#' Clickme: use R to create interactive visualizations
#'
#' @section Package options:
#'
#' Clickme uses the following \code{options} to configure behaviour:
#'
#' \itemize{
#'
#' \item \code{clickme_templates_path}: path where the templates are stored
#'
#' \item \code{clickme_output_path}: path where the generated visualizations are saved (along with their dependencies)
#'
#' }
#' @docType package
#' @name clickme
#' @import methods yaml stringr knitr rjson
#' @author Nacho Caballero <\url{http://reasoniamhere.com}>
#' @references Full documentation: \url{https://github.com/nachocab/clickme/wiki};
NULL
# document datasets
#' 500 genes with the highest fold-change between two conditions
#'
#' A microarray dataset showing the expression values of 500 genes
#' The variables include:
#'
#' \itemize{
#' \item logFC. Fold change between two conditions (log2)
#' \item magnitude. Average magnitude of the change (log2)
#' \item P.Value. t-test-derived p-value
#' \item adj.P.Val. Benjamini-Hochberg corrected p-value
#' \item probe_name. Agilent v2 probe name
#' \item gene_name. Gene symbol
#' \item significance. -log10(adj.P.Val)
#' ...
#' }
#'
#' @docType data
#' @keywords datasets
#' @format A data frame with 500 rows and 7 variables
#' @name microarray
NULL
set_default_paths <- function() {
opts <- options()
opts_clickme <- list(
clickme_templates_path = file.path(system.file(package = "clickme"), "templates"),
clickme_output_path = file.path(system.file(package = "clickme"), "output")
)
# only set options that have not already been set by the user
to_set <- !(names(opts_clickme) %in% names(opts))
if(any(to_set)) options(opts_clickme[to_set])
}
.onLoad <- function(libname, pkgname) {
# I need to load it explicitly or I get an error when running in non-interactive mode
library(methods)
set_default_paths()
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.