R/package.R

In bmbroom/NGCHMR: Utilities for Creating Next Generation Clustered Heat Maps

#' Next Generation Clustered Heat Map (NGCHM) Construction Library
#'
#' NGCHM provides tools for defining the contents of a new NGCHM,
#' and for compiling and installing it on a NGCHM server.
#'
#' Typical usage (see example) is to create a base NGCHM using chmNew; extend it with at
#' least one ngchmLayer; typically extend it further with an additional
#' ngchmLayer, row and column dendrograms, classification bars, and popup menu entries;
#' compile and install it on an available ngchmServer.
#'
#' @section Initialization:
#' When first loaded the NGCHM library reads configuration files in
#' the directories specified by the NGCHMCONFIGPATH environment variable.  This is
#' a colon (:) separated list of directory names.  If not set it defaults to
#' /etc/ngchm:/usr/local/ngchm:/opt/ngchm:$HOME/.ngchm.
#' See NGCHM-initialization for details.
#'
#' @seealso [chmNew()]
#' @seealso [chmAdd()]
#' @seealso [chmExportToFile()]
#' @seealso [chmExportToPDF()]
#' @seealso [chmSetCollection()]
#' @seealso [chmInstall()]
#' @seealso [ngchm-class]
#'
#' @docType package
#' @name NGCHM
#' @rdname NGCHM-package
#' @aliases NGCHM-package
#'
#' @examples
#' data(TCGA.BRCA.ExpressionData)
#' chm1 <- chmNew('brca', TCGA.BRCA.ExpressionData[1:50,1:50], rowAxisType='bio.gene.hugo', colAxisType='bio.tcga.barcode.sample.vial.portion.analyte.aliquot');
#'\dontrun{chmExportToFile(chm1, 'brca.ngchm');
#' chmExportToPDF(chm1, 'brca.pdf');
#'}
#'
#' mat <- matrix(rnorm(100),nrow=10)
#' rownames(mat) <- sprintf ("ABCA%d", 1:10)
#' colnames(mat) <- sprintf ("Sample%d", 1:10)
#' chm <- chmNew ('my-chm', mat)
#'\dontrun{chmSetCollection ('//server/collection')
#' chmInstall (chm)
#'}
NULL

#' Sample dataset containing RNA expression data from Affymetrix U133A chips
#' for TCGA Glioblastoma Multiforme samples.
#'
#' @name TCGA.BRCA.ExpressionData
#' @docType data
#' @keywords data
#'
#' @examples
#' data(TCGA.BRCA.ExpressionData)
#' sample.type <- 'bio.tcga.barcode.sample.vial.portion.analyte.aliquot'
#' chm <- chmNew ('my-brca-chm', TCGA.BRCA.ExpressionData, rowAxisType='bio.gene.hugo',
#'                 colAxisType=sample.type)
#'\dontrun{
#' chmMake ('my-server', chm)
#' chmInstall ('my-server', chm)
#'}
NULL