mergeSummaryPlot {BindingSiteFinder} | R Documentation |
Bar charts produced for the different filter steps in the binding site
merging routine. Depending on the selected option (select
) all or
only a user defined filter can be shown.
mergeSummaryPlot( object, select = c("all", "filter", "inputRanges", "minClSites", "mergeCrosslinkSites", "minCrosslinks", "centerIsClSite", "centerIsSummit"), ... )
object |
a BSFDataObject, with the makeBindingSites function already run |
select |
one of "all", "filter", "inputRanges", "minCLSites", "mergeCrosslinkSites", "minCrosslinks", "centerIsClSite" or "centerIsSummit". Defines which parameter is selected for plotting. |
... |
further arguments passed to ggplot |
If object
is a single BSFDataObject a single coverage plot will be
drawn, whereas if it is a list of BSFDataObjects, then faceting is used to
make a plot for each list element.
a plot of type ggplot after the makeBindingSites
function was run
# load data files <- system.file("extdata", package="BindingSiteFinder") load(list.files(files, pattern = ".rda$", full.names = TRUE)) # plotting a single object bds0 <- makeBindingSites(object = bds, bsSize = 9, minWidth = 2, minCrosslinks = 2, minClSites = 1) mergeSummaryPlot(bds0) # plotting mulitple obejcts bds1 <- makeBindingSites(object = bds, bsSize = 9, minWidth = 2, minCrosslinks = 2, minClSites = 1, sub.chr = "chr22") bds2 <- makeBindingSites(object = bds, bsSize = 9, minWidth = 2, minCrosslinks = 2, minClSites = 3, sub.chr = "chr22") l = list(`1. bsSize = 3` = bds1, `2. bsSize = 9` = bds2) rangeCoveragePlot(l, width = 20)