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Last data update: 2014.03.03

R: Plot the 3D-ROC curve

Calculate3D

R Documentation

Plot the 3D-ROC curve

Description

This is the main function of the HUM package. It plots the 3D-ROC curve using the point coordinates, computed by the function CalculateHUM_ROC. Optionally visualizes the optimal threshold point, which gives the maximal accuracy of the classifier(feature) (see CalcROC).

Usage

Calculate3D(sel,Sn,Sp,S3,optSn,optSp,optS3,thresholds,HUM,name,print.optim=TRUE)

Arguments

`sel`	a character value, which is the name of the selected feature.
`Sn`	a numeric vector of the x-coordinates of the ROC curve..
`Sp`	a numeric vector of the y-coordinates of the ROC curve.
`S3`	a numeric vector of the z-coordinates of the ROC curve.
`optSn`	the first coordinate of the optimal threshold
`optSp`	the second coordinate of the optimal threshold
`optS3`	the third coordinate of the optimal threshold
`thresholds`	a numeric vector with threshold values to calculate point coordinates.
`HUM`	a numeric vector of HUM values, calculated using function.
`name`	a character vector of class labels.
`print.optim`	a boolean parameter to plot the optimal threshold point on the graph. The default value is TRUE.

Details

This function's main job is to plot the 3D-ROC curve according to the given point coordinates.

Value

The function doesn't return any value.

Errors

If there exists NA values for specificity or sensitivity values, or HUM values the plotting fails and an error is triggered with message “Values are missing”

References

Li, J. and Fine, J. P. (2008): ROC Analysis with Multiple Tests and Multiple Classes: methodology and its application in microarray studies.Biostatistics. 9 (3): 566-576.

Examples

data(sim)
indexF=names(sim[,c(3),drop = FALSE])
indexClass=2
label=unique(sim[,indexClass])
indexLabel=label[1:3]
out=CalculateHUM_seq(sim,indexF,indexClass,indexLabel)
HUM<-out$HUM
seq<-out$seq
out=CalculateHUM_ROC(sim,indexF,indexClass,indexLabel,seq)
Calculate3D(indexF,out$Sn,out$Sp,out$S3,out$optSn,out$optSp,out$optS3,
out$thresholds,HUM,indexLabel[seq])

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(HUM)
Loading required package: gtools
Loading required package: Rcpp
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/HUM/Calculate3D.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Calculate3D
> ### Title: Plot the 3D-ROC curve
> ### Aliases: Calculate3D
> ### Keywords: multivariate nonparametric plot roc auc
> 
> ### ** Examples
> 
> data(sim)
> indexF=names(sim[,c(3),drop = FALSE])
> indexClass=2
> label=unique(sim[,indexClass])
> indexLabel=label[1:3]
> out=CalculateHUM_seq(sim,indexF,indexClass,indexLabel)
> HUM<-out$HUM
> seq<-out$seq
> out=CalculateHUM_ROC(sim,indexF,indexClass,indexLabel,seq)
> Calculate3D(indexF,out$Sn,out$Sp,out$S3,out$optSn,out$optSp,out$optS3,
+ out$thresholds,HUM,indexLabel[seq])
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>