plotRegulome

Description

plotRegulome is an R package that integrates different types of genomic and epigenomic data into the Islet Regulome Browser characteristic plot.

For a detailed description of all plot elements you can visit isletregulome.com and go to Info > Description of the plot or read the package vignette (see below).

How to install

To install the current version:

devtools::install_github("mireia-bioinfo/plotRegulome", 
                         build_opts = c("--no-resave-data", 
                                        "--no-manual"),
                         build_vignettes = TRUE)

To install the development version:

devtools::install_github("mireia-bioinfo/plotRegulome", 
                         ref="devel",
                         build_opts = c("--no-resave-data", 
                                        "--no-manual"),
                         build_vignettes = TRUE)

Required packages

• CRAN
  • scales
  • ggrepel
  • dplyr
  • cowplot
  • ggplot2
  • Hmisc
• Bioconductor
  • GenomicRanges
  • regioneR

Quick start

library(plotRegulome)

## Download IRB database
dir <- "~/data/"
path <- downloadIRB(output_dir=dir) # Download IRB data, returns path for database

## Define parameters for plotting
coordinates <- "chr5:50678921-51318155"
snps_dataset <- "diagram"
contacts_dataset <- "ISL1"
maps_dataset <- "openChromatinClasses"
cluster_dataset <- "enhancerClusters"
tfs_dataset <- "adult"

## Call ploRegulome function
plotRegulome(coordinates=coordinates,
             snps_dataset=snps_dataset,
             contacts_dataset=contacts_dataset,
             maps_dataset=maps_dataset,
             cluster_dataset=cluster_dataset,
             tfs_dataset=tfs_dataset,
             path=path)

More information on datasets and plotting with plotRegulome can be found in the package vignette:

vignette("using_plotRegulome", package="plotRegulome")