  xlab("Variable")+ylab("Adjusted Relative Risk with 95% Confidence Interval")+theme_classic()+scale_y_discrete(limits = rev(labels))+
  scale_x_log10(limits = c(0.25, 4), breaks = c(0.25, 0.5, 1, 2, 4), labels=c("0.25", "0.5", "1", "2", "4"), expand = c(0,0))
p

但是，我无法让带有标签的左侧面板工作：

#dataframe for table
fplottable <- structure(list(labels = structure(c(1L, 30L, 7L, 33L, 27L, 4L, 
6L, 35L, 32L, 31L, 26L, 11L, 2L, 24L, 34L, 12L, 10L, 8L, 14L, 
9L, 5L, 18L, 17L, 16L, 3L, 13L, 29L, 36L, 28L, 15L, 21L, 20L, 
25L, 19L, 22L, 23L), .Label = c("Age*", "Alcohol use - vs. never", 
"Allergic rhinitis", "Asian", "Asthma", "Black", "Body-mass index*,1 ", 
"Cancer", "Chronic obstructive pulmonary disease2", "Comorbidity", 
"Current", "Daily or almost daily", "Depression", "Diabetes", 
"Hemoglobin concentration", "Hypercholesterolemia", "Hypothyroidism", 
"Ischemic heart disease3", "Lymphocyte count", "Mean corpuscular hemoglobin concentration", 
"Mean corpuscular volume", "Monocyte count", "Neutrophil count", 
"Once or twice a week", "Platelet count", "Previous", "Race - vs. white", 
"Red blood cell count", "Serology", "Sex – male vs. female", 
"Smoking - vs. never", "Social habit", "Systolic blood pressure*", 
"Three or four times a week", "Townsend deprivation index", "White blood cell count"
), class = "factor"), No..of.Events = c(1073L, 581L, 1061L, 1031L, 
NA, 57L, 68L, 1072L, NA, NA, 442L, 117L, NA, 262L, 191L, 172L, 
NA, 96L, 107L, 41L, 146L, 86L, 52L, 170L, 66L, 84L, NA, 1009L, 
1009L, 1009L, 1009L, 1009L, 1009L, 1005L, 1005L, 1005L), ARR..95..CI. = c("1.18 (1.08-1.28)", 
"1.45 (1.28-1.64)", "1.76 (1.57-1.97)", "0.98 (0.95-1.02)", "", 
"2.16 (1.63-2.86)", "2.65 (2.03-3.44)", "1.09 (1.07-1.11)", "", 
"", "1.35 (1.18-1.55)", "1.15 (0.94-1.42)", "", "0.73 (0.58-0.90)", 
"0.63 (0.49-0.79)", "0.63 (0.50-0.81)", "", "1.23 (0.99-1.53)", 
"1.34 (1.08-1.66)", "1.51 (1.09-2.09)", "1.12 (0.93-1.34)", "1.46 (1.15-1.85)", 
"0.96 (0.71-1.30)", "1.10 (0.92-1.31)", "1.18 (0.91-1.52)", "1.38 (1.10-1.74)", 
"", "1.03 (1.02-1.04)", "0.87 (0.73-1.03)", "0.93 (0.87-0.98)", 
"1.00 (0.99-1.01)", "0.94 (0.88-1.01)", "1.00 (1.00-1.00)", "1.03 (1.01-1.05)", 
"1.17 (1.03-1.32)", "1.06 (1.01-1.10)")), class = "data.frame", row.names = c(NA, 
-36L))

###NOT WORKING CODE THAT TRIES TO MAKE TABLE LEFT OF FOREST PLOT
data_table <- geom_text(data=fplottable,aes(y=labels)) +
  geom_text(label=eventnum) +
  geom_text(label=arr)
data_table

grid.arrange(data_table,p, ncol=2)

我的灵感来自： Reproduce table and plot from journal 并试图获得类似于森林图中粉红色框显示的内容

【问题讨论】：

当我按照您发布的代码运行您的代码时，我遇到了错误。具体来说，当试图复制你的p 时，我得到了Error in x[length(x):1L] : object of type 'closure' is not subsettable，这似乎与scale_y_discrete(limits=rev(labels)) 有关。同样，在尝试复制data_table 时，我在两台不同的机器上得到了Error: unexpected '<' in: ", class = c("data.table",。只是我还是你没有检查你的代码？ :)
感谢 davidnortes。 data_table 之前的代码现在应该可以正常工作了。 data_table 是我不知道怎么写的代码。 data_table 代码的目的是希望在我的 ggplot 左侧创建一个与每个框对齐的表，如链接“从日志中复制表和绘图”中所示。我无法将 geom_text 与我的情节点对齐
没有名为 forestplottable 或 groupData 的数据框。此外，任何地方都没有名为ID 的变量。 fplottable 数据框定义后可能缺少某些代码。
@davidk 这不是森林地块。森林图是一种评估元分析问题的工具。当您对相同的风险比或优势比有多个估计值时，您可以将它们绘制为置信带，并将它们的标准误差作为 y 轴标准，顶部最大，底部最小。如果没有发表偏倚，置信带的包络应该是 V。我想知道你的情节被称为“森林情节”。您使用该术语的来源是什么？

标签： r ggplot2 plot geom-text forestplot

【解决方案1】：

@efz 指出了一些问题。此外，您需要重构第二列中的标签，以使它们与第一列中的标签匹配。表格旁边的 y 轴标签和标题可能看起来很乱，所以这些也可以删除。

这会给你留下类似的东西：

forestdf$colour <- rep(c("white", "gray95"), 18)
p <- ggplot(forestdf, aes(x = rr, y = labels, xmin = rrlow, xmax = rrhigh)) +
  geom_hline(aes(yintercept = labels, colour = colour), size = 7) + 
  geom_pointrange(shape = 22, fill = "black") +
  geom_vline(xintercept = 1, linetype = 3) +
  xlab("Variable") +
  ylab("Adjusted Relative Risk with 95% Confidence Interval") +
  theme_classic() +
  scale_colour_identity() +
  scale_y_discrete(limits = rev(forestdf$labels)) +
  scale_x_log10(limits = c(0.25, 4), 
                breaks = c(0.25, 0.5, 1, 2, 4), 
                labels = c("0.25", "0.5", "1", "2", "4"), expand = c(0,0)) +
  theme(axis.text.y = element_blank(), axis.title.y = element_blank())

names(fplottable) <- c("labels", "eventnum", "arr")
fplottable$labels <- factor(fplottable$labels, rev(levels(forestdf$labels)))
fplottable$colour <- rep(c("white", "gray95"), 18)

data_table <- ggplot(data = fplottable, aes(y = labels)) +
  geom_hline(aes(yintercept = labels, colour = colour), size = 7) +
  geom_text(aes(x = 0, label = labels), hjust = 0) +
  geom_text(aes(x = 5, label = eventnum)) +
  geom_text(aes(x = 7, label = arr), hjust = 1) +
  scale_colour_identity() +
  theme_void() + 
  theme(plot.margin = margin(5, 0, 35, 0))

grid.arrange(data_table,p, ncol = 2)

【讨论】：

非常感谢！有没有办法添加交替的灰色和白色带？太难也不用担心！谢谢！
@davidk 有点繁琐，不过我加了几行
你是个了不起的人
这种类型的图的广义名称只是一个“区间图”（它包含作为子类型的森林图）。在您的情况下，您可以将其称为“效果大小图”。我认为@IRTFM 的观点是，在实际的森林图中，每条线代表一个完整的研究，并显示了治疗组与对照组的二元结果的测量优势比（及其置信区间）。结合多项研究时，它用于荟萃分析。您的图显示了单个研究中各个变量的影响大小，因此从技术上讲不是森林图。
顺便说一句，我经常对医学期刊的论文进行同行评审（我猜@IRTFM 也是如此），我不得不承认我可能会让这种命名法的不准确滑落，除非我特别特别脾气暴躁。将其称为“效果大小图”或“区间图”甚至只是“图”可能更安全，只要清楚您要展示的内容即可。

【解决方案2】：

您可以通过将两个数据框合并为fdf <- full_join(forestdf, fplottable, by = "labels") 并在fdf 上运行p 来进一步简化。然后p + geom_text(aes(x=22, label=paste(" ", arr," ",eventum, sep=' '))) 将给出以下输出：output

显然，limits需要扩大到100才能包含表格，完整代码如下：

p <- ggplot(fdf, aes(x=rr, y=labels, xmin=rrlow, xmax=rrhigh))+
  geom_pointrange(shape=22, fill="black") +
  geom_vline(xintercept = 1, linetype=3) +
  xlab("Variable")+ylab("Adjusted Relative Risk with 95% Confidence Interval") +
  theme_bw() +
  #scale_y_discrete(limits = rev(labels))+
  scale_x_log10(limits = c(0.25, 100), 
                breaks = c(0.25, 0.5, 1, 2, 4, 100),
                labels=c("0.25", "0.5", "1", "2", "4", ""), 
                expand = c(0,0)
  )+
  geom_text(aes(x=22, label=paste("  ",  arr,"  ",eventum, sep='   ')))
p

【讨论】：

【解决方案3】：

假设 names(fplottable)<-c('labels','eventum','arr')

那么data_table 的代码存在一些问题。如果我理解正确，您的意思是： data_table <- ggplot(data=fplottable)+geom_text(aes(x= 1, y=labels, label=arr))+geom_text(aes(x= 1.5, y=labels, label=eventum))。你可以玩 x 的值并且只有一个 geom_text 其中label=paste(arr, eventum, sep=' ')

在这种情况下，命令grid.arrange(data_table,p, ncol=2) 似乎工作正常。您可以使用width 定义每个面板的空间。

【讨论】：