stateProfile: create a ggplot2 visualization of chromatin states over...

In erma: epigenomic road map adventures

Description

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

Usage

stateProfile(ermaset, symbol = "IL33", upstream = 2000, 
   downstream = 200, ctsize = 10, 
   shortCellType = TRUE, tsswidth=3 )
stateProf(ermaset, shortCellType=TRUE, ctsize=10, iniSym="IL7R")
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
iniSym	a character(1) gene symbol
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

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

erma documentation built on Nov. 8, 2020, 5:39 p.m.