clusterPlot {TIN} | R Documentation

## clusterPlot

### 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")

[Package TIN version 1.14.0 Index]