R/krsa_violin_plot.R

In CogDisResLab/KRSA: KRSA: Kinome Random Sampling Analyzer

#' Generates violin plots based on peptides signals intensities
#'
#' Takes in the scaled dataset from krsa_scaleModel() and plot violin figures using ggplot2
#'
#' @param data the scaled dataset from krsa_scaleModel
#' @param peptides vector of peptides
#' @param facet_factor Column used to facet by. Will be used in facet_wrap(). Needs argument facet to be True.
#' @param facet boolean to facet the plot by a variable
#' @param samples (optional) a vector of sample names
#' @param groups (optional) a vector of group names
#' @param show_legend to show legend (default = FALSE)
#'
#'
#' @return ggplot figure
#'
#' @family plots
#'
#' @export
#'
#' @examples
#' TRUE
krsa_violin_plot <- function(data, peptides, facet_factor, facet = T, samples = NULL, groups = NULL, show_legend = F) {
    data %>%
        dplyr::filter(Peptide %in% peptides) %>%
        {
            if (!is.null(samples)) dplyr::filter(., SampleName %in% samples) else .
        } %>%
        {
            if (!is.null(groups)) dplyr::filter(., Group %in% groups) else .
        } %>%
        ggplot2::ggplot(ggplot2::aes(if (facet_factor == "Group") SampleName else Group, slope)) +
        ggplot2::geom_violin(ggplot2::aes(fill = Group), show.legend = show_legend) +
        ggplot2::geom_point(size = 1.5) +
        ggplot2::geom_line(ggplot2::aes(group = Peptide), alpha = 1 / 2) +
        ggplot2::labs(
            x = "",
            y = "Signal Intensity"
        ) +
        ggplot2::theme(axis.text.x = ggplot2::element_text(size = 6)) +
        ggplot2::theme_bw() -> gg

    if (facet == T) {
        gg + ggplot2::facet_wrap(facet_factor, scales = "free")
    } else {
        gg
    }
}