R: Pairs plot visualization of clusters statistics

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

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 2.22.0 Index]