mergeSummaryPlot: Plot summarized results of the different binding site merging...

In ZarnackGroup/BindingSiteFinder: Binding site defintion based on iCLIP data

Plot summarized results of the different binding site merging and filtering steps

Description

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.

Usage

mergeSummaryPlot(
  object,
  select = c("all", "filter", "inputRanges", "minClSites", "mergeCrosslinkSites",
    "minCrosslinks", "centerIsClSite", "centerIsSummit"),
  ...
)

Arguments

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

Details

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.

Value

a plot of type ggplot after the makeBindingSites function was run

See Also

makeBindingSites

Examples

# 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)
mergeSummaryPlot(l, width = 20)

ZarnackGroup/BindingSiteFinder documentation built on Nov. 24, 2024, 10:41 a.m.