SigCheck (version 1.0.2)

sigCheckPlot: Plot results of a signature check

Description

Plots a histogram of the classification performance scores for a check, showing how it compares to classification performance of the signature being checked, as well as to a hypothetical classifier that uses the mode of the training samples.

Usage

sigCheckPlot(checkResults, ...)

Arguments

checkResults

The list value returned by sigCheckRandom, sigCheckKnown, or sigCheckPermuted (or one the elements of the list returned by sigCheck).

Can also be the list returned by sigCheck, which which case each of the four results lists will be plotted in turn.

...

Additional arguments to be passed to the plot function.

Value

none

Details

Draws a line plot version of a histogram, with the x-axis representing the range of classification performance scores computed in the check, and the y-axis representing how many times that score was obtained. In addition, vertical lines are plotted representing the classification performance of the originally specified signature (solid red line) and the performance of a classifier that always predicts the mode value of the training samples (dotted red line).

See Also

sigCheck, sigCheckRandom, sigCheckKnown, sigCheckPermuted

Examples

library(breastCancerNKI)
data(nki)
nki <- nki[,!is.na(nki$e.dmfs)]
data(knownSignatures)
results <- sigCheckRandom(nki, classes="e.dmfs", 
                          signature=knownSignatures$cancer$VANTVEER, 
                          annotation="HUGO.gene.symbol", 
                          validationSamples=275:319, nIterations=25)
sigCheckPlot(results)