R/genes.R

#' Data linking genes and pathways.
#'
#' Table knownGene from track UCSC Genes was downloaded from the UCSC table
#' browser for the human genome assembly (hg18, May 2006) and filtered for a
#' selection of pathways associated with human metabolism was obtained from KEGG
#' PATHWAY database. Bioconductor package KEGG.db was used to provide mappings
#' between gene and pathway identifiers.
#'
#' @references Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS,
#' Goldman M, Barber GP, Clawson H, Coelho A, Diekhans M, Dreszer TR, Giardine
#' BM, Harte RA, Hillman-Jackson J, Hsu F, Kirkup V, Kuhn RM, Learned K, Li CH,
#' Meyer LR, Pohl A, Raney BJ, Rosenbloom KR, Smith KE, Haussler D, Kent WJ. The
#' UCSC Genome Browser database: update 2011. Nucleic Acids Res. 2010 Oct 18.
#' \url{http://genome.ucsc.edu/index.html?org=Human&db=hg19&hgsid=289810087}
#'
#' Marc Carlson, Seth Falcon, Herve Pages and Nianhua Li (). KEGG.db: A set
#' of annotation maps for KEGG. R package version 2.6.1.
#'
#' Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., and Tanabe, M.; KEGG for
#' integration and interpretation of large-scale molecular datasets. Nucleic
#' Acids Res. 40, D109-D114 (2012)
#'
#' Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes.
#' Nucleic Acids Res. 28, 27-30 (2000).
#' @examples
#' library(ggplot2)
#' library(RColorBrewer)
#' genes$chrom <- factor(genes$chrom, levels=c(paste("chr", 1:22, sep=""),
#'   "chrX", "chrY"))
#' ggparallel(
#'   list("path", "chrom"),
#'   text.offset = c(0.03, 0,-0.03),
#'   data = genes,
#'   width = 0.1,
#'   order = c(1, 0),
#'   angle = 0,
#'   color = "white",
#'   factorlevels =  c(sapply(unique(genes$chrom), as.character),unique(genes$path))
#' ) +
#'  scale_fill_manual(
#'    values = c(brewer.pal("YlOrRd", n = 9), rep("grey80", 24)),
#'    guide = "none"
#'  ) +
#'  scale_colour_manual(
#'    values = c(brewer.pal("YlOrRd", n = 9), rep("grey80", 24)),
#'    guide = "none"
#'  ) +
#'  coord_flip()
"genes"
heike/ggparallel documentation built on Sept. 14, 2017, 5:48 a.m.