SWAP.PlotKTSP.GenePairClassesBoxplot: Plots a feature pair as seperated by class as boxplots.

In marchion/switchBox: Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithm

Description

Plots two genes or features, each as a pair of boxplots seperated to two classes or phenotypes.

Usage

SWAP.PlotKTSP.GenePairClassesBoxplot(genes, inputMat, Groups, 
  classes=NULL, points=FALSE, ordering="byGene", 
  colors=c(), point_colors=c(), point_directions=FALSE, ...)

Arguments

genes	is a vector of length two providing the pair (from the rownames of inputMat) of features to be plotted.
inputMat	is a matrix of data with rows being the features (such as gene names, if the matrix if gene expression data) and columns being the samples.
Groups	is a factor or a vector providing the phenotype class each sample belongs to. It should correspond to the order of samples given by the columns of inputMat.
classes	is a vetor of length 2 providing the two phenotype or class labels of Groups.
points	is a logical value indicating whether to overlay the boxplot with points for individual samples or not.
ordering	can be either 'byGene' or 'byClass' respectively indicating whether to plot two adjacent boxplots for each class/phenotype or two adjacent boxplots for each gene/features.
colors	is a character vector indicating the color to be used for each class or gene boxplots.
point_colors	is a character vector indicating the color to be used for the points.
point_directions	is a logical indicating whether to color the points by whether the first gene is less than the second gene.
...	any further arguments are supplied to the boxplot function.

Value

Produces a pair of boxplots indicating the distribution of the measured values for the pair of features/genes.

Author(s)

Bahman Afsari [e-mail], Luigi Marchionni [e-mail], Wikum Dinalankara [e-mail]

References

See switchBox for the references.

See Also

SWAP.PlotKTSP.GenePairBoxplot

Examples

### Load gene expression data
data(trainingData)

### train 1-TSP
classifier = SWAP.Train.1TSP(matTraining, trainingGroup)

### plot top pair
SWAP.PlotKTSP.GenePairClassesBoxplot(classifier$TSPs, matTraining,
  trainingGroup, levels(trainingGroup),
  points=TRUE, ordering="byGene")

marchion/switchBox documentation built on May 9, 2019, 4:07 p.m.