plotStatistics {wavClusteR} | R Documentation

## Pairs plot visualization of clusters statistics

### Description

Graphical representation of cluster statistics, featuring pairwise correlations in the upper panel.

### Usage

    plotStatistics(clusters, corMethod = 'spearman', lower =
    panel.smooth, ...)

### Arguments

`clusters` | GRanges object containing individual clusters as identified by the getClusters function
`corMethod` | A character defining the correlation coefficient to be computed. See the help page of the `cor` function for possible options. Default is "spearman". Hence, rank-based Spearman's correlation coefficients are computed
`lower` | A function compatible with the `lower` panel argument of the `pairs` function
`...` | Additional parameters to be passed to the `pairs` function

### Value

called for its effect

### Author(s)

Federico Comoglio

### See Also

`getClusters`

### Examples

    require(BSgenome.Hsapiens.UCSC.hg19)

    data( model, package = "wavClusteR" )

    filename <- system.file( "extdata", "example.bam", package = "wavClusteR" )
    example <- readSortedBam( filename = filename )
    countTable <- getAllSub( example, minCov = 10, cores = 1 )
    highConfSub <- getHighConfSub( countTable, supportStart = 0.2, supportEnd = 0.7, substitution = "TC" )
    coverage <- coverage( example )
    clusters <- getClusters( highConfSub = highConfSub,
                             coverage = coverage,
                             sortedBam = example,
    	                 method = 'mrn',
    	                 cores = 1,
    	                 threshold = 2 )

    fclusters <- filterClusters( clusters = clusters,
    		             highConfSub = highConfSub,
            		     coverage = coverage,
    			     model = model,
    			     genome = Hsapiens,
    		             refBase = 'T',
    		             minWidth = 12 )
    plotStatistics( clusters = fclusters )

[Package wavClusteR version 2.12.1 Index]