R/normTableForExport.R

In Scavetta/complexomics: Complexome Profiling Analysis package

#' Convert Normalized Dataframe to Export format
#'
#' This is a convenient function for plotting
#'
#' @param labTab a dataframe
#' @param unlabTab a dataframe
#' @param comboTab a dataframe
#'
#' @importFrom stringr str_remove
#' @importFrom tidyr gather separate
#'
#' @return a dataframe
normTableForExport <- function(labTab, unlabTab, comboTab) {
    
    # Clean up labeled
    names(labTab) <- str_remove(names(labTab), "_.*$")
    max_frac <- max(suppressWarnings(as.numeric(names(labTab))), na.rm = TRUE)
    labTab$scenario <- "A"
    labTab$label <- TRUE
    labTab <- labTab[c("Protein Group Accessions", "Protein Descriptions", 
                        "scenario", "label", seq_len(max_frac))]
    
    # Clean up unlabeled
    names(unlabTab) <- str_remove(names(unlabTab), "_.*$")
    unlabTab$scenario <- "A"
    unlabTab$label <- FALSE
    unlabTab <- unlabTab[c("Protein Group Accessions", "Protein Descriptions", 
                            "scenario", "label", seq_len(max_frac))]
    
    # Clean up combined
    comboTab %>%
        gather("key", "value",
                -c(`Protein Group Accessions`, `Protein Descriptions`)) %>%
        separate("key", c("Fraction", "label"), "_") %>%
        spread(Fraction, "value") %>%
        mutate(scenario = "B",
                label = as.logical(label)) -> comboTab
    #comboTab <- comboTab[c("Protein Group Accessions", "Protein Descriptions", 
    #                        "scenario", "label", seq_len(max_frac))]
    
    return(labTab %>%
                bind_rows(unlabTab) %>%
                bind_rows(comboTab))
}