plotHistone: LocusExplorer - ENCODE histone track plot

In oncogenetics/oncofunco: Custom function for Oncogenetics team

LocusExplorer - ENCODE histone track plot

Description

ENCODE Histone plot for LocusExplorer. H3K27Ac Mark (Often Found Near Active Regulatory Elements) on 7 cell lines from ENCODE http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRegMarkH3k27ac/

Usage

plotHistone(
  folder = NULL,
  file = c("wgEncodeBroadHistoneGm12878H3k27acStdSig.bigWig",
    "wgEncodeBroadHistoneH1hescH3k27acStdSig.bigWig",
    "wgEncodeBroadHistoneHsmmH3k27acStdSig.bigWig",
    "wgEncodeBroadHistoneHuvecH3k27acStdSig.bigWig",
    "wgEncodeBroadHistoneK562H3k27acStdSig.bigWig",
    "wgEncodeBroadHistoneNhekH3k27acStdSig.bigWig",
    "wgEncodeBroadHistoneNhlfH3k27acStdSig.bigWig"),
  name = c("GM12878", "H1-hESC", "HSMM", "HUVEC", "K562", "NHEK", "NHLF"),
  colour = c("#FF1F1F", "#FFB41F", "#2ADFAF", "#1FB4FF", "#1F1FFF", "#B41FFF",
    "#FF1FB4"),
  alpha = 0.7,
  chr = NULL,
  xStart = NULL,
  xEnd = NULL,
  pad = TRUE,
  title = NULL
)

Arguments

folder	folder path for bigWig files
file	bigWig file(s) names, defaults to encode filenames.
name	defaults to encode names: c("GM12878","H1-hESC","HSMM","HUVEC","K562","NHEK","NHLF")
colour	colour for bigWig files, defaults to encode colours: c("#FF1F1F","#FFB41F","#2ADFAF","#1FB4FF","#1F1FFF","#B41FFF","#FF1FB4")
alpha	transparency for overlayed tracks, default 0.7.
chr, xStart, xEnd	subset bigWig, chromosome number, postion start and end.
pad	Default is TRUE, to align plots pad strings with spaces, using oncofunco::strPadLeft().
title	character string for plot title. Default is NULL, i.e.: no plot title.

Value

a ggplot object

Author(s)

Tokhir Dadaev

oncogenetics/oncofunco documentation built on March 9, 2024, 5:23 p.m.