Penguins

TidyTuesday week 31

Load the necessary libraries

library(tidyverse)
library(visdat)
library(cowplot)
library(ggrepel)
library(mapproj) # polar orthographic map projection
library(ggthemes) 
library(here)
library(extrafont)
library(extrafont)
library(knitr)

Download the Penguins data from Tidytuesday

# Get the data 
penguins <- readr::read_csv('https://raw.githubusercontent.com/rfordatascience/tidytuesday/master/data/2020/2020-07-28/penguins.csv')

kable(head(penguins), caption = "Penguins data. Source: Gorman, Williams and Fraser, 2014 ")

Penguins data. Source: Gorman, Williams and Fraser, 2014

species	island	bill_length_mm	bill_depth_mm	flipper_length_mm	body_mass_g	sex	year
Adelie	Torgersen	39.1	18.7	181	3750	male	2007
Adelie	Torgersen	39.5	17.4	186	3800	female	2007
Adelie	Torgersen	40.3	18.0	195	3250	female	2007
Adelie	Torgersen	NA	NA	NA	NA	NA	2007
Adelie	Torgersen	36.7	19.3	193	3450	female	2007
Adelie	Torgersen	39.3	20.6	190	3650	male	2007

Make a plot of the ocurrences of the penguin species

# Get geospatial data for Antarctica only
antarctica <- map_data("world", region = "Antarctica")

# map of antartica
df_penguinloc <-
  tibble(
    island = c("Dream", "Biscoe", "Torgersen"),
    lat_y = c(-64.7333, -65.4333, -64.7666636),
    long_x = c(-64.2333, -65.5000, -64.083333)
  ) 


df_penguinloc <- penguins %>% 
  group_by(island) %>%  summarise(amount=n()) %>% 
  left_join(df_penguinloc, by = "island")

# barplot

d <- penguins %>% filter(year==2009) %>% 
  mutate(island = factor(island), 
         island = factor(island, levels = rev(levels(island)))) %>%  
  ggplot() +
  stat_count(aes(island, fill = species), alpha = 0.8) +
  annotate("text", y=3,  x= "Torgersen", label= "Torgersen", color = "#1874CD")+
  annotate("text", y=3,  x= "Dream", label= "Dream", color = "#c02728")+
  annotate("text", y=3,  x= "Biscoe", label= "Biscoe", color = "#53868B")+
  scale_fill_manual(values = c("#66c2a5","#fc8d62","#8da0cb")) +
  scale_y_reverse()+
  labs(caption = "Source: Gorman, Williams and Fraser, 2014 | Graphics: Julián Avila-Jiménez") +
  theme_minimal() +
  theme(legend.position = c(0.2,0.3),
        axis.title = element_blank(),
        axis.text.x = element_blank(),
        panel.grid = element_blank(),
        plot.background = element_rect(fill="#f9f9f9", color = "#f9f9f9"))
d

Make a nice map of the localities of the penguin species

# main map
p <- ggplot(antarctica, aes(long, lat, group = group)) +
  geom_polygon(fill = "#506B8E", alpha = .8) +
  coord_map("ortho", orientation = c(-90, 0, 0),
            xlim = c(-62, -55),
            ylim = c(-75, - 60)) +
  geom_text_repel(df_penguinloc, mapping=aes(long_x, lat_y, label = island), 
                  group=1, color = c("#53868B", "#c02728", "#1874CD"), 
                   box.padding = 0.5,
                   nudge_y = 1,  nudge_x = -2, min.segment.length = 0) +
  geom_point(df_penguinloc, mapping=aes(long_x, lat_y,  
                                        group = 1, 
                                        colour = island), 
             alpha =.7)+
  scale_color_manual(values = c("#53868B", "#c02728", "#1874CD"))+
  labs(title = "Penguins in Palmer Archipelago",
       subtitle = "Recorded penguins in 2009 and their nesting Islands") +
  theme_map() +
  theme(legend.position = "none",
        plot.title = element_text(hjust = 0.5, size = 20),
        plot.subtitle =  element_text(hjust = 0.5),
        plot.background = element_rect(fill="#f9f9f9", color = "#f9f9f9"))
p

# inset map
inset <- ggplot(antarctica, aes(long, lat, group = group)) +
  geom_polygon(fill = "#506B8E", alpha = .5) +
  coord_map("ortho", orientation = c(-90, 0, 0)) +
  geom_point(df_penguinloc, mapping=aes(long_x, lat_y,  
                                        group = island, 
                                        colour = island), 
             alpha =.5, size = 1)+
  annotate("rect", color="black", fill = "transparent",
           xmin = -68, xmax = -54,
           ymin = -75, ymax = -60)+
  labs(title = "Antarctica") +
  theme_map() +
  theme(legend.position = "none",
        panel.grid.major.y = element_line(colour="grey"),
        plot.title = element_text(hjust = 0.5),
        plot.background = element_rect(fill="#f9f9f9", color = "#f9f9f9"))
inset

# draw together inset and main map
a <- ggdraw(p ) +
  draw_plot(inset, .47, .38, .5, .4)
a

Final map

# plot everything together
p1 <- plot_grid(a,d, ncol = 1, rel_widths = c(4, 2), rel_heights = c(2,1))+
  theme(plot.background = element_rect(fill="#f9f9f9")) +
  labs(title = "Penguins in Palmer Archipelago")

# import image
penguin <-here("/penguin.png")
                    
# draw plot with image
p2 <- ggdraw() + 
  draw_plot(p1) +
  draw_image(penguin, x = 0.2, y = 0.34, hjust = 1, width = 0.20, height = 0.25)
p2

# save plot

ggsave(here("/penguinplot.png"))