Plot regions

Description

A function to plot regions

Usage

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## 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

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