R/isoplot_generic.R

In andreabz/pbratios: Processing Pb isotope ratio data

#' Customisable three-isotope plots.
#'
#' The function plots Pb isotope ratio data in a three-isotope diagram, calculates a regression line
#' and saves the plot in PDF, PNG and SVG formats.
#'
#' @import data.table
#' @import ggplot2
#' @import grid
#' @import scales
#' @import MASS
#' @import svglite
#'
#' @param data A data.table generated by \code{corr.mbf} function and subsetted to cointain only
#'   samples to be plotted in the three-isotope diagram. Data should contain the columns
#'   \code{Pb208207}, \code{Pb206207}, \code{Pb208206} and \code{Pb207206} with the  measured Pb
#'   isotope ratios for 208Pb/207Pb, 206Pb/207Pb, 208Pb/206Pb and 207Pb/206Pb, respectively.
#'
#' @param x,y The string \code{"Pb20x20y"} to be plotted on the x and y-axis. Default values are
#'   \code{"Pb208207"} and \code{"Pb206207"}, respectively.
#'
#' @param factor A factor within the data.table that can be used to differentiate data points with
#'   different colours. Default value is \code{NULL}.
#'
#' @param regression Logical. If \code{TRUE}, a regression line and its \eqn{R^2} value are added to
#'   the plot. Default is \code{FALSE}.
#'
#' @param save Logical. If \code{TRUE}, the plot is saved in the "output" folder with the file name
#'   "data_gen" in PDF, PNG and SVG formats.
#'
#' @return The function prints a three-isotope plot on screen. Additionally, if \code{save = TRUE},
#'   three files named "data_gen" are saved in the "output" folder with the file name "data_gen" in
#'   PDF, PNG and SVG formats.
#'
#' @examples
#' data(pm10nya)
#' isoplot_generic(pm10nya, save = FALSE)
#'
#' @seealso \code{\link{corr_mbf}} \code{\link{isoplot_pm10}}
#'
#' @export
isoplot_generic <- function(data,
                            x = "Pb208207",
                            y = "Pb206207",
                            factor = NULL,
                            regression = FALSE,
                            save = FALSE){

  # Preparing axis labels
  x.str <- as.character(x)
  y.str <- as.character(y)

  x.n <- gsub("[[:alpha:]]", "", x.str)
  y.n <- gsub("[[:alpha:]]", "", y.str)

  x.num <- gsub("([0-9]{3}).*", "\\1", x.n)
  y.num <- gsub("([0-9]{3}).*", "\\1", y.n)

  x.den <- gsub(".{3}([0-9]{3})", "\\1", x.n)
  y.den <- gsub(".{3}([0-9]{3})", "\\1", y.n)

  xlab <- bquote(phantom(.) ^ .(x.num) * Pb ~ "/" * phantom(.) ^ .(x.den) * Pb)
  ylab <- bquote(phantom(.) ^ .(y.num) * Pb ~ "/" * phantom(.) ^ .(y.den) * Pb)

  # Defining the plot
  p <- ggplot(data, aes_string(x = x, y = y)) +
    geom_point(aes_string(colour = factor)) +
    # Limits of the plot and breaks
    scale_x_continuous(breaks = pretty_breaks(n = 8)) +
    scale_y_continuous(breaks = pretty_breaks(n = 6)) +
    xlab(xlab) + ylab(ylab) +
    theme_linedraw() +
    theme(
      panel.grid.major = element_blank(),
      panel.grid.minor = element_blank(),
      legend.title = element_blank(),
      legend.justification = c(0, 1),
      legend.position = c(0.01, 0.99)
    )

  # Computing the regression line
  if (regression == FALSE) {

    p

  } else {

    yx <- as.formula(paste(y.str, x.str, sep = " ~ "))
    print(yx)
    lm.sum <- summary(lm(data = data, yx))
    r2 <- lm.sum$r.squared
    print(lm.sum)

    r2.text <- sprintf("%.3f", round(r2, 3))

    r2.note <- grobTree(textGrob(
      bquote(R ^ 2 * "=" ~ .(r2.text)), x = 0.98, y = 0.1, hjust = 1
    ))

    p <- p + geom_smooth(method = rlm, se = FALSE, colour = "black", size = 0.5) +
      annotation_custom(r2.note)

  }

  if (save == TRUE) {

    filename <- gsub("\\[.*?\\]", "\\1", deparse(substitute(data)))
    filename <- gsub("\\.", "", filename)

    if (dir.exists("output") == TRUE) {

    } else {
    dir.create("output")
    }

    ggsave(
    filename = paste0("output/", filename, "_gen", ".pdf"),
    plot = p, width = 13, height = 8.03, units = "cm", device = "pdf", dpi = 600)

    ggsave(
    filename = paste0("output/", filename, "_gen", ".png"),
    plot = p, width = 13, height = 8.03, units = "cm", device = "png", dpi = 600)

    ggsave(
    filename = paste0("output/", filename, "_gen", ".svg"),
    plot = p, width = 13, height = 8.03, units = "cm", device = "svg", dpi = 600)

    p

  } else {

    p

  }


}
# End of file