SWAP.PlotKTSP.GenePairScatter {switchBox} | R Documentation |
Makes a scatter plot of a pair of features/genes.
SWAP.PlotKTSP.GenePairScatter(inputMat, Groups, classes, genes, colors=c(), legends=c(), ...)
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 |
classes |
is a vetor of length 2 providing the two phenotype or
class labels of |
genes |
is a vector of length one or more providing the names
(from the rownames of |
colors |
is a character vector indicating the color to be used for each phenotype. |
legends |
is a character vector providing any additional information to be appended to the phenotype label in the legend. |
Produces a scatter plot containing points for each sample colored by the phenotype, with two axes being the measurements for the given two features.
Bahman Afsari bahman.afsari@gmail.com, Luigi Marchionni marchion@jhu.edu, Wikum Dinalankara wdinala1@jhmi.edu
See switchBox for the references.
### Load gene expression data data(trainingData) ### train 1-TSP classifier = SWAP.Train.1TSP(matTraining, trainingGroup) ### plot top pair SWAP.PlotKTSP.GenePairScatter(matTraining, trainingGroup, levels(trainingGroup), classifier$TSPs)