R语言绘图包11--森林图的绘制(2)：forestploter

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R语言绘图包系列：

• R语言绘图包01--优秀的拼图包patchwork
• R语言绘图包02--热图pheatmap
• R语言绘图包03--火山图EnhancedVolcano
• R语言绘图包04--GOplot：富集分析结果可视化
• R语言绘图包05--韦恩图的绘制：ggvenn和VennDiagram
• R语言绘图包06--基因表达相关性绘图corrplot
• R语言绘图包07--多集合可视化UpSetR
• R语言绘图包08--森林图的绘制：forestplot
• R语言绘图包09--序列分析图的绘制ggseqlogo
• R语言绘图包10--Circos图的绘制：circlize包

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• 加载包

install.packages('forestploter')
library(forestploter)

• 准备数据

# Read provided sample example data
dt <- read.csv(system.file("extdata", "example_data.csv", package = "forestploter"))

# Keep needed columns
dt <- dt[,1:6]

# indent the subgroup if there is a number in the placebo column
dt$Subgroup <- ifelse(is.na(dt$Placebo),
                      dt$Subgroup,
                      paste0("   ", dt$Subgroup))

# NA to blank or NA will be transformed to carachter.
dt$Treatment <- ifelse(is.na(dt$Treatment), "", dt$Treatment)
dt$Placebo <- ifelse(is.na(dt$Placebo), "", dt$Placebo)
dt$se <- (log(dt$hi) - log(dt$est))/1.96

# Add blank column for the forest plot to display CI.
# Adjust the column width with space.
dt$` ` <- paste(rep(" ", 20), collapse = " ")

# Create confidence interval column to display
dt$`HR (95% CI)` <- ifelse(is.na(dt$se), "",
                           sprintf("%.2f (%.2f to %.2f)",
                                   dt$est, dt$low, dt$hi))
View(dt)

注意倒数第二列是空白的(不是NA，是"")，是留出来画图空间的

• 绘图

# Define theme
tm <- forest_theme(base_size = 10,
                   refline_col = "red",
                   footnote_col = "#636363",
                   footnote_fontface = "italic")

p <- forest(dt[,c(1:3, 8:9)],
            est = dt$est,
            lower = dt$low,
            upper = dt$hi,
            sizes = dt$se,
            ci_column = 4, #指定图绘制在第几列
            ref_line = 1,
            arrow_lab = c("Placebo Better", "Treatment Better"),
            xlim = c(0, 4),
            ticks_at = c(0.5, 1, 2, 3),
            footnote = "This is the demo data. Please feel free to change\nanything you want.",
            theme = tm)

# Print plot
plot(p)