plotRegion: Plot regions

In soGGi: Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Genomic Intervals

Description

A function to plot regions

Usage

## S4 method for signature 'ChIPprofile'
plotRegion(object,
gts,sampleData,groupData,summariseBy,
colourBy,lineBy,groupBy,
plotregion,outliers,freeScale)

## S4 method for signature 'ChIPprofile'
plotRegion(object = "ChIPprofile", gts = NULL,
  sampleData = NULL, groupData = NULL, summariseBy = NULL,
  colourBy = NULL, lineBy = NULL, groupBy = NULL, plotregion = "full",
  outliers = NULL, freeScale = FALSE)

Arguments

object	A ChIPprofile object
gts	A list of character vectors or GRangesList
plotregion	region to plot. For combined plots with style "region", may be "start" or "end" to show full resolution of plot of edges.
groupData	Dataframe of metadata for groups
sampleData	Dataframe of metadata for sample
summariseBy	Column names from GRanges elementmetadata. Formula or character vector of column names to use to collapse genomic ranges to summarised profiles. summariseBy can not be used injustion with groups specified by gts argument.
colourBy	Character vector or formula of either column names from colData(object) containing sample metadata or character vector "group" to colour by groups in gts
lineBy	Character vector or formula of either column names from colData(object) containing sample metadata or character vector "group" to set line type by groups in gts
groupBy	Character vector or formula of either column names from colData(object) containing sample metadata or character "group" to colour by groups in gts
outliers	A numeric vector of length 1 containing proportion from limits to windsorise.]
freeScale	TRUE or FALSE to set whether ggplot 2 facets have their own scales. Useful for comparing multiple samples of differing depths without normalisation. Default is FALSE.

Value

A gg object from ggplot2

Author(s)

Thomas Carroll

Examples

data(chipExampleBig)
plotRegion(chipExampleBig[[2]])

soGGi documentation built on Nov. 8, 2020, 5:24 p.m.