bindingSiteCoveragePlot: Plot signal coverage of selected ranges

View source: R/coveragePlots.R

bindingSiteCoveragePlotR Documentation

Plot signal coverage of selected ranges

Description

Function plots the coverage of the CLIP data in the signal slot and plots it as coverage. The plot is centered around a given binding site, which can be selected by an index.

Usage

bindingSiteCoveragePlot(
  object,
  plotIdx,
  flankPos,
  shiftPos = NULL,
  mergeReplicates = FALSE,
  autoscale = FALSE,
  highlight = TRUE,
  showCentralRange = TRUE,
  customRange = NULL,
  customRange.name = "custom",
  customAnnotation = NULL,
  customAnnotation.name = "anno",
  title = NULL,
  colorPalette = NULL
)

Arguments

object

a BSFDataSet object

plotIdx

integer, index of the range to plot

flankPos

numeric, number of nucleotides by which the plotting frame is symmetrically extended

shiftPos

numeric, nucleotide positions by which the current plotting range should be shifted

mergeReplicates

logical, if replicates should be merge per condition (TRUE) or if every replicates should be shown separately (FALSE)

autoscale

logical, if y-axis should be scaled to the maximum for all replicates (TRUE), or not (FALSE)

highlight

logical, if the central range should be highlighted (TRUE), or not (FALSE)

showCentralRange

logical, if the central range should be shown (TRUE), or not (FALSE)

customRange

GenomicRanges, a custom range object to be shown underneath the coverage tracks

customRange.name

character, the name of the customRange track

customAnnotation

GenomicRanges or TxDb, a custom annotation for eg. gene, exons, etc. to be shown underneath the coverage tracks

customAnnotation.name

character, the name of the customAnnotation track

title

character, set plotting title

colorPalette

vector, hex colors used for the conditions

Value

an object of class GVIZ

See Also

BSFDataSet, BSFind

Examples

# load data
files <- system.file("extdata", package="BindingSiteFinder")
load(list.files(files, pattern = ".rda$", full.names = TRUE))

bindingSiteCoveragePlot(bds, plotIdx = 3, flankPos = 10)


ZarnackGroup/BindingSiteFinder documentation built on May 31, 2024, 3:29 a.m.