plotStatistics: Pairs plot visualization of clusters statistics

Description Usage Arguments Value Author(s) See Also Examples

View source: R/plotStatistics.R

Description

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

Usage

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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

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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, 
	                        threshold = 2 ) 

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

wavClusteR documentation built on Nov. 8, 2020, 6:54 p.m.