R/plot_coeff.R

In ChristofSeiler/CytoGLMM: Conditional Differential Analysis for Flow and Mass Cytometry Experiments

#' Helper function to plot regression coeffcient
#'
#' @import ggplot2
#' @import tibble
#' @import magrittr
#' @import dplyr
#' @importFrom stats median quantile
#' @importFrom rlang .data
#'
#' @param tb A data frame
#' @param title_str Title string for summary plot
#' @param title_str_right Title for bootstrap sample plot
#' @param xlab_str Label on x-axis
#' @param redline Point on x-axis to draw the red line
#' @param order Order the markers according to the mangintute of the
#'   coefficients
#' @param separate Plot both summary and bootstrap samples
#' @return \code{\link[ggplot2]{ggplot2}} object or list of two objects if
#'   separate is true
#'
plot_coeff <- function(tb, title_str, title_str_right, xlab_str, redline = 0,
                      order = FALSE, separate = FALSE) {

  tb$run %<>% as.factor

  # median over seeds
  tb_summary <- tb %>%
    group_by(.data$protein_name) %>%
    summarize(
      coeff_median = median(.data$coeff),
      min_median = quantile(.data$coeff, probs = 0.05),
      max_median = quantile(.data$coeff, probs = 0.95)
    )
  if(order) {
    ind <- sort.int(tb_summary$coeff_median,index.return=TRUE)$ix
    reordered_names <- tb_summary$protein_name[ind]
    tb_summary$protein_name %<>% factor(levels = reordered_names)
    tb$protein_name %<>% factor(levels = reordered_names)
  }

  # plot all bootstrap runs
  pall <- ggplot(tb, aes(x = .data$coeff, y = .data$protein_name,
                         color = .data$protein_name)) +
    geom_vline(xintercept = redline,color = "red") +
    geom_jitter(size = 1, width = 0.001, alpha = 0.5) +
    ggtitle(title_str) +
    xlab(xlab_str) +
    theme(legend.position="none",
          axis.title.y = element_blank())

  # plot summary
  psummary <- ggplot(tb_summary,
                     aes(x = .data$coeff_median, y = .data$protein_name)) +
    geom_vline(xintercept = redline, color = "red") +
    geom_point(size = 2) +
    geom_errorbarh(aes(xmin = .data$min_median, xmax = .data$max_median)) +
    ggtitle(title_str_right) +
    xlab(xlab_str) +
    theme(axis.title.y = element_blank())

  # combine
  if(separate) {
    return(list(pall=pall,psummary=psummary))
  } else {
    psummary
  }

}