Calculate3D {HUM} | 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.
See Also
CalculateHUM_seq
, CalculateHUM_ROC
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])