所用R包: forestplot , forestploter
示例数据
单列森林图（forestplot包）
官方文档：Introduction to forest plots
#forestplot包森林图代码附注释
library(forestplot)
data <- read.xlsx("森林图示例数据.xlsx",sheet=1)
fig<-forestplot(data[,c(1:5)],
mean=data[,6],
lower=data[,7],
upper=data[,8],
zero=1,
lwd.zero=1, # 森林图参考线
lty.zero=2, # 森林图参考线类型
boxsize=0.2,
graph.pos= 5 ,#森林图的显示位置
hrzl_lines=list("1" = gpar(lty=1,lwd=2), #虚线
"2" = gpar(lty=1,lwd=2), #表格上框线
"18"= gpar(lwd=2,lty=1,columns=c(1:4)) ),#表格下框线，column设置其覆盖的列
graphwidth = unit(0.15,"npc"), #森林图占整张图的比例 这里是0.3即30%
xlab="←Esmketamine Better Placebo Better→",#森林图坐标轴标签
xticks=c(0,1,2,3) , #森林图坐标轴上的刻度
is.summary=c(T,F,T,F,F,T,F,F,T,F,F,T,F,F,T,F,F,T,F),#设置有无加粗行，这样即只有第一行表头字体加粗
txt_gp=fpTxtGp(
label=gpar(cex=1), #表格字符的文字大小
ticks=gpar(cex=1), #森林图刻度的文字大小
xlab=gpar(cex=0.5), #森林图标题的文字大小
title=gpar(cex=3)), #图标题文字大小
lwd.ci=1.5, # 森林图置信区间的线宽
lwd.xaxis=2, #森林图x轴线宽
lty.ci=1.5, #森林图置信区间线型
ci.vertices =F, #森林图置信区间左右端点是否显示竖直线条
ci.vertices.height=0.4, #森林图置信区间左右端点线条长度
clip=c(0,3), #森林图HR坐标轴显示的范围
ineheight=unit(1, 'mm'), # 每个研究条目的高度
line.margin=unit(1, 'mm'),# 线的边距
colgap= unit(4, 'mm'),# 表格列之间的间隔。
fn.ci_norm="fpDrawDiamondCI", #绘制置信区间的函数应该不用改
col=fpColors(box ='#021eaa',
lines ='black')) # 框、线和参考线的颜色
fig示例图形
单列森林图（forestploter包）
官方文档: Introduction to forestploter
data <- read.xlsx("森林图示例数据.xlsx",sheet=2)
#数据处理
#有缺失的地方变成一个空格
data$Pvalue <- as.character(data$Pvalue)
data <- data %>% mutate(across(2:5,~if_else(is.na(.),"",.)))
#生成一个变量se，它在绘图的时候表示正方形的大小
data$se <- (log(data$h) - log(data$e))/1.96
#生成一个绘图区间，等下用来绘图
data$` ` <- paste(rep(" ", 20), collapse = " ") #该变量长度决定森林图列的宽度
#图型设置
tm <- forest_theme(base_size = 10, #文本的大小
# Confidence interval point shape, line type/color/widatah
ci_pch = 15, #可信区间点的形状
ci_col = "#762a83", #CI的颜色
ci_fill = "blue", #ci颜色填充
ci_alpha = 0.8, #ci透明度
ci_lty = 1, #CI的线型
ci_lwd = 1.5, #CI的线宽
ci_Theight = 0.2, # Set an T end at the end of CI ci的高度，默认是NULL
# Reference line widatah/type/color 参考线默认的参数，中间的竖的虚线
refline_lwd = 1, #中间的竖的虚线
refline_lty = "dashed",
refline_col = "grey20",
# Vertical line widatah/type/color 垂直线宽/类型/颜色 可以添加一条额外的垂直线，如果没有就不显示
vertline_lwd = 1, #可以添加一条额外的垂直线，如果没有就不显示
vertline_lty = "dashed",
vertline_col = "grey20",
# Change summary color for filling and borders 更改填充和边框的摘要颜色
summary_fill = "yellow", #汇总部分大菱形的颜色
summary_col = "#4575b4",
#change arrow
arrow_type = c("open"),
arrow_length = 0.05,
arrow_gp = gpar(cex=0.5),
# Footnote font size/face/color 脚注字体大小/字体/颜色
footnote_cex = 0.6,
footnote_fontface = "italic",
footnote_col = "red")
#绘图
p <- forest(data[,c(1:3,10,4:5)],
est = data$e,
lower = data$l,
upper = data$h,
sizes = data$se,
is_summary = c(TRUE,rep(FALSE, nrow(data)-1)),
ci_column = 4,
ref_line = 1,
arrow_lab = c("Placebo Better", "Treatment Better"),
xlim = c(0, 3),
ticks_at = c(0, 1, 2, 3),
background = "white", # 设置背景为白色，去除条纹
panel = "blank" , # 使用空白面板（如果条纹是由面板产生的）
footnote = "This is the demo data. Please feel free to change\nanything you want.",
theme = tm)
p
#细节调整
# 背景改为全白
p <- edit_plot(p, which = "background",
gp = gpar(fill = "white"))
p
#数据显示位置
p <- edit_plot(p,
row = c(3,4,6,7,9,10,12,13,15,16),
col = 1,
which = "text",
hjust = unit(0.2, "npc"),
x = unit(0.2, "npc"))
p <- edit_plot(p,
col = c(2,3,5,6),
which = "text",
hjust = unit(0.5, "npc"),
x = unit(0.5, "npc"))
# 把2, 5, 10, 13, 17, 20行的文本变成粗体
p <- edit_plot(p,
row = c(2, 5, 8, 11, 14),
gp = gpar(fontface = "bold"))
# 在顶部插入文本
p <- insert_text(p,
text = "No. of cases/total number（incidence rate, %）",
col = 2:3,
part = "header",
gp = gpar(fontface = "bold",cex=1))
# 在标题下方加一条下划线
p <- add_border(p, row=1,part = "header",where="top",gp = gpar(lwd = 2))
p <- add_border(p,row=2, part = "header",where="bottom",gp = gpar(lwd = 2))
p <- add_border(p,row=16, col=c(1:3),part = "body",where="bottom",gp = gpar(lwd = 2))
p <- add_border(p,row=16, col=c(5:6),part = "body",where="bottom",gp = gpar(lwd = 2))
p
# 其他可做的修改
# 更改3,6,10,11行方块及长条的颜色为绿色
p <- edit_plot(p,
row = c(3, 6, 11, 13),
col = 4,
which = "ci",
gp = gpar(col = "green"))
p
# 第三行变成红色
p <- edit_plot(p, row = 3, gp = gpar(col = "red", fontface = "italic"))
p
# 在第十行位置插入文本
p <- insert_text(p,
text = "This is a long text. Age and gender summarised above.\nBMI is next",
row = 10,
just = "left",
gp = gpar(cex = 0.6, col = "green", fontface = "italic"))
p图形示例
双组多结局森林图 (forestploter包)
forestdata<- read.xlsx("森林图示例数据.xlsx",sheet=3)
forestdata$KM聚类结局 <- paste(rep(" ", 10), collapse = " ")
forestdata$GMM聚类结局 <- paste(rep(" ", 10), collapse = " ")
forestdata$lpa聚类结局 <- paste(rep(" ", 10), collapse = " ")
forestdata$` ` <-""
forestdata$` ` <-""
tm <- forest_theme(base_size = 10,
refline_lty = "dashed", #参考线类型
ci_pch = c(15, 18),
ci_col = c("#377eb8", "#4daf4a"),
footnote_col = "blue",
legend_name = "结局", #设置标题名字
legend_value = c("行为问题", "体格问题"), #设置分组名字
vertline_lty = c("dashed", "dotted"),
vertline_col = c("#d6604d", "#bababa"),
refline_lwd = 1, #中间的竖的虚线
refline_col = "grey20")
p <- forest(
forestdata[,c(1,2,23,26,24,27,25)],
est = list(forestdata$OR_1,
forestdata$OR_3,
forestdata$OR_5,
forestdata$OR_2,
forestdata$OR_4,
forestdata$OR_6), # 分成两组的估计值
lower = list(forestdata$lci_1,
forestdata$lci_3,
forestdata$lci_5,
forestdata$lci_2,
forestdata$lci_4,
forestdata$lci_6), # 分成两组的下限
upper = list(forestdata$uci_1,
forestdata$uci_3,
forestdata$uci_5,
forestdata$uci_2,
forestdata$uci_4,
forestdata$uci_6), # 分成两组的上限
sizes=0.4,
ci_column = c(3,5,7), # 两列CI
ref_line = 1,
xlim = c(0,5),
ticks_at = c(0,1,2,3,4,5),
footnote = "This is the demo data",
nudge_y = 0.4, #调整两组间距
xlab=c(""," OR",""),
theme=tm)
p
#去除背景
p <- edit_plot(p, which = "background",
gp = gpar(fill = "white"))
#调整标题行对齐位置
p <- edit_plot(p,
col=c(2:7),
part="header",
which = "text",
hjust = unit(0.4, "npc"),
x = unit(0.4, "npc"))
#添加框线
# 在标题下方加一条下划线
p <- add_border(p, row=1,part = "header",where="top",gp = gpar(lwd = 2))
p <- add_border(p,row=1, part = "header",where="bottom",gp = gpar(lwd = 2))
p
