original_codes/original_actogram.R

In nasserdr/digiRhythm: Analyzing Animal's Rhythmicity

#libraries import
library(ggplot2)
library(lubridate)
library(dplyr)


#Example
data("df516b_2")
df <- df516b_2
activity <- names(df)[2]
start <- "2020-05-01" #year-month-day
end <- "2020-08-13" #year-month-day

activity_alias <- 'Motion Index'
save <- 'sample_results/actogram' #if NULL, don't save the image

#Start of the function
start <- lubridate::date(start)
end <- lubridate::date(end)

names(df)[1] <- 'datetime'

df$date <- lubridate::date(df$datetime)
data_to_plot <- df %>%
  filter(lubridate::date(datetime) >= start) %>%
  filter(lubridate::date(datetime) <= end)
data_to_plot$time <- format(data_to_plot$datetime, format = "%H:%M", tz = "CET")
data_to_plot <- data_to_plot %>% select(-datetime)

data_to_plot$date_numeric <- xtfrm(as.Date(data_to_plot$date, format='%Y-%m-%d'))


equally_spaced_select <- function(x) {
  indices <- seq(1, length(x), by = 5)
  return(x[indices])
}

if (length(unique(data_to_plot$date_numeric)) > 15) {
  breaks_for_y_axis = equally_spaced_select(unique(data_to_plot$date_numeric))
  labels_for_y_axis = equally_spaced_select(unique(data_to_plot$date))
} else {
  breaks_for_y_axis = unique(data_to_plot$date_numeric)
  labels_for_y_axis = unique(data_to_plot$date)
}

act_plot <- ggplot(data_to_plot,
                   aes(x = time,
                       y = date_numeric,
                       fill = .data[[activity]])) +

  geom_tile()+
  xlab("Time")+
  ylab("Date") +
  scale_fill_gradient(name = activity_alias,
                      low = "#FFFFFF",
                      high = "#000000",
                      na.value = "yellow")+
  theme_classic() +
  theme(plot.title = element_text(hjust = 0.5)) +
  scale_x_discrete(breaks = c("03:00", "09:00", "15:00", "21:00")) +
  theme(
    text = element_text(size = 15, color = 'black'),
    axis.text = element_text(color = 'black'),
    panel.background = element_rect(fill = "white"),
    axis.line = element_line(size = 0.5)
    ) +  scale_y_reverse(breaks = breaks_for_y_axis,
                  labels = labels_for_y_axis)

if (!is.null(save)) {

  cat("Saving image in :", save, "\n")
  ggsave(
    paste0(save, '.tiff'),
    act_plot,
    device = 'tiff',
    width = 15,
    height = 6,
    units = "cm",
    dpi = 600
  )
}

print(act_plot)