R语言（pROC）绘图

任务描述：采取R语言绘制ROC曲线

参考文献：link.

专业背景：临床医学（心血管病学）

数据库：R语言的公共数据库

软件环境

R version 3.6.2 (2019-12-12) -- "Dark and Stormy Night"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

> library(pROC)
Type 'citation("pROC")' for a citation.

载入程辑包：‘pROC’

The following objects are masked from ‘package:stats’:

    cov, smooth, var

> aSAH
    gos6 outcome gender age wfns s100b   ndka
29     5    Good Female  42    1  0.13   3.01
30     5    Good Female  37    1  0.14   8.54
31     5    Good Female  42    1  0.10   8.09
32     5    Good Female  27    1  0.04  10.42
33     1    Poor Female  42    3  0.13  17.40
34     1    Poor   Male  48    2  0.10  12.75
##### Build a ROC object and compute the AUC
> roc(aSAH$outcome,aSAH$s100b)

Call:
roc.default(response = aSAH$outcome, predictor = aSAH$s100b)

Data: aSAH$s100b in 72 controls (aSAH$outcome Good) < 41 cases (aSAH$outcome Poor).
Area under the curve: 0.7314
//# Smooth ROC curve
> roc(aSAH$outcome,aSAH$s100b,smooth = TRUE)

Call:
roc.default(response = aSAH$outcome, predictor = aSAH$s100b,     smooth = TRUE)

Data: aSAH$s100b in 72 controls (aSAH$outcome Good) < 41 cases (aSAH$outcome Poor).
Smoothing: binormal 
Area under the curve: 0.74
> levels(aSAH$outcome)
[1] "Good" "Poor"
//# more options, CI and plotting
> roc1 <- roc(aSAH$outcome,aSAH$s100b,smooth = TRUE,percent = TRUE,partial.auc = c(100,90),partial.auc.correct = TRUE,partial.auc.focus = "sens",ci = TRUE,boot.n = 100,ci.alpha = 0.9,stratified = FALSE,plot = TRUE,auc.polygon = TRUE,max.auc.polygon = TRUE,grid = TRUE)

Call:
roc.default(response = aSAH$outcome, predictor = aSAH$s100b,     percent = TRUE, smooth = TRUE, ci = TRUE, plot = TRUE, partial.auc = c(100,         90), partial.auc.correct = TRUE, partial.auc.focus = "sens",     boot.n = 100, ci.alpha = 0.9, stratified = FALSE, auc.polygon = TRUE,     max.auc.polygon = TRUE, grid = TRUE)

Data: aSAH$s100b in 72 controls (aSAH$outcome Good) < 41 cases (aSAH$outcome Poor).
Smoothing: binormal 
Corrected partial area under the curve (sensitivity 100%-90%): 55.63%
95% CI: 50.02%-66.08% (100 stratified bootstrap replicates)
//计算曲线下面积和部分曲线下面积
> auc(roc1)
Area under the curve: 74%>
> auc(roc1,partial.auc =c(1,10))
Partial area under the curve (specificity 10%-1%): 8.857%
> auc(roc1,partial.auc =c(1,0))
Partial area under the curve (specificity 1%-0%): 0.9985%
> auc(roc1,partial.auc =c(0,100))
Partial area under the curve (specificity 100%-0%): 74%

绘图部分

#######  加载程序包  ########
> library(pROC)
> library(ggplot2)
######  查看数据库  #######
> summary(aSAH$outcome)
Good Poor 
  72   41 
######  构建方程  #########
> rocs100b <- roc(aSAH$outcome, aSAH$s100b)
Setting levels: control = Good, case = Poor
Setting direction: controls < cases
> rocage <- roc(aSAH$outcome, aSAH$age)
Setting levels: control = Good, case = Poor
Setting direction: controls < cases
#########  1.0版本的图像  ############
> g <- ggroc(rocs100b)
#########  2.0版本的图像  ############
> ggroc(rocs100b, alpha = 0.5, colour = "red", linetype = 2, size = 2)
#########  3.0版本的图像  ############
> g + theme_minimal() + ggtitle("My ROC curve") +
     geom_segment(aes(x = 1, xend = 0, y = 0, yend = 1), colour = "grey", linetype = "dashed")
#########  4.0版本的图像（改变X轴) ########
> g1 <- ggroc(rocs100b, legacy.axes = TRUE)
> g1
> g1 + xlab("FRR") + ylab("TRR") +
     geom_segment(aes(x = 0, xend = 1, y = 0, yend = 1), colour = "darkgrey", linetype = "dashed")

######### 绘制多条曲线 ##########
> g2 <- ggroc(list(s100b = rocs100b, age = rocage), legacy.axes = TRUE)
> g2