使用 table ggplot 编码的森林图
Forest plot with table ggplot coding
我正在尝试将 table 与我的林地并排放置，但我遇到了很多麻烦。
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，我无法使带有标签的左侧面板正常工作：
#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 并尝试获得类似于森林图中粉红色框所示的内容
假设
names(fplottable)<-c('labels','eventum','arr')
data_table 的代码存在一些问题。如果我理解正确的话，你的意思是这样的：
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，只有一个 geom_text where 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 space
@efz 指出了一些问题。此外，您需要重构第二列中的标签，以使其与第一列中的标签相匹配。 table 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。
这给你留下了类似的东西：
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)
您可以通过将两个数据帧合并为 fdf <- full_join(forestdf, fplottable, by = "labels") 和 运行 您的 p on fdf 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 需要扩展到 100 以包含 table，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
我正在尝试将 table 与我的林地并排放置，但我遇到了很多麻烦。
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，我无法使带有标签的左侧面板正常工作：
#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 并尝试获得类似于森林图中粉红色框所示的内容
假设
names(fplottable)<-c('labels','eventum','arr')
data_table 的代码存在一些问题。如果我理解正确的话，你的意思是这样的：
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，只有一个 geom_text where 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.
@efz 指出了一些问题。此外，您需要重构第二列中的标签，以使其与第一列中的标签相匹配。 table 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。
这给你留下了类似的东西：
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)
您可以通过将两个数据帧合并为 fdf <- full_join(forestdf, fplottable, by = "labels") 和 运行 您的 p on fdf 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 需要扩展到 100 以包含 table，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