stateProfile {erma} | R Documentation |
Create a ggplot2 visualization of chromatin states over genomic addresses for a family of cell types managed in an ErmaSet instance.
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)
ermaset |
instance of |
symbol |
gene symbol resolvable in |
upstream, downstream |
parameters passed to |
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 |
if useShiny is FALSE, an instance of c("gg", "ggplot") is returned
ermaset = makeErmaSet() # set useShiny=TRUE for interactive display csProfile(ermaset[,1:5], "CD28")