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

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

Description

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

Usage

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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 bahman.afsari@gmail.com, Luigi Marchionni marchion@jhu.edu, Wikum Dinalankara wdinala1@jhmi.edu

References

See switchBox for the references.

See Also

SWAP.PlotKTSP.GenePairBoxplot

Examples

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### 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.