plotRegion: Plot regions

Description

A function to plot regions

Usage

"plotRegion"(object,
gts,sampleData,groupData,summariseBy,
colourBy,lineBy,groupBy,
plotregion,outliers,freeScale)
"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

sampleData

Dataframe of metadata for sample

groupData

Dataframe of metadata for groups

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

plotregion

region to plot. For combined plots with style "region", may be "start" or "end" to show full resolution of plot of edges.

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

Examples

Run this code

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

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