#' Shiny gadget to upload groups and select contrasts
#'
#' @param eset ExpressionSet
#' @param gse_name GEO accession for the series.
#' @param prev Previous result of \code{diff_expr}. Used to allow rechecking previous selections.
#' @param app_dir Directory to shiny app. For local development use 'inst/select_contrasts'. Default is
#' in 'select_contrasts' sub directory of crossmeta package.
#' @inheritParams shiny::runGadget
#'
#' @return result of \link{setup_prev}. Used to specify sample groups and contrasts for differential expression analysis.
#' @keywords internal
#'
#' library(lydata)
#' # location of data
#' data_dir <- system.file("extdata", package = "lydata")
#'z
#' # gather GSE names
#' gse_name <- "GSE9601"
#'
#' # load previous analysis
#' eset <- load_raw(gse_name, data_dir)[[1]]
#' run_select_contrasts(eset, gse_name)
#'
run_select_contrasts <- function(eset,
gse_name,
prev = NULL,
app_dir = system.file('select_contrasts', package = 'crossmeta', mustWork = TRUE),
port = 3838) {
# pass arguments to app through options then run
shiny::shinyOptions(eset = eset, gse_name = gse_name, prev = prev)
# auto-reload if update app files
options(shiny.autoreload = TRUE)
shiny::runGadget(shinyAppDir(app_dir),port = port, viewer = browserViewer(), stopOnCancel = FALSE)
}
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