R/spider_plot.R

In muhohl/geochem: Wrangling, Analysing, And Visualization Of Geochemical Data

#' Spider Plot faceted
#'
#' Produces spider plots highlighting different groups per facet and compares them
#' to the remaining groups.
#'
#' @param data
#' Dataframe
#' @param elements
#' Select the elements to include in the plot as vector.
#' @param group
#' Select the grouping of the data set as character variable. This needs to be the
#' name of a column in the data frame.
#' @param levels
#' Select sequence of elements.
#' @param ribbon
#' If TRUE the fourth and first quantile are summarised to a ribbon, if FALSE
#' single lines for those samples are plotted.
#' @param ncol
#' Number of facet columns.
#' @param ...
#' Arguments passed on to ggplot2::theme().
#'
#' @return
#' @export
#'
#' @examples
#'
#' @import magrittr
spider_plot <- function(data,
                        elements,
                        group,
                        levels = elements,
                        ribbon = TRUE,
                        ncol = NULL,
                        ...) {

    By_Group <- function(data, group, elements, levels) {
        quo_group <-  ggplot2::sym(group)
        data <- data %>% dplyr::select(elements)
        ncols <- ncol(data)
        data %>%
            tidyr::pivot_longer(2:ncols, names_to = "elements", values_to = "ppm") %>%
            dplyr::group_by(!! quo_group, elements) %>%
            dplyr::summarise(Median = stats::median(ppm, na.rm = TRUE)) %>%
            dplyr::mutate(elements = factor(elements,
                                     levels = levels))
    }

    By_Gather <- function(data, elements, levels) {
        data <- data %>% dplyr::select(elements)
        ncols <- ncol(data)
        data %>%
            dplyr::mutate(ID = 1: dplyr::n()) %>%
            tidyr::pivot_longer(2:ncols, names_to = "elements", values_to = "ppm") %>%
            dplyr::mutate(elements = factor(elements,
                                     levels = levels))
    }

    By_Gather_Ribbon <- function(data, group, elements, levels) {
        quo_group <- dplyr::sym(group)
        By_Gather(data = data,
                  elements = elements,
                  levels = levels) %>%
            dplyr::group_by(elements, !! quo_group) %>%
            dplyr::summarise(min = stats::quantile(ppm, na.rm = TRUE)[[2]],
                      max = stats::quantile(ppm, na.rm = TRUE)[[4]],
                      median = stats::median(ppm, na.rm = TRUE)) %>%
            dplyr::mutate(ID = 1: dplyr::n())
    }

    quo_group <- ggplot2::sym(group)

    data1 <- By_Group(data = data,
                      group = group,
                      elements = elements,
                      levels = levels)

    data2 <- data1
    data2 <- dplyr::rename(data2, "XXX" = 1)

    if (ribbon == FALSE) {

        spider_p <- By_Gather(data = data,
                  elements = elements,
                  levels = levels) %>%
            ggplot2::ggplot(ggplot2::aes(elements,
                       ppm,
                       group = ID,
                       color = !! quo_group)) +
            ggplot2::geom_line(alpha = 0.2) +
            ggplot2::geom_line(data = data2, ggplot2::aes(elements,
                                        Median,
                                        group = XXX),
                      alpha = 0.6,
                      color = "grey70",
                      size = 2) +
            ggplot2::geom_line(data = data1, ggplot2::aes(elements,
                                        Median,
                                        color = !! quo_group,
                                        group = !! quo_group),
                               size = 2.5)

    } else {

        spider_p <- By_Gather_Ribbon(data = data,
                         group = group,
                         elements = elements,
                         levels = levels) %>%
            ggplot2::ggplot(ggplot2::aes(group = ID,
                       color = !! quo_group)) +
            ggplot2::geom_ribbon(ggplot2::aes(ymin = min,
                            ymax = max,
                            x = elements,
                            fill = !! quo_group,
                            color = !! quo_group),
                        linetype = "blank",
                        alpha = 0.2) +
            ggplot2::geom_line(data = data2, ggplot2::aes(elements,
                                        Median,
                                        group = XXX,
                                        color = XXX),
                      alpha = 0.6,
                      size = 1) +
            ggplot2::geom_line(ggplot2::aes(elements,
                          median,
                          color = !! quo_group,
                          group = !! quo_group),
                          size = 2)
    }

    spider_p <- spider_p +
        ggplot2::facet_wrap(quo_group, ncol = ncol) +
        ggplot2::scale_y_log10(labels = prettyNum) +
        viridis::scale_fill_viridis(discrete = TRUE) +
        viridis::scale_color_viridis(discrete = TRUE) +
        ggplot2::theme_dark() +
        ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 45, hjust = 1),
                       ...) +
        ggplot2::labs(x = "", y = "")

    return(spider_p)
}