SWAP.PlotKTSP.Genes: Plot features seperated by phenotype

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

Description

Makes line plots of one or more features seperated by phenotype.

Usage

SWAP.PlotKTSP.Genes(inputMat, Groups, classes, genes, 
  colors=c(), legends=c(), ...)

Arguments

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.
genes	is a vector of length one or more providing the names (from the rownames of inputMat) of the features to be plotted.

Value

Produces a plot containing a line for each feature plotted, the x-axis being the ordering of samples and the y-axis being the measured value (such as gene expression).

Author(s)

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

References

See switchBox for the references.

See Also

SWAP.PlotKTSP.GenePairScatter

Examples

### Load gene expression data
data(trainingData)

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

### plot top pair
SWAP.PlotKTSP.Genes(matTraining, trainingGroup, levels(trainingGroup), classifier$TSPs)

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