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Separate reference and comparison gene sets

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This commit is contained in:
Elias Projahn 2022-08-18 09:02:53 +02:00
parent 7f0090620b
commit e9033883a5
5 changed files with 28 additions and 19 deletions
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19
R/app.R
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@ -1,13 +1,14 @@
#' Run the application server.
#'
#' @param gene_sets A list of predefined gene sets. This should be a named list
#' containing vectors of gene IDs for each set. The names will be used to
#' present the gene set throughout the user interface. You have to provide *at
#' least one gene set* which will be selected as the initial reference gene
#' set.
#' @param reference_gene_sets A list of predefined gene sets to be used as
#' reference genes. This should be a named list containing vectors of gene IDs
#' for each set. You have to provide *at least one gene set* which will be
#' selected as the initial reference gene set.
#' @param species_sets A list of predefined species sets. This should be a named
#' list containing vectors of species IDs for each set. The names will be used
#' to present the species set throughout the user interface.
#' @param comparison_gene_sets A named list of predefined gene sets to be used
#' as comparison genes.
#' @param locked Whether the application should be locked and prohibit
#' performing custom analyses. If this is set to `TRUE`, only the predefined
#' gene and species sets are available for customizing the analysis. This may
@ -16,12 +17,13 @@
#' @param port The port to serve the application on.
#'
#' @export
run_app <- function(gene_sets,
run_app <- function(reference_gene_sets,
species_sets = NULL,
comparison_gene_sets = NULL,
locked = FALSE,
title = "Gene Position Analysis",
port = 3464) {
stopifnot(!is.null(gene_sets) & !is.null(gene_sets[[1]]))
stopifnot(!is.null(reference_gene_sets) & !is.null(reference_gene_sets[[1]]))
# These function calls make the required java scripts available.
shinyjs::useShinyjs()
@ -29,8 +31,9 @@ run_app <- function(gene_sets,
# Bundle of global options to redue broilerplate.
options <- list(
gene_sets = gene_sets,
reference_gene_sets = reference_gene_sets,
species_sets = species_sets,
comparison_gene_sets = comparison_gene_sets,
locked = locked,
title = title
)