R/tidyHeatmap-package.R

In tidyHeatmap: A Tidy Implementation of Heatmap

#' tidyHeatmap: A Tidy Implementation of Heatmap
#'
#' @description
#' tidyHeatmap is a package that introduces tidy principles to the creation of
#' information-rich heatmaps. This package uses ComplexHeatmap as graphical engine.
#' The goal of this package is to interface a tidy data frame with this powerful
#' tool. Some of the advantages are: Row and/or columns colour annotations are easy
#' to integrate just specifying one parameter (column names). Custom grouping of
#' rows is easy to specify providing a grouped tbl. For example: df %>% group_by(...).
#' Labels size adjusted by row and column total number. Default use of Brewer and
#' Viridis palettes.
#'
#' @details
#' The tidyHeatmap package provides a tidy interface to create information-rich
#' heatmaps using the powerful ComplexHeatmap engine. The package integrates
#' seamlessly with the tidyverse ecosystem, allowing you to use familiar dplyr
#' and tidyr verbs.
#'
#' The main functions and methods are:
#'
#' \itemize{
#' \item \code{\link{heatmap}} - Create a heatmap from a tidy data frame
#' \item \code{\link{annotation_group}} - Add group annotation strips
#' \item \code{\link{annotation_tile}} - Add tile annotations
#' \item \code{\link{annotation_point}} - Add point annotations
#' \item \code{\link{annotation_bar}} - Add bar annotations
#' \item \code{\link{annotation_numeric}} - Add numeric annotations
#' \item \code{\link{annotation_line}} - Add line annotations
#' \item \code{\link{layer_text}} - Add text layers
#' \item \code{\link{layer_point}} - Add point layers
#' \item \code{\link{layer_square}} - Add square symbol layers
#' \item \code{\link{layer_diamond}} - Add diamond symbol layers
#' \item \code{\link{layer_arrow_up}} - Add arrow up symbol layers
#' \item \code{\link{layer_arrow_down}} - Add arrow down symbol layers
#' \item \code{\link{layer_asterisk}} - Add asterisk symbol layers
#' \item \code{\link{layer_star}} - Add star symbol layers
#' \item \code{\link{get_heatmap_data}} - Extract matrix and dendrograms from heatmap
#' \item \code{\link{as_ComplexHeatmap}} - Convert to ComplexHeatmap object
#' \item \code{\link{save_pdf}} - Save heatmap to PDF
#' \item \code{\link{scale_robust}} - Robust scaling function
#' \item \code{\link{split_columns}} - Split columns in heatmap
#' }
#'
#' The package uses a pipe-friendly syntax that allows you to build complex
#' heatmaps by adding layers of annotations and customizations step by step.
#'
#' For detailed information on usage, see the package vignette, by typing
#' \code{vignette("introduction", package = "tidyHeatmap")}.
#'
#' The code can be viewed at the GitHub repository:
#'
#' \url{https://github.com/stemangiola/tidyHeatmap}
#'
#' @references
#' Mangiola, S. and Papenfuss, A.T., 2020. "tidyHeatmap: an R package for
#' modular heatmap production based on tidy principles." Journal of Open Source Software,
#' 5(52), 2472. \doi{10.21105/joss.02472}
#'
#' Gu, Z., Eils, R., and Schlesner, M. 2016. "Complex heatmaps reveal patterns
#' and correlations in multidimensional genomic data." Bioinformatics, 32(18), 2847-2849.
#'
#' @seealso
#' Useful links:
#' \itemize{
#'   \item \url{https://github.com/stemangiola/tidyHeatmap}
#'   \item Report bugs at \url{https://github.com/stemangiola/tidyHeatmap/issues}
#' }
#'
#' @author Stefano Mangiola
#'
#' @docType package
#' @name tidyHeatmap-package
#' @aliases tidyHeatmap
#' @keywords internal
"_PACKAGE"