forestPlot,ModelComparison-method {PDATK} | R Documentation |
validationStats
slot of a PCOSP
model object.Render a forest plot from the validationStats
slot of a PCOSP
model object.
## S4 method for signature 'ModelComparison' forestPlot( object, stat, groupBy = "cohort", colourBy = "model", vline, ..., xlab, ylab, transform, colours, title )
object |
A |
stat |
A |
groupBy |
A |
colourBy |
A |
vline |
An |
... |
Force subsequent parameters to be named, not used. |
xlab |
A |
ylab |
A |
transform |
The name of a numeric function to transform the statistic before making the forest plot. |
colours |
A |
title |
A |
A ggplot2
object.
data(sampleValPCOSPmodel) data(sampleClinicalModel) data(sampleCohortList) # Set parallelization settings BiocParallel::register(BiocParallel::SerialParam()) # Train the models trainedClinicalModel <- trainModel(sampleClinicalModel) # Predict risk/risk-class ClinicalPredCohortL <- predictClasses(sampleCohortList[c('PCSI', 'TCGA')], model=trainedClinicalModel) # Validate the models validatedClinicalModel <- validateModel(trainedClinicalModel, valData=ClinicalPredCohortL) # Compare the models modelComp <- compareModels(sampleValPCOSPmodel, validatedClinicalModel) # Make the forest plot modelComp <- modelComp[modelComp$isSummary == TRUE, ] modelCindexCompForestPlot <- forestPlot(modelComp, stat='concordance_index')