R/generateReport.R

In BioAlvaro/MQmetrics: Quality Control of Protemics Data

#' Generates a report including all the plots of MQmetrics.
#'
#' @param MQPathCombined The directory to the "combined" folder where the
#'  MaxQuant results are stored.
#'
#' @param output_dir The directory where the results will be stored. By default
#'  is the working directory.
#'
#' @param name_output_file The name of the report generated.
#'
#' @param remove_contaminants Whether or not to remove contaminants,
#' reverse and identified by one one peptide.
#'
#' @param log_base The logarithmic scale for the intensity. Default is 2.
#'
#' @param long_names If TRUE, samples having long names will be considered, and
#'  the name will be split by sep_names. By default = FALSE.
#'
#' @param sep_names If long_names is TRUE, sep_names has to be selected. Samples
#'  names will be split. By default is NULL.
#'
#' @param intensity_type The type of intensity of interest. Values: 'Intensity'
#'  or 'LFQ'. Default = 'Intensity'.
#'
#' @param palette The palette from the Package RColorBrewer.
#' By default is 'Set2'.
#'
#' @param UniprotID Uniprot ID of the protein of interest.
#' \code{PlotProteinCoverage()}.
#'
#' @param segment_width Width of the segments to improve visualization.
#' Default is 1. (PlotProteinCoverage).
#'
#' @param show_shade Creates a shade showing where the \code{percent_proteins}
#' are. Default is TRUE. \code{PlotAllDynamicRange(),
#' PlotCombinedDynamicRange()}.
#'
#' @param percent_proteins  Determines the percentage for the show_shade
#' parameter. Default is 0.90 (90\% of the proteins).
#' \code{PlotAllDynamicRange(),  PlotCombinedDynamicRange()}.
#'
#' @param show_calibrated_rt  If TRUE, it will also show the calibrated
#' retention time of each iRT peptide. By default = FALSE. \code{PlotiRT()}.
#'
#' @param tolerance Error maximum to find the iRT peptides by m/z value.
#'  By default is 0.001.
#' @param show_max_value If TRUE, it will show the max TIC value of each sample.
#'  \code{PlotTotalIonCurrent()}.
#'
#' @param peptides_modified Minimum number of peptides modified. Default  is 5.
#' \code{PlotPTM()}.
#'
#' @param show_median If true it will show the median of each group, as a red
#'  dashed line.By default is TRUE. \code{PlotHydrophobicity()}.
#'
#' @param size_median The width of the median line in the plots.
#'
#' @param binwidth Selects the binwidth of the histogram. By default = 0.2.
#' \code{PlotHydrophobicity()}.
#'
#' @param plot_unmodified_peptides If TRUE, it will show the Unmodified
#' peptides. \code{PlotPTM()}.
#'
#' @param aggregate_PTMs If TRUE, same PTM that occur multiple times in the
#'  same peptides,  will be aggregated together.
#'
#' @param combine_same_residue_ptms Combine the PTMs that happen in the same
#' residue such as Dimethyl (KR), Trimethyl (KR) into only one group:
#' Methyl (KR).
#'
#' @param PTM_of_interest Post-Translation Modification of interest. It is
#' important they are defined exactly as MaxQuant does:
#' Examples:
#' 'Oxidation (M)', 'Acetyl (Protein N-term)', 'Unmodified', etc.
#'
#' @param plots_per_page Establish the maximum number of plots per page.
#'
#'
#' @return A pdf document with all the results of MQmetrics package.
#'
#'
#' @export
#'
#' @examples
#' \dontrun{
#' MQPathCombined <- system.file('extdata/combined/', package = 'MQmetrics')
#' generateReport(MQPathCombined)
#' }
#'
generateReport = function(MQPathCombined,
                        output_dir = getwd(),
                        name_output_file = "MQmetrics_report.pdf",
                        remove_contaminants = TRUE,
                        log_base = 2,
                        long_names = FALSE,
                        sep_names = NULL,
                        intensity_type = 'Intensity',
                        palette = 'Set2',
                        UniprotID = NULL,
                        segment_width = 1,
                        show_shade = TRUE,
                        percent_proteins = 0.90,
                        show_calibrated_rt = FALSE,
                        tolerance = 0.001,
                        show_max_value = TRUE,
                        peptides_modified = 1,
                        show_median = TRUE,
                        size_median = 1.5,
                        binwidth = 0.1,
                        plot_unmodified_peptides = FALSE,
                        aggregate_PTMs = TRUE,
                        combine_same_residue_ptms = TRUE,
                        PTM_of_interest = 'Oxidation (M)',
                        plots_per_page = 5){

    #Determine the template
    input = system.file("rmd/template_report.Rmd", package="MQmetrics")

    rmarkdown::render(
        input = input,
        params = list(
            input_dir = MQPathCombined,
            remove_contaminants = remove_contaminants,
            log_base = log_base,
            long_names = long_names,
            sep_names = sep_names,
            intensity_type = intensity_type,
            palette = palette,
            UniprotID = UniprotID,
            segment_width = segment_width,
            show_shade = show_shade,
            percent_proteins = percent_proteins,
            show_calibrated_rt = show_calibrated_rt,
            tolerance = tolerance,
            show_max_value = show_max_value,
            peptides_modified = peptides_modified,
            show_median = show_median,
            size_median = size_median,
            binwidth = binwidth,
            plot_unmodified_peptides = plot_unmodified_peptides,
            aggregate_PTMs = aggregate_PTMs,
            combine_same_residue_ptms = combine_same_residue_ptms,
            PTM_of_interest = PTM_of_interest,
            plots_per_page = plots_per_page),
        output_file = name_output_file,
        output_dir = output_dir,
        clean = TRUE)
}