SWAP.PlotKTSP.GenePairBoxplot: Plots a feature pair 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 as a pair of boxplots; optionally, individual samples can be plotted on top of the boxplots as points; for this points can be colored by either gene, or class, or whether first gene < second gene is TRUE or FALSE for each sample.

Usage

SWAP.PlotKTSP.GenePairBoxplot(genes, inputMat, Groups=NULL, 
  classes=NULL, points=FALSE, point_coloring="byGene", 
  colors=c(), point_colors=c(), ...)

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.
point_coloring	can be either 'byGene' or 'byClass' indicating whether to color the points by gene/feature or by phenotype. A third option is 'byDirection' indicating to color the points by whether the first gene is less than the second gene.
colors	is a character vector indicating the color to be used for each boxplot.
point_colors	is a character vector indicating the color to be used for the points.
...	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.GenePairClassesBoxplot

Examples

### Load gene expression data
data(trainingData)

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

### plot top pair
SWAP.PlotKTSP.GenePairBoxplot(classifier$TSPs, matTraining, 
  points=TRUE, point_coloring="byGene")

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