R/package.R

In NGCHM: 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.
#'
#' Note:
#'   - `chmNew()` requires **git** to be installed.
#'   - `chmExportToFile()`, `chmExportToHTML()`, and `chmExportToPDF()` require
#'      **Java 11** and the **[NGCHMSupportFiles](https://github.com/MD-Anderson-Bioinformatics/NGCHMSupportFiles)**
#'      package. The NGCHMSupportFiles package
#'      can be installed with: \cr\cr
#'      \code{install.packages('NGCHMDemoData', } \cr
#'      \code{repos = c('https://md-anderson-bioinformatics.r-universe.dev',} \cr
#'      \code{'https://cloud.r-project.org'))}
#'
#' @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
#'
#' @import htmltools
#'
#' @examples
#' # Examples using `chmNew()` require git to be installed.
#' # The NGCHMSupportFiles package is required by chmExportToFile and chmExportToPDF
#' # The NGCHMDemoData package is used to create a demo NGCHM
#' \dontrun{
#'   if (requireNamespace("NGCHMSupportFiles", quietly = TRUE)) {
#'     if (requireNamespace("NGCHMDemoData", quietly = TRUE)) {
#'       library(NGCHMSupportFiles)
#'       library(NGCHMDemoData)
#'       data(TCGA.GBM.EXPR, package = "NGCHMDemoData")
#'       chm1 <- chmNew("gbm", TCGA.GBM.EXPR[1:50, 1:50],
#'         rowAxisType = "bio.gene.hugo",
#'         colAxisType = "bio.tcga.barcode.sample.vial.portion.analyte.aliquot"
#'       )
#'       chmExportToFile(chm1, tempfile("gbm", fileext = ".ngchm"))
#'       chmExportToPDF(chm1, tempfile("gbm", fileext = ".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)
#' }
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