R/psiplot-package.R

In kcha/psiplot: Generate plots of PSI values generated by vast-tools

#' Produce PSI and GE plots based on output from vast-tools
#'
#' \code{psiplot} is an R package for generating plots of percent spliced-in (PSI)
#' values of alternatively spliced exons. It requires input from
#' \href{https://www.github.com/vastgroup/vast-tools}{VAST-TOOLS}, an RNA-Seq
#' pipeline for alternative splicing analysis.
#'
#' @details
#' This package uses input data generated by vast-tools. A sample dataset
#' (\code{psi}, \code{crpkm} and \code{crpkm_counts}) and sample configuration file
#' (\code{config}) is provided.
#'
#' The main functions to generate plots is \code{\link{plot_event}} and
#' \code{\link{plot_expr}} for PSI and cRPKM values, respectively. Two other
#' functions, \code{\link{plot_multievent}} and \code{\link{plot_multi}}, allow
#' plotting of multiple events in scatterplots or heatmaps.
#'
#' \code{\link{plot_multi}} can be used to plot multiple events in the form
#' of a heatmap.
#'
#'See \code{vignette('psiplot-usage', package="psiplot")} for usage details.
#'
#' Report bugs and issues to \url{https://github.com/kcha/psiplot/issues}.
#'
#' @name psiplot
#' @docType package
#' @seealso \url{https://www.github.com/kcha/psiplot}
#' @seealso \url{https://www.github.com/vastgroup/vast-tools}
#' @seealso \url{https://www.vastdb.crg.eu}
#' @examples
#' library(psiplot)
#' plot_event(psi[1,])
#' plot_event(psi[1,], config=config, subg=FALSE)
#' plot_expr(crpkm[1,])
#' plot_expr(crpkm[1,], config=config)

NULL