肿瘤免疫反应瀑布图（源于The Miller Lab）

数据格式

绘图

①根据剂量

②根据type

③根据治疗响应度

添加水平线

数据格式

肿瘤免疫响应数据

复制代码

rm(list = ls()) 
library(tidyverse)
library(dplyr)
library(knitr)

#模拟数据
# We will randomly assign the two doses, 80 mg or 150 mg, to the 56 subjects
Merkel <- data.frame(
  id=c(1:56), 
  type = sample((rep(c("laMCC", "metMCC"), times =28))), 
  response = c(30, sort(runif(n=53,min=-10,max=19), decreasing=TRUE),-25,-31), 
  dose= sample(rep(c(80, 150), 28)))

# Let's assign Best Overall Response (BOR)
Merkel$BOR= (c("PD", rep(c("SD"), times =54),"PR"))

复制代码

head(Merkel)
  id   type response dose BOR
1  1 metMCC 30.00000  150  PD
2  2 metMCC 18.99641   80  SD
3  3  laMCC 18.78160   80  SD
4  4 metMCC 17.98778  150  SD
5  5 metMCC 16.61512   80  SD
6  6 metMCC 16.30297   80  SD

绘图

①根据剂量

复制代码

##颜色设置
col <- ifelse(Merkel$dose == 80, 
              "steelblue", # if dose = 80 mg, then the color will be steel blue
              "cadetblue") # if dose != 80 mg (i.e. 150 mg here), then the color will be cadet blue
MCC<- barplot(Merkel$response, 
              col=col, 
              border=col, 
              space=0.5, 
              ylim=c(-50,50),
              main = "Waterfall plot for Target Lesion Tumor Size", 
              ylab="Change from baseline (%)",
              cex.axis=1.5, 
              legend.text= c( "80mg", "150mg"),
              #添加图例
              args.legend=list(title="Treatment Dose", fill=c("steelblue", "cadetblue"), border=NA, cex=0.9))

dev.off()

②根据type

复制代码

col <- ifelse(Merkel$type == "laMCC", 
              "#BC5A42", # if type of disease = locally MCC, then the color will be #BC5A42 (deep red)
              "#009296") # if type of disease != locaally MCC (i.e. mMCC), then the color will be ##009296 (greenish-blue)

MCC<- barplot(Merkel$response, 
              col=col, 
              border=col, 
              space=0.5, 
              ylim=c(-50,50),
              main = "Waterfall plot for Target Lesion Tumor Size", 
              ylab="Change from baseline (%)",
              cex.axis=1.5, 
              legend.text= c( "locally advanced MCC", "Metastatic MCC"),
              args.legend=list(title="Disease", fill=c("#BC5A42", "#009296"), border=NA, cex=0.9))

③根据治疗响应度

复制代码

col <- ifelse(Merkel$BOR == "CR", 
              "green", # if a subject had a CR the bar will be green, if they did not have a CR....
              ifelse(Merkel$BOR == "PR", 
                     "steelblue", # then, if a subject had a PR the bar will be steel blue, if they did not have a PR or CR....
                     ifelse(Merkel$BOR == "PD", 
                            "red", # then, if a subject had a PD the bar will be red, otherwise if they did not have a PR or CR or PD.... 
                            ifelse(Merkel$BOR == "SD", 
                                   "cadetblue", # then they must have ahd a SD, so the bar will be cadetblue, otherwise....
                                   "") # the color will be blank (which is not really an option, b/c they must have either a CR, PR, PD or SD)
                     )))


MCC<- barplot(Merkel$response, 
              col=col, 
              border=col, 
              space=0.5, 
              ylim=c(-50,50),
              main = "Waterfall plot for Target Lesion Tumor Size", ylab="Change from baseline (%)",
              cex.axis=1.5, 
              legend.text= c( "CR: Complete Response", "PR: Partial Response", "SD: Stable Disease", "PD: Progressive Disease"),
              args.legend=list(title="Best Overall Response", fill=c("green","steelblue",  "cadetblue", "red"), border=NA, cex=0.9))

添加水平线

复制代码

abline(h=20, col = "black", lwd=0.5) # The "PD" line
abline(h=-30, col = "black", lwd=0.5) # This "PR" line

来源：

The Miller Lab - Visualizing Tumor Response using Waterfall Charts with R