Calculate3D: Plot the 3D-ROC curve

Description Usage Arguments Details Value Errors References See Also Examples

View source: R/ROC_Plot.R

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

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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.

See Also

CalculateHUM_seq, CalculateHUM_ROC

Examples

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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])

Example output

Loading required package: gtools
Loading required package: Rcpp
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
3: .onUnload failed in unloadNamespace() for 'rgl', details:
  call: fun(...)
  error: object 'rgl_quit' not found 

HUM documentation built on May 29, 2017, 2:55 p.m.