create a ggplot2 visualization of chromatin states over genomic addresses for a family of cell types managed in an ErmaSet instance

Description

Create a ggplot2 visualization of chromatin states over genomic addresses for a family of cell types managed in an ErmaSet instance.

Usage

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stateProfile(ermaset, symbol = "IL33", upstream = 2000, 
   downstream = 200, ctsize = 10, 
   shortCellType = TRUE, tsswidth=3 )
stateProf(ermaset, shortCellType=TRUE, ctsize=10)
csProfile(ermaset, symbol, upstream = 2000, downstream = 200,
                 useShiny = FALSE, ctsize = 10, shortCellType = TRUE,
                 tsswidth = 3)

Arguments

ermaset

instance of ErmaSet-class

symbol

gene symbol resolvable in Homo.sapiens

upstream, downstream

parameters passed to promoters to limit region to view

ctsize

font size for cell type labels

shortCellType

logical, if FALSE, full cell type labels are used, otherwise ad hoc abbreviations are used for facet labeling

useShiny

logical; if TRUE, shiny app is run permitting interactive selection of gene, and scope of view

tsswidth

width in base pairs of the base of a black rectangle used to depict location of transcription start site

Value

if useShiny is FALSE, an instance of c("gg", "ggplot") is returned

Examples

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ermaset = makeErmaSet()
# set useShiny=TRUE for interactive display
csProfile(ermaset[,1:5], "CD28")