R/launchApp.R

In ComputationalProteomics/FusariumResponseInOatMethods: Interactively illustrate proteogenomics oat dataset

#' launches the shinyAppDemo app
#'
#' @export launchApp
#' @return shiny application object
#' @param query_proteins_arg_fp Argamak peptide assembly
#' @param query_proteins_bel_fp Belinda peptide assembly
#' @param search_fasta_fp Annotation BLAST database
#' @param rds_obj_fp List of SummarizedExperiment objects saved to RDS file
#' @import shiny SummarizedExperiment dplyr rlang
launchApp <- function(data_dir) {
    # query_proteins_arg_fp = "../../FusariumResponseInOatMethods_files/shiny_data/transcripts-shortid_fa_transdecoder-Arg-shortid_pep.fasta",
    # query_proteins_bel_fp = "../../FusariumResponseInOatMethods_files/shiny_data/transcripts-shortid_fa_transdecoder-Bel-shortid_pep.fasta",
    # search_fasta_fp = "../../FusariumResponseInOatMethods_files/shiny_data/search_protein.fasta",
    # rds_obj_fp = "../../FusariumResponseInOatMethods_files/shiny_data/combined_flat_ses.rds") {
    
    query_proteins_arg_fp <- sprintf("%s/%s", data_dir, "transcripts-shortid_fa_transdecoder-Arg-shortid_pep.fasta")
    query_proteins_bel_fp <- sprintf("%s/%s", data_dir, "transcripts-shortid_fa_transdecoder-Bel-shortid_pep.fasta")
    search_fasta_fp <- sprintf("%s/%s", data_dir, "search_protein.fasta")
    rds_obj_fp <- sprintf("%s/%s", data_dir, "combined_flat_ses.rds")
    
    shiny::shinyOptions(
        query_proteins_arg_fp = query_proteins_arg_fp,
        query_proteins_bel_fp = query_proteins_bel_fp,
        search_fasta_fp = search_fasta_fp,
        rds_obj_fp = rds_obj_fp
    )
    
    ggplot2::theme_set(cowplot::theme_cowplot())
    
    if (any(is.null(c(query_proteins_arg_fp, query_proteins_bel_fp, search_fasta_fp, rds_obj_fp)))) {
        stop(sprintf(
            "All four input files are required, obtained: \nquery_proteins_arg_fp: %s\nquery_proteins_bel_fp: %s\nsearch_fasta_fp: %s\nrds_obj_fp: %s",
            query_proteins_arg_fp, query_proteins_bel_fp, search_fasta_fp, rds_obj_fp
        ))
    }
    shinyApp(ui = ui, server = server)
}