R/plot_acf_results.R

In edpclau/circadian-dynamics: Period and Rythm Analysis of Timeseries Data

#' Plot Raw Values
#'
#' @param df Use the second output from 'simplify_data'.
#'
#' @return Returns a list of plots for the autocorrelation results.
#' @export
#'
#' @examples plots = plot_acf_results(df = simplified_data$autocorrelation)
#'
#' @import magrittr
#' @importFrom dplyr select distinct filter mutate
#' @importFrom tidyr nest
#' @importFrom future plan sequential
#' @importFrom furrr future_map2
#' @importFrom ggplot2 ggplot geom_line labs theme element_text element_blank element_line scale_x_continuous element_rect geom_hline
plot_acf_results <- function(df) {

  if (!'window' %in% names(df)) {df$window = 1}
  #Preprocess the data to plot
auto_df = df %>%
    select(data, window, rythm_strength, gc_raw_to_cos, gc_cos_to_raw, period) %>%
    distinct() %>%
    mutate(window = as.numeric(window),
           granger = ifelse(gc_raw_to_cos < gc_cos_to_raw, gc_raw_to_cos, gc_cos_to_raw)) %>%
    nest(cols = -data) %>%
    as.list()
  names(auto_df$cols) = auto_df$data
  id = auto_df$data
  auto_df = auto_df$cols

  # Plot the figures
  plan(sequential)
  period_plots = future_map2(.x = auto_df,
                          .y = id,
                          .f = ~ {
                            ggplot(.x, aes(x = window, y = period)) +
                              geom_point(na.rm = TRUE) +
                              geom_line(na.rm = TRUE) +
                              labs(y = 'Hours', title = 'Autocorrelation Period', x = 'Window') +
                              scale_x_continuous(labels = window, limits = c(NA,NA)) +
                              theme(
                                panel.spacing = unit(0, "cm", data = NULL),
                                axis.title = element_text(face = "bold", size = 12),
                                # axis.ticks = element_blank(),
                                axis.line = element_blank(),
                                axis.line.x = element_blank(),
                                axis.text.y = element_text(size = 12),
                                axis.text.x = element_text(size = 12),
                                strip.background = element_blank(),
                                strip.placement = "outside",
                                strip.text.y.left = element_text(
                                  angle = 0,
                                  size = 12,
                                  vjust = 0
                                ),
                                plot.margin = unit(c(0, 0.5, 0, 0), "cm"),
                                panel.border = element_rect(colour = "black", fill=NA, size = 1),
                                panel.background = element_blank(),
                                plot.title = element_text(hjust = 0.5, vjust =  -0.5),
                                legend.position = 'none'
                              )
                          })

  rhythm_plots = future_map2(.x = auto_df,
                             .y = id,
                             .f = ~ {
                               ggplot(.x, aes(x = window, y = rythm_strength)) +
                                 geom_point(na.rm = TRUE) +
                                 geom_line(na.rm = TRUE) +
                                 geom_hline(aes(yintercept = 1), lty = 'dashed') +
                                 labs(y = '', title = 'Autocorrelation Rhythm Strength', x = 'Window') +
                                 scale_x_continuous(labels = window, limits = c(NA,NA)) +
                                 theme(
                                   panel.spacing = unit(0, "cm", data = NULL),
                                   axis.title = element_text(face = "bold", size = 12),
                                   # axis.ticks = element_blank(),
                                   axis.line = element_blank(),
                                   axis.line.x = element_blank(),
                                   axis.text.y = element_text(size = 12),
                                   axis.text.x = element_text(size = 12),
                                   strip.background = element_blank(),
                                   strip.placement = "outside",
                                   strip.text.y.left = element_text(
                                     angle = 0,
                                     size = 12,
                                     vjust = 0
                                   ),
                                   plot.margin = unit(c(0, 0.5, 0, 0), "cm"),
                                   panel.border = element_rect(colour = "black", fill=NA, size = 1),
                                   panel.background = element_blank(),
                                   plot.title = element_text(hjust = 0.5, vjust =  -0.5),
                                   legend.position = 'none'
                                 )
                             })

  granger_plots = future_map2(.x = auto_df,
                                               .y = id,
                                               .f = ~ {
                                                 ggplot(.x, aes(x = window, y = granger)) +
                                                   geom_point(na.rm = TRUE) +
                                                   geom_line(na.rm = TRUE) +
                                                   geom_hline(aes(yintercept = 0.05), lty = 'dashed') +
                                                   labs(y = 'p.value', title = 'Autocorrelation Granger Test', x = 'Window') +
                                                   scale_x_continuous(labels = window, limits = c(NA,NA)) +
                                                   theme(
                                                     panel.spacing = unit(0, "cm", data = NULL),
                                                     axis.title = element_text(face = "bold", size = 12),
                                                     # axis.ticks = element_blank(),
                                                     axis.line = element_blank(),
                                                     axis.line.x = element_blank(),
                                                     axis.text.y = element_text(size = 12),
                                                     axis.text.x = element_text(size = 12),
                                                     strip.background = element_blank(),
                                                     strip.placement = "outside",
                                                     strip.text.y.left = element_text(
                                                       angle = 0,
                                                       size = 12,
                                                       vjust = 0
                                                     ),
                                                     plot.margin = unit(c(0, 0.5, 0, 0), "cm"),
                                                     panel.border = element_rect(colour = "black", fill=NA, size = 1),
                                                     panel.background = element_blank(),
                                                     plot.title = element_text(hjust = 0.5, vjust =  -0.5),
                                                     legend.position = 'none'
                                                   )
                                               })

  return(list(
    period_plots = period_plots,
    rhythm_plots = rhythm_plots,
    granger_plots = granger_plots
  ))
}