R/plot_VK_25perc_groups.R

In robertyoung3/MSanalyzeNOM: Utilities for Analyzing Complex Natural Organic Matter (NOM) Mixtures After Formula Assignment

#' plot_VK_25perc_groups
#'
#' This function makes a traditional van Krevelen diagram (H/c vs. O/C). This
#' plot shows the distribution of the assigned formulas as a function of
#' elemental ratios, and shows the intensities of the detected ions by their
#' percent contribution to total assigned abundance.
#'
#' The area above the horizontal line at H/C = 1.5 is designated as the
#' aliphatic region in accordance with D'Andrilli et al. 2015 and Lv et al.
#' 2017. The area below the diagonal line from H/C = 1.1 is designated as the
#' aromatic region based on a modified aromaticity index >= 0.5 in accordance
#' with Koch & Dittmar 2006.
#'
#' @param data a tibble containing the following column names: "HtoC", "OtoC",
#'   "group_25perc" (from the get_25perc_groups() function), and "rel_abund"
#' @param plot_title a character string containing the sample name
#' @param panel a logical value specifying whether a panel will be used (default
#'   = FALSE)
#' @param var_panel a character string containing the column name specifying the
#'   factor variable to be used for faceting
#' @param num_col an integer specifying the number of panel columns (default =
#'   2)
#'
#' @importFrom rlang .data
#' @importFrom ggplot2 aes element_text
#'
#' @export
plot_VK_25perc_groups <- function(data, plot_title = "", panel = FALSE,
                                  var_panel, num_col = 2) {
  # plotting highest values on top
  data <- data %>%
    dplyr::arrange(.data$rel_abund)

  # RColorBrewer::display.brewer.pal(n = 9, name = "GnBu")
  # RColorBrewer::brewer.pal(n = 9, name = "GnBu")
  # assign colors to levels
  blueGreenPalette <- c("#084081", "#4EB3D3", "#A8DDB5", "#E0F3DB")
  names(blueGreenPalette) <- levels(.data$group_25perc)

  #create plot
  VK <- ggplot2::ggplot(data, aes(x = .data$OtoC, y = .data$HtoC)) +
    ggplot2::geom_point(aes(color = .data$group_25perc), size = 2, na.rm = TRUE, alpha = 0.8) +
    ggplot2::scale_color_manual(name = "Ranked by\n% Abund.", values = blueGreenPalette) +
    ggthemes::theme_tufte(base_size = 14, base_family = "sans") +
    ggplot2::theme(plot.title = element_text(size = 16, face = "bold"),
                   legend.title = element_blank(),
                   legend.text = element_text(size = 12),
                   strip.text = element_text(size = 14, face = "bold"),
                   axis.title = element_text(face = "bold")) +
    ggplot2::guides(color = ggplot2::guide_legend(override.aes = list(size = 4))) +
    ggplot2::ggtitle(plot_title) +
    ggplot2::labs(x = "O/C", y = "H/C") +
    ggplot2::scale_x_continuous(limits = c(0, 1.5), breaks = seq(0.0, 1.2, by = 0.3)) +
    ggplot2::scale_y_continuous(limits = c(0, 2.5), breaks = seq(0.0, 2.5, by = 0.5)) +
    ggplot2::geom_hline(yintercept = 1.5) +
    # arrow: label = "\u2192 ALIPH"
    ggplot2::geom_abline(intercept = 1.1, slope = -0.44) +
    ggplot2:: annotate("text", x = 1.4, y = 1.6, label = "MOSTLY\nALIPH",
                       size = 3.5, vjust = "outward") +
    ggplot2:: annotate("text", x = 1.4, y = 0.37, label = "MOSTLY\nAROM",
                       size = 3.5, vjust = "outward")

  # implement panel
  if (panel == TRUE) {
    VK + ggplot2::facet_wrap(~ .data[[var_panel]], ncol = num_col)
  } else {
    VK
  }
}