README.md

In elise-is/multiROC: Calculating and Visualizing ROC and PR Curves Across Multi-Class Classifications

multiROC

Calculating and Visualizing ROC and PR Curves Across Multi-Class Classifications

The receiver operating characteristic (ROC) and precision recall (PR) is an extensively utilized method for comparing binary classifiers in various areas. However, many real-world problems are designed to multiple classes (e.g., tumor, node, and metastasis staging system of cancer), which require an evaluation strategy to assess multiclass classifiers. This package aims to fill the gap by enabling the calculation of multiclass ROC-AUC and PR-AUC with confidence intervals and the generation of publication-quality figures of multiclass ROC curves and PR curves.

A user-friendly website is available at https://metabolomics.cc.hawaii.edu/software/multiROC/.

1 Citation

Please cite our paper once it is published: (Submitted).

2 Installation

Install multiROC from GitHub:

install.packages('devtools')
require(devtools)
install_github("WandeRum/multiROC")
require(multiROC)

Install multiROC from CRAN:

install.packages('multiROC')
require(multiROC)

3 A demo example

This demo is about the comparison between random forest and multinomial logistic regression based on Iris data.

3.1 data preparation

require(multiROC)
data(iris)
head(iris)

3.2 60% training data and 40% testing data

set.seed(123456)
total_number <- nrow(iris)
train_idx <- sample(total_number, round(total_number*0.6))
train_df <- iris[train_idx, ]
test_df <- iris[-train_idx, ]

3.3 Random forest

rf_res <- randomForest::randomForest(Species~., data = train_df, ntree = 100)
rf_pred <- predict(rf_res, test_df, type = 'prob') 
rf_pred <- data.frame(rf_pred)
colnames(rf_pred) <- paste(colnames(rf_pred), "_pred_RF")

3.4 Multinomial logistic regression

mn_res <- nnet::multinom(Species ~., data = train_df)
mn_pred <- predict(mn_res, test_df, type = 'prob')
mn_pred <- data.frame(mn_pred)
colnames(mn_pred) <- paste(colnames(mn_pred), "_pred_MN")

3.5 Merge true labels and predicted values

true_label <- dummies::dummy(test_df$Species)
true_label <- data.frame(true_label)
colnames(true_label) <- gsub(".*?\\.", "", colnames(true_label))
colnames(true_label) <- paste(colnames(true_label), "_true")
final_df <- cbind(true_label, rf_pred, mn_pred)

3.6 multiROC and multiPR

roc_res <- multi_roc(final_df, force_diag=T)
pr_res <- multi_pr(final_df, force_diag=T)

3.7 Plot

plot_roc_df <- plot_roc_data(roc_res)
plot_pr_df <- plot_pr_data(pr_res)

require(ggplot2)
ggplot(plot_roc_df, aes(x = 1-Specificity, y=Sensitivity)) +
  geom_path(aes(color = Group, linetype=Method), size=1.5) +
  geom_segment(aes(x = 0, y = 0, xend = 1, yend = 1), 
                        colour='grey', linetype = 'dotdash') +
  theme_bw() + 
  theme(plot.title = element_text(hjust = 0.5), 
                 legend.justification=c(1, 0), legend.position=c(.95, .05),
                 legend.title=element_blank(), 
                 legend.background = element_rect(fill=NULL, size=0.5, 
                                                           linetype="solid", colour ="black"))

ggplot(plot_pr_df, aes(x=Recall, y=Precision)) + 
  geom_path(aes(color = Group, linetype=Method), size=1.5) + 
  theme_bw() + 
  theme(plot.title = element_text(hjust = 0.5), 
                 legend.justification=c(1, 0), legend.position=c(.95, .05),
                 legend.title=element_blank(), 
                 legend.background = element_rect(fill=NULL, size=0.5, 
                                                           linetype="solid", colour ="black"))

4 multiROC in a nutshell

library(multiROC)
data(test_data)
head(test_data)

##   G1_true G2_true G3_true G1_pred_m1 G2_pred_m1 G3_pred_m1 G1_pred_m2 G2_pred_m2 G3_pred_m2
## 1       1       0       0  0.8566867  0.1169520 0.02636133  0.4371601  0.1443851 0.41845482
## 2       1       0       0  0.8011788  0.1505448 0.04827643  0.3075236  0.5930025 0.09947397
## 3       1       0       0  0.8473608  0.1229815 0.02965766  0.3046363  0.4101367 0.28522698
## 4       1       0       0  0.8157730  0.1422322 0.04199482  0.2378494  0.5566147 0.20553591
## 5       1       0       0  0.8069553  0.1472971 0.04574766  0.4067347  0.2355822 0.35768312
## 6       1       0       0  0.6894488  0.2033285 0.10722271  0.1063048  0.4800507 0.41364450

This example dataset contains two classifiers (m1, m2), and three groups (G1, G2, G3).

4.1 multi_roc and multi_pr function

roc_res <- multi_roc(test_data, force_diag=T)
pr_res <- multi_pr(test_data, force_diag=T)

The function multi_roc and multi_pr are core functions for calculating multiclass ROC-AUC and PR-AUC.

Arguments of multi_roc and multi_pr:

• data is the dataset contains both of true labels and corresponding predicted scores. True labels (0 - Negative, 1 - Positive) columns should be named as XX_true (e.g., S1_true, S2_true) and predictive scores (continuous) columns should be named as XX_pred_YY (e.g., S1_pred_SVM, S2_pred_RF). Predictive scores can be probabilities among [0, 1] or other continuous values. For each classifier, the number of columns should be equal to the number of groups of true labels.

• If force_diag equals TRUE, true positive rate (TPR) and false positive rate (FPR) will be forced to across (0, 0) and (1, 1).

Outputs of multi_roc:

• Specificity contains a list of specificities for each group of different classifiers.

• Sensitivity contains a list of sensitivities for each group of different classifiers.

• AUC contains a list of AUC for each group of different classifiers. Micro-average ROC-AUC was calculated by stacking all groups together, thus converting the multi-class classification into binary classification. Macro-average ROC-AUC was calculated by averaging all groups results (one vs rest) and linear interpolation was used between points of ROC.

• Methods shows names of different classifiers.

• Groups shows names of different groups.

Outputs of multi_pr:

• Recall contains a list of recalls for each group of different classifiers.

• Precision contains a list of precisions for each group of different classifiers.

• AUC contains a list of AUC for each group of different classifiers. Micro-average PR-AUC was calculated by stacking all groups together, thus converting the multi-class classification into binary classification. Macro-average PR-AUC was calculated by averaging all groups results (one vs rest) and linear interpolation was used between points of ROC.

• Methods shows names of different classifiers.

• Groups shows names of different groups.

4.2 Confidence Intervals

4.2.1 List of AUC results

unlist(roc_res$AUC)

##     m1.G1     m1.G2     m1.G3  m1.macro  m1.micro     m2.G1     m2.G2     m2.G3  m2.macro  m2.micro
## 0.7233607 0.5276190 0.9751462 0.7420609 0.8824221 0.3237705 0.3723810 0.4020468 0.3665670 0.4174394

This list shows the following AUC information:

1) AUC of G1 v.s. the rest in the classifier m1; 2) AUC of G2 v.s. the rest in the classifier m1; 3) AUC of G3 v.s. the rest in the classifier m1; 4) AUC of Macro in the classifier m1; 5) AUC of Micro in the classifier m1; 6) AUC of G1 v.s. the rest in the classifier m2; 7) AUC of G2 v.s. the rest in the classifier m2; 8) AUC of G3 v.s. the rest in the classifier m2; 9) AUC of Macro in the classifier m2; 10) AUC of Micro in the classifier m2.

4.2.2 Bootstrap

roc_ci_res <- roc_ci(test_data, conf= 0.95, type='basic', R = 100, index = 4)
pr_ci_res <- pr_ci(test_data, conf= 0.95, type='basic', R = 100, index = 4)

## BOOTSTRAP CONFIDENCE INTERVAL CALCULATIONS
## Based on 100 bootstrap replicates
## 
## CALL : 
## boot.ci(boot.out = res_boot, conf = conf, type = type, index = index)
## 
## Intervals : 
## Level       BCa          
## 95%   ( 0.649,  0.861 )  
## Calculations and Intervals on Original Scale
## Some BCa intervals may be unstable


## BOOTSTRAP CONFIDENCE INTERVAL CALCULATIONS
## Based on 100 bootstrap replicates
## 
## CALL : 
## boot.ci(boot.out = res_boot, conf = conf, type = type, index = index)
## 
## Intervals : 
## Level       BCa          
## 95%   ( 0.4242,  0.6547 )  
## Calculations and Intervals on Original Scale
## Warning : BCa Intervals used Extreme Quantiles
## Some BCa intervals may be unstable

The function roc_ci and pr_ci are used to calculate confidence intervals of multiclass ROC-AUC and PR-AUC.

Arguments of roc_ci and pr_ci:

• data is the dataset contains both of true labels and corresponding predicted scores. True labels (0 - Negative, 1 - Positive) columns should be named as XX_true (e.g., S1_true, S2_true) and predictive scores (continuous) columns should be named as XX_pred_YY (e.g., S1_pred_SVM, S2_pred_RF). Predictive scores can be probabilities among [0, 1] or other continuous values. For each classifier, the number of columns should be equal to the number of groups of true labels.

• conf contains the required level of confidence intervals, and the default number is 0.95.

• type includes five different types of equi-tailed two-sided nonparametric confidence intervals (e.g., "norm","basic", "stud", "perc", "bca", "all").

• R is the number of bootstrap replicates, the default number is 100.

• index is the position of the list of AUC results in 3.2.1.

Here, we set index = 4 to calculate 95% CI of AUC of Macro in the classifier m1 based on 1000 bootstrap replicates as an example.

4.2.3 Output All Results

roc_auc_with_ci_res <- roc_auc_with_ci(test_data, conf= 0.95, type='bca', R = 100)
roc_auc_with_ci_res
pr_auc_with_ci_res <- pr_auc_with_ci(test_data, conf= 0.95, type='bca', R = 100)
pr_auc_with_ci_res

##         Var       AUC  lower CI higher CI
## 1     m1.G1 0.7233607 0.5555556 0.8406849
## 2     m1.G2 0.5276190 0.3141490 0.6991112
## 3     m1.G3 0.9751462 0.9156118 0.9969245
## 4  m1.macro 0.7420420 0.6162905 0.8469999
## 5  m1.micro 0.8824221 0.7942627 0.9318145
## 6     m2.G1 0.3237705 0.2039669 0.4888149
## 7     m2.G2 0.3723810 0.2322795 0.5126755
## 8     m2.G3 0.4020468 0.2266853 0.5944778
## 9  m2.macro 0.3665214 0.2796633 0.4970809
## 10 m2.micro 0.4174394 0.3449170 0.5036827


##         Var        AUC   lower CI higher CI
## 1     m1.G1 0.81104090 0.69394085 0.9219133
## 2     m1.G2 0.18898097 0.09755974 0.3404294
## 3     m1.G3 0.67479141 0.34789377 0.9871966
## 4  m1.macro 0.54968868 0.43208030 0.6663112
## 5  m1.micro 0.75125213 0.61651803 0.8635095
## 6     m2.G1 0.60633468 0.49548427 0.7510816
## 7     m2.G2 0.13298786 0.06840618 0.2092138
## 8     m2.G3 0.08150105 0.03931745 0.1388464
## 9  m2.macro 0.27320882 0.23863708 0.3009619
## 10 m2.micro 0.27540471 0.23380391 0.3087388

The function roc_auc_with_ci and pr_auc_with_ci are used to calculate confidence intervals of multiclass ROC-AUC, PR-AUC, and output a dataframe with AUCs, lower CIs, and higher CIs of all methods and groups.

Arguments of roc_auc_with_ci and pr_auc_with_ci:

• data is the dataset contains both of true labels and corresponding predicted scores. True labels (0 - Negative, 1 - Positive) columns should be named as XX_true (e.g., S1_true, S2_true) and predictive scores (continuous) columns should be named as XX_pred_YY (e.g., S1_pred_SVM, S2_pred_RF). Predictive scores can be probabilities among [0, 1] or other continuous values. For each classifier, the number of columns should be equal to the number of groups of true labels.

• conf contains the required level of confidence intervals, and the default number is 0.95.

• type includes five different types of equi-tailed two-sided nonparametric confidence intervals (e.g., "norm","basic", "stud", "perc", "bca").

• R is the number of bootstrap replicates, the default number is 100.

5 Plots

5.1 change the format of AUC results to a ggplot2 friendly format.

plot_roc_df <- plot_roc_data(roc_res)
plot_pr_df <- plot_pr_data(pr_res)

5.2 Plot

5.2.1 ROC Plot

ggplot(plot_roc_df, aes(x = 1-Specificity, y=Sensitivity)) + geom_path(aes(color = Group, linetype=Method)) + geom_segment(aes(x = 0, y = 0, xend = 1, yend = 1), colour='grey', linetype = 'dotdash') + theme_bw() + theme(plot.title = element_text(hjust = 0.5), legend.justification=c(1, 0), legend.position=c(.95, .05), legend.title=element_blank(), legend.background = element_rect(fill=NULL, size=0.5, linetype="solid", colour ="black"))

5.2.2 PR Plot

ggplot(plot_pr_df, aes(x=Recall, y=Precision)) + geom_path(aes(color = Group, linetype=Method), size=1.5) + theme_bw() + theme(plot.title = element_text(hjust = 0.5), legend.justification=c(1, 0), legend.position=c(.95, .05), legend.title=element_blank(), legend.background = element_rect(fill=NULL, size=0.5, linetype="solid", colour ="black"))

6 Bug Reports

For sending comments, suggestions, bug reports of multiROC, please email to Runmin Wei ([e-mail]) or report it via thus URL: https://github.com/WandeRum/multiROC/issues

7 License

GPL-3

elise-is/multiROC documentation built on Nov. 24, 2020, 1:40 a.m.