R/PlotIsotopePattern.R

In BioAlvaro/ProteoMS: Quality Control of Protemics Data

#' Plot Isotope Pattern and Isotope Pattern Sequenced
#'
#' @param MQCombined Object list containing all the files from the MaxQuant
#' output. It is the result from using \code{make_MQCombined}.
#' @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 position_dodge_width Position of the columns within each others.
#' @param palette The palette from the Package RColorBrewer. By default is
#' 'Set2'.
#'
#' @return Returns a plot Isotope Pattern and Isotope Pattern Sequenced.
#' @export
#'
#' @examples
#' MQPathCombined <- system.file('extdata/combined/', package = 'MQmetrics')
#' MQCombined <- make_MQCombined(MQPathCombined)
#' PlotIsotopePattern(MQCombined)
#'
PlotIsotopePattern <- function(MQCombined,
                            long_names = FALSE,
                            sep_names = NULL,
                            position_dodge_width=1,
                            palette = 'Set2'){

    summary <- MQCombined$summary.txt

    `Isotope patterns sequenced` <- `Isotope Patterns Sequenced` <-  NULL
    value <- variable <- `Isotope patterns`  <- `Isotope Patterns` <- NULL
    Experiment <- NULL

    MaxQuant_version <- MQCombined$parameters$Value[
        MQCombined$parameters$Parameter == 'Version']

    #Detect MaxQuant Version to read column names accordingly.

    if (base::startsWith(MaxQuant_version, '1'))  {

        a <- summary %>% select(c(Experiment,
                                  `Isotope Patterns`,
                                  `Isotope Patterns Sequenced`))

    } else{
        a <- summary %>% select(c(Experiment,
                                  `Isotope patterns`,
                                  `Isotope patterns sequenced`))
    }

    a_melt <- melt(a, id.vars = 'Experiment' )





    b <- ggplot(a_melt, aes(x=Experiment,
                            y = value,
                            group = variable,
                            fill= variable))+
        geom_bar(stat = 'identity',
                colour='black',
                position = position_dodge(width = position_dodge_width))+
        theme_bw()+
        ylab('Frequency Isotope Patterns')+
        ggtitle('Isotope Patterns detected and sequenced')+
        scale_fill_brewer(palette = palette)+
        theme(legend.position = 'bottom')+
        labs(fill = element_blank())

    if (long_names == TRUE) {
        b + scale_x_discrete(labels = function(x) {
                stringr::str_wrap(gsub(sep_names," ", x),3)})
    }  else{
        b
    }

}