R/LEEF_2_plot_tocs_per_bottle.R

In LEEF-UZH/LEEF.analysis: Access Functions, Tests and Basic Analysis of the RRD Data from the LEEF Project

#' Plot diagnostic plot to check number of species per timestamp
#'
#' @param db fully qualified path to the sqlite database. Default, read from option \code{RRDdb}.
#'   If not set, defaults to option \code{RRDdb}; if this is not set, defaults to \code{LEEF.RRD.sqlite}
#' @param type the type of the measurement which should be displayed. A vector with the types.
#'   Possible values are: "TOC", "TN", "IC", "TN", "".
#' @param treatment_begin_day begin of treatment (vertical red line in plot). If \code{NULL} none is plotted.
#' @param treatment_end_day end of treatment (vertical red line in plot). If \code{NULL} none is plotted.
#' @param arrow if \code{TRUE} read data from arrow instead of sqlite database
#'
#' @return \code{ggplot} object of the plot
#'
#' @importFrom dplyr collect mutate
#' @importFrom rlang !!
#' @import ggplot2
#'
#' @export
#'
#' @examples
LEEF_2_plot_tocs_per_bottle_per_timestamp <- function(
  db = getOption("RRDdb", "LEEF.RRD.sqlite"),
  type = c("IC", "TC", "TN", "TOC"),
  treatment_begin_day = 70,
  treatment_end_day = 154,
  arrow = FALSE
){

  if (arrow) {
    toc <- arrow_read_toc(getOption("RRDarrow"))
  } else {
    toc <- db_read_toc(db)
  }

  options(dplyr.summarise.inform = FALSE)


  ## plot

  data <- toc %>%
    filter(type %in% !!type) %>%
    dplyr::collect()

  if (nrow(data) < 1) {
    warning("No data for available!")
  } else {
    data$label <- paste0("t: ", data$temperature, "\n r: ", data$resources, "\n s: ", data$salinity)
    data <- data %>%
      dplyr::mutate(bottle = fix_bottle(bottle)) %>%
      group_by(day, bottle, type, salinity, resources, temperature, replicate)

    p <- ggplot2::ggplot(data, ggplot2::aes(x = .data$day, y = .data$concentration)) +
      ggplot2::geom_line(ggplot2::aes(y = .data$concentration, colour = .data$type)) +
      ggplot2::facet_grid(rows = vars(replicate), cols = vars(label),scales = "free_y") +
      ggplot2::geom_text(
        data = data,
        ggplot2::aes(x = -Inf, y = Inf, label = bottle, group = bottle),
        hjust = -0.5,
        vjust = 1.4,
        size = 3
      ) +
      ggplot2::scale_colour_manual(values = 1:40) +
      ggplot2::xlab("Day of Experiment") +
      ggplot2::ylab("concentration") +
      ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 45)) # +
      # geom_vline(xintercept = range(ls$day), colour = "lightgrey")
    if (!is.null(treatment_begin_day)) {
      p <- p + geom_vline(xintercept = range(treatment_begin_day), colour = "red")
    }
    if (!is.null(treatment_end_day)) {
      p <- p + geom_vline(xintercept = range(treatment_end_day), colour = "red")
    }
    p
  }
}