# INBO CODING CLUB

26 March 2024

Welcome!

## Share your code snippet

If you want to share your code snippet, copy paste your snippet within a section of three backticks (```):

As an **example**:

library(tidyverse)

(*you can copy paste this example and add your code further down*)

## Yellow sticky notes

No yellow sticky notes online. Put your name + " | " and add a "*" each time you solve a challenge (see below).

## Participants

Name | Challenges
--- | ---
Raïsa Carmen | ***
Jorre Vannieuwenhuyze | ***
Adriaan Seynaeve |
Wouter Depaepe |
Heleen Deroo | *
Anja Leyman |
Leen Govaere |
An |**

## Challenge 1

### Raïsa's solution (example)

Copy paste this section to show your solutions.

# dummy code
print("This is how to insert code.")

### Heleen's solution

plot1 <- ggplot(rodents) +
  geom_bar(aes(x = year, fill = institutionCode)) +
  labs(y = "observations")
plot1
ggplotly(plot1)

plot2 <- ggplot(rodents) +
  geom_bar(mapping = aes(x = month, fill = species)) +
  facet_wrap(~species, scales = "free") +
  labs(y = "observations") +
  scale_x_continuous(breaks = pretty_breaks())
plot2

rodents_n_2000 <- rodents %>%
  dplyr::filter(year >= 2000) %>%
  dplyr::group_by(species,year, month) %>%
  dplyr::count() %>%
  mutate(date = make_date(year, month, 1))

plot3 <- ggplot(data = rodents_n_2000,
                mapping = aes(x = date, y = n, color = species)) +
  geom_line() +
  facet_wrap(~species, scales = "free") +
  labs(y = "observations") +
  scale_x_date(
    NULL,
    breaks = scales::breaks_width("5 years"), 
    labels = scales::label_date("'%y")) + 
  scale_y_continuous(
    labels = scales::label_number(scale_cut = scales::cut_short_scale()))
plot3

#jorre
plot1 <- plot1 |> ggplotly()

plot2 <- plot2 + scale_x_continuous(breaks=pretty_breaks())

plot3 <- plot3 +
  scale_x_date(labels = scales::label_date("'%y")) +
  scale_y_continuous( labels = scales::label_number(scale_cut = scales::cut_short_scale()))

## Challenge 2

# Jorre
plot1 + plot2 + plot3 + plot4 + plot_layout(nrow = 2, byrow = FALSE)


plot1 +  facet_zoom(x = year %in% 2016:2020)

# Wouter
plot1 + plot2 + plot3 + plot4

plot4 | (plot1 / plot2) + 
  plot_annotation(title = "I like this layout, I disabled plot4's legend")

plot1 + facet_zoom(x = year == c(2016,2020))

### Raïsa's solution

#Save some space by grouping the legends as much as possible
library(viridis) #other colors for the institution then for the species
((plot1 + scale_fill_viridis(discrete = TRUE)) +
    plot2 +
    (plot3 + theme(legend.position = "none")) +
    (plot4 + theme(legend.position = "none"))) +
  plot_layout(guides = 'collect') #puts all legends to the side


# Using ggforce, add a "facet zoom"  to `plot1` focussing on the last 5 years.
plot1 +
  facet_zoom(year >= 2015)

## Challenge 3

# jorre
plot4_anim <- rodents |>
  filter(!is.na(decimalLatitude),!is.na(decimalLongitude)) |>
  sample_n(2000) |> # sample 2000 rows for this exercise to increase speed
  ggplot() +
  geom_point(mapping = aes(x = decimalLongitude,
                           y = decimalLatitude,
                           color = species)) +
  labs(x = "latitude", y = "longitude") +
  transition_states(species) + 
  ggtitle('Now showing {closest_state}',
          subtitle = 'Frame {frame} of {nframes}')
plot4_anim


plot4_anim2 <- rodents |>
  filter(!is.na(decimalLatitude),!is.na(decimalLongitude)) |>
  filter(year %in% 2015:2020) |> # only last 5 years for speed
  ggplot() +
  geom_point(
    mapping = aes(
      x = decimalLongitude,
      y = decimalLatitude,
      color = species,
      group= seq_along(year)
      )
    ) +
  labs(x = "latitude", y = "longitude") +
  transition_states(year) + 
  ggtitle('Now showing {closest_state}',
    subtitle = 'Frame {frame} of {nframes}'
    ) +
  enter_fade() + 
  exit_shrink()
plot4_anim2  |> animate(nframes=50,fps=5)

### Raïsa's solution

anim1 <- plot4 +
  ggtitle('Now showing {closest_state}',
          subtitle = 'Frame {frame} of {nframes}') +
  transition_states(species) +
  enter_fade() +
  exit_fade()
animate(anim1)
anim_save("./src/20240326/20240326_animation_plot4_by_species.tif")


#' 2. Create an animation showing the observations year by year. By default the animation has 100 frames and 10 frame per seconds
# (fps), i.e. a duration of 10s. How to change these values?

# rewritten plot4 with `year` as "group" in aesthetics of `geom_point()`.
# Without the group gganimate thinks to group by color.
anim2 <- ggplot(rodents %>%
                  filter(!is.na(decimalLatitude),
                         !is.na(decimalLongitude))) +
  geom_point(mapping = aes(x = decimalLongitude,
                           y = decimalLatitude,
                           group = seq_along(year),
                           color = species)) +
  transition_time(year) +
  labs(x = "latitude",
       y = "longitude",
       title = 'Year: {frame_time}') +
  enter_fade() +
  exit_shrink()
animate(anim2, nframes = 400) # It can take long
anim_save("./src/20240326/20240326_animation_plot4_by_year.tif")

## BONUS challenge

### Raïsa's solution

logo_file <- "./data/20240326/coding_club_logo_1.png"
logo <- image_read(logo_file)

# Add logo as an annotation raster with ggplot
image <- image_fill(logo, 'none')
raster <- as.raster(image)
plot1 +
  annotation_raster(raster,
                    xmin = 2010, xmax = 2020,
                    ymin = 14000, ymax = 17500)

### Jorre

Function below was taken from https://themockup.blog/posts/2019-01-09-add-a-logo-to-your-plot/.
It is not the most efficient solution because it doesn't work on your ggplot object directly, you first have to save it as a another image on disk. But it might be more robust.

add_logo <- function(plot_path, logo_path, logo_position, logo_scale = 10){
  
  # Requires magick R Package https://github.com/ropensci/magick
  
  # Useful error message for logo position
  if (!logo_position %in% c("top right", "top left", "bottom right", "bottom left")) {
    stop("Error Message: Uh oh! Logo Position not recognized\n  Try: logo_positon = 'top left', 'top right', 'bottom left', or 'bottom right'")
  }
  
  # read in raw images
  plot <- magick::image_read(plot_path)
  logo_raw <- magick::image_read(logo_path)
  
  # get dimensions of plot for scaling
  plot_height <- magick::image_info(plot)$height
  plot_width <- magick::image_info(plot)$width
  
  # default scale to 1/10th width of plot
  # Can change with logo_scale
  logo <- magick::image_scale(logo_raw, as.character(plot_width/logo_scale))
  
  # Get width of logo
  logo_width <- magick::image_info(logo)$width
  logo_height <- magick::image_info(logo)$height
  
  # Set position of logo
  # Position starts at 0,0 at top left
  # Using 0.01 for 1% - aesthetic padding
  
  if (logo_position == "top right") {
    x_pos = plot_width - logo_width - 0.01 * plot_width
    y_pos = 0.01 * plot_height
  } else if (logo_position == "top left") {
    x_pos = 0.01 * plot_width
    y_pos = 0.01 * plot_height
  } else if (logo_position == "bottom right") {
    x_pos = plot_width - logo_width - 0.01 * plot_width
    y_pos = plot_height - logo_height - 0.01 * plot_height
  } else if (logo_position == "bottom left") {
    x_pos = 0.01 * plot_width
    y_pos = plot_height - logo_height - 0.01 * plot_height
  }
  
  # Compose the actual overlay
  magick::image_composite(plot, logo, offset = paste0("+", x_pos, "+", y_pos))
  
}


logo_file <- "./data/20240326/coding_club_logo_1.png"
plot_file <- "./data/20240326/plot1.png"

ggsave(plot_file,plot1)

add_logo(
  plot_path=plot_file, 
  logo_path=logo_file, 
  logo_position="top right", 
  logo_scale = 10
  )