SWAP.PlotKTSP.Genes: Plot features seperated by phenotype

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/exportedFuncs.R

Description

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

Usage

1
2
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 [email protected], Luigi Marchionni [email protected], Wikum Dinalankara [email protected]

References

See switchBox for the references.

See Also

SWAP.PlotKTSP.GenePairScatter

Examples

1
2
3
4
5
6
7
8
### 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)

switchBox documentation built on Nov. 1, 2018, 2:46 a.m.