plotRegulome package

Plotting Islet Regulome data

By providing the coordinates and IRB datasets of interest, it will produce the characteristic Islet Regulome Broser plot.

plotRegulome(coordinates, snps_dataset = "", snps_col = "dark red",
  contacts_dataset = "", contacts_col = c(`0` = "grey", `3` = "blue",
  `5` = "dark orange"), maps_dataset = "", clusters_dataset = "",
  cluster_col = "dark green", tfs_dataset = "",
  tfs_col = "dark blue", genes_col = c(gene = "dark grey", spec =
  "darkorchid3", lnc = "black"), showLongestTranscript = TRUE,
  randomIRB = FALSE, genome = "hg19", path = "~/data/IRB/")

Arguments

coordinates	Either a GRanges object, data.frame or character string (i.e. chr11:17227951-17589050) indicating the coordinates for the region the user wants to plot.
snps_dataset	GWAS SNPs dataset name to use for the analysis. The value should be one of the defined below (column Dataset). Defaults to "", which will produce an empty plot. Name Dataset Reference 70KforT2D 70KforT2D S. Bonàs-Guarch et al. (2018) Diagram diagram A. P. Morris et al. (2012) Magic magic R. A. Scott et al. (2012)
snps_col	Color for the GWAS SNPs. Default: "dark red"
contacts_dataset	BaitID or bait gene name for the virtual 4C data (Miguel-Escalada et al. (2019)) to plot.
contacts_col	Named vector ("0", "3" and "5"), with the colors for each group of CHiCAGO contacts.
maps_dataset	Name of the chromatin maps to plot. The value should be one of the defined below (column Dataset). Defaults to "", which will produce an empty plot. Name Dataset Reference Adult Islets - Chromatin Classes chromatinClassesReduced Miguel-Escalada et al. (2019) Adult Islets - Chromatin Classes openChromatinClasses Pasquali et al. (2014) Pancreatic Progenitors progenitors Cebola et al. (2015) Adult Islets - Chromatin States chromatinStates Parker et al. (2013)
clusters_dataset	Name of the enhncer cluster data to plot. The value should be one of the defined below (column Dataset). Defaults to "", which will produce an empty plot. Name Dataset Reference Enhancer Hubs enhancerHubs Miguel-Escalada et al. (2019) Super Enhancers superEnhancers Miguel-Escalada et al. (2019) Enhancer Clusters enhancerClusters Pasquali et al. (2014) Stretch Enhancers stretchEnhancers Parker et al. (2013) COREs cores K. J. Gaulton et al. (2010)
cluster_col	Color for the clusters. Default: "dark green"
tfs_dataset	Name of the TF dataset to plot. The value should be one of the defined below (column Dataset). Defaults to "", which will produce an empty plot. Name Dataset Reference Adult Islets – Structural structure Miguel-Escalada et al. (2019) Pancreatic Progenitors progenitors Cebola et al. (2015) Adult Islets – Tissue-specific adult Pasquali et al. (2014)
tfs_col	Color for the TFs circle border.
genes_col	Named character vector ("gene", "lnc" and "spec") with the colors for each type of feture plotted in the gene annotation track.
showLongestTranscript	When plotting gene data, set to TRUE (default) if you want to reduce the number of transcripts by only plotting the longest transcript per gene. If set to FALSE, will plot all available transcripts.
randomIRB	Generate random combinations of IRB datasets.
genome	Character string indicating the genome for the coordinates. Default: hg19.
path	Path containing the genomes folder (for example "hg19"). Default: "~/data/IRB/"

Value

A ggplot2 object that can be plotted or saved with ggsave. Recomended device size in inches is: width=11, height=6

Details

See the README on GitHub

Examples

if (FALSE) {
    coordinates <- "chr5:131817301-131826490"
    snps_dataset <- "70KforT2D"
    contacts_dataset <- 570519 #183446
    maps_dataset <- "progenitors"
    clusters_dataset <- ""
    tfs_dataset <- ""
    path <- "~/data/IRB/"

    plotRegulome(coordinates=coordinates,
                 snps_dataset=snps_dataset,
                 contacts_dataset=contacts_dataset,
                 maps_dataset=maps_dataset,
                 clusters_dataset=clusters_dataset,
                 tfs_dataset=tfs_dataset,
                 path=path)
}