clusterPlot: clusterPlot

In TIN: Transcriptome instability analysis

Description

Create plot from hierarchical clustering analysis of the samples, based on splicing factor expression levels.

Usage

    clusterPlot(geneSummaries, tra, distmethod, clustermethod, fileName)

Arguments

geneSummaries	The data.frame with gene-level expression values for each sample, returned from the function 'readGeneSummaries'.
tra	The list returned from the function 'aberrantExonUsage', containing sample-wise total relative amounts of aberrant exon usage.
distmethod	Which distance measure to be used. Possible options are "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski".
clustermethod	Which clustering algorithm to be used. Possible options are "ward", "single", "complete", "average", "mcquitty", "median" or "centroid".
fileName	Output filename. File format is optional, but must be one of png, jpg, eps or pdf.

Value

clusterPlot is used for the side-effect of producing a hierarchical clustering plot showing how the samples are separated based on expression levels for the splicing factors in each sample.

Examples

    fs <- firmaAnalysis(useToyData=TRUE)
    gs <- readGeneSummaries(useToyData=TRUE)
    tra <- aberrantExonUsage(1.0, fs)
# create cluster plot with the samples
    clusterPlot(gs, tra, "euclidean", "complete", "cluster.png")

TIN documentation built on Nov. 8, 2020, 5:58 p.m.