R/plot_timeseries.R

In WDNR-Water-Use/CSLSchem: CSLS Water Chemistry Analysis

# ------------------------------------------------------------------------------
#' Parameter plot
#'
#' Plots Wells vs. Lake measurements for a parameter of interest at all lakes.
#'
#'
#' @param df subsetted version of SWIMS data for parameter of interest.
#' @param yaxis_type defaults to "number" to use continuous y axis. Can also be
#'                   "log" for semi-log plot.
#' @param text_size size of text on plots, defaults to 12pt.
#' @param site_types possible site types to plot
#' @param site_labels how to display names of site types in legends
#' @param site_colors colors to use for site types
#' @param site_shapes shapes to use for site types
#'
#' @return plot_obj, the plot object created by ggplot.
#'
#' @import ggplot2
#' @import extrafont
#' @importFrom rlang .data
#' @importFrom magrittr %>%
#'
#' @export

plot_timeseries <- function(df,
                            yaxis_type = "number",
                            text_size = 12,
                            site_types = c("upgradient",
                                           "nogradient",
                                           "downgradient",
                                           "lake", "lake_bottom"),
                            site_labels = c("Upgr.", "Nogr.", "Downgr.",
                                            "Lake Surf", "Lake Bot."),
                            site_colors = c("#33A02C", "#B15928", "#B2DF8A",
                                            "#FB9A99", "#E31A1C"),
                            site_shapes = c(21, 21, 21, 24, 24)){
  ylabel   <- sprintf("%s (%s)",
                      unique(df$name),
                      str_to_lower(unique(df$units)))
  df       <- df %>% arrange(.data$date)

  plot_obj <- ggplot(df,
                     aes(x = floor_date(.data$date, unit = "day"),
                         y = .data$result,
                         group = .data$site_id,
                         color = .data$site_type,
                         fill = .data$site_type,
                         shape = .data$site_type)) +
              geom_hline(aes(yintercept = min(.data$loq, na.rm = TRUE),
                             linetype = "LOQ"),
                         color = "grey40",
                         size = 1) +
              geom_hline(aes(yintercept = min(.data$lod, na.rm = TRUE),
                             linetype = "LOD"),
                         color = "grey40",
                         size = 1) +
              geom_path() +
              geom_point(size = 2.5) +
              facet_grid(~lake) +
              labs(x = "", y = ylabel, color = "Site") +
              scale_x_datetime(breaks = "6 months",
                               date_labels = "%b %y") +
              scale_linetype_manual(name = "",
                                    breaks = c("LOQ", "LOD"),
                                    values = c("longdash", "dotted")) +
              scale_color_manual(name = "Sites",
                                 breaks = site_types,
                                 limits = site_types,
                                 labels = site_labels,
                                 values = site_colors) +
              scale_fill_manual(name = "Sites",
                                breaks = site_types,
                                limits = site_types,
                                labels = site_labels,
                                values = site_colors) +
              scale_shape_manual(name = "Sites",
                                 breaks = site_types,
                                 limits = site_types,
                                 labels = site_labels,
                                 values = site_shapes) +
              theme_bw() +
              theme(text = element_text(family = "Segoe UI Semilight",
                                        size = text_size),
                    legend.position = "top")
  if (yaxis_type == "log") {
    plot_obj <- plot_obj + scale_y_log10()
  }
  return(plot_obj)
}