plotSizeDistribution {wavClusteR} | R Documentation |
Produce an histogram of cluster sizes
plotSizeDistribution( clusters, showCov = FALSE, ... )
clusters |
GRanges object containing individual clusters as identified by the getClusters function |
showCov |
logical, if TRUE a scatter plot of average cluster coverage vs. cluster size is shown along with a loess fit. Default is FALSE. |
... |
Additional parameters to be passed to the |
Called for its effect, returns a histogram.
Federico Comoglio
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 ) plotSizeDistribution(fclusters, breaks = 30, col = 'skyblue2')