Lecture 6.2 KEY – EDS 240

TODO

UPDATE FACECTED PLOT

Note

This template follows lecture 6.2 slides. Please be sure to cross-reference the slides, which contain important information and additional context!

Lobster plot

Setup

#.........................load libraries.........................
library(tidyverse)

#..........................read in data..........................

# read in Google Sheet ----
lobs <- googlesheets4::read_sheet("https://docs.google.com/spreadsheets/d/1DkDVcl_9rlaqznHfa_v1V1jtZqcuL75Q6wvAHpnCHuk/edit#gid=2143433533") |>
  mutate(temp = as.factor(temp))

# alternatively, read in csv file ----
# lobs <- read_csv(here::here("week6", "data", "metabolism-foraging-data.csv")) |>
#   mutate(temp = as.factor(temp))

Create base plot

#..........................create theme..........................
lob_theme <- function(){
  theme_light() +
    theme(
      axis.title.x = ggtext::element_markdown(size = 16,
                                              lineheight = 1.5,
                                              margin = margin(t = 10, r = 0, b = 0, l = 0)),
      axis.title.y = ggtext::element_markdown(size = 16,
                                              lineheight = 1.5,
                                              margin = margin(t = 0, r = 10, b = 0, l = 0)),
      axis.text = element_text(color = "black", 
                               size = 14),
      axis.ticks = element_line(color = "black"),
      panel.border = element_rect(colour = "black", 
                                  linewidth = 0.7),
      panel.grid = element_blank(),
      legend.title = element_text(size = 15),
      legend.text = element_text(size = 13),
      legend.position = c(0.95, 0.95),
      legend.justification = c(0.95, 0.95),
      legend.box.background = element_rect(linewidth = 0.9)
    )
}

#..........................create scales.........................
lob_palette <- c("11" = "#7B8698",
                 "16" = "#BAD7E5",
                 "21" = "#DC7E7C",
                 "26" = "#7D3E40")

lob_shapes <-  c("11" = 15,
                 "16" = 16,
                 "21" = 17,
                 "26" = 18)

lob_sizes <- c("11" = 6,
               "16" = 6,
               "21" = 6,
               "26" = 7)

#........................create plot text........................
x_axis_lab <- glue::glue("Resting Metabolic Rate<br>
                         (mg O<sub>2</sub> kg<sup>-1</sup> min<sup>-1</sup>)")

y_axis_lab <- glue::glue("Maximum Consumption Rate<br>
                         (prey consumed predator<sup>-1</sup> 24hr<sup>-1</sup>)")

#............................plot data...........................
lob_plot <- ggplot(lobs, aes(x = SMR, y = avg_eaten,
                             color = temp, shape = temp, size = temp)) +
  geom_point() +
  scale_color_manual(values = lob_palette, name = "Temperature (ºC)") +
  scale_shape_manual(values = lob_shapes, name = "Temperature (ºC)") +
  scale_size_manual(values = lob_sizes, name = "Temperature (ºC)") +
  scale_x_continuous(breaks = seq(0, 1.5, by = 0.2)) +
  scale_y_continuous(breaks = seq(0, 35, by = 5)) +
  labs(x = x_axis_lab,
       y = y_axis_lab) +
  lob_theme()

lob_plot

Adding annotations using `geom_text()` & `geom_rect()`

bounding box + text

# create bounding box, text ----
lob_plot +
  geom_text(
    x = 0.1,
    y = 25,
    label = "Important lobsters",
    size = 4,
    color = "black",
    hjust = "inward",
  ) +
  geom_rect(
    xmin = 0.25, xmax = 0.85,
    ymin = 8.5, ymax = 18,
    alpha = 0.5,
    fill = "gray40", color = "black",
    show.legend = FALSE
  )

Adding annotations using `annotate()`

bounding box + text + arrow

# create bounding box, text, arrow ----
lob_plot +
  annotate(
    geom = "text",
    x = 0.1,
    y = 25,
    label = "Important lobsters",
    size = 4,
    color = "black",
    hjust = "inward"
  ) +
  annotate(
    geom = "rect",
    xmin = 0.25, xmax = 0.85,
    ymin = 8.5, ymax = 18,
    alpha = 0.5,
    fill = "gray70", color = "black"
  ) +
  annotate(
    geom = "curve",
    x = 0.3, xend = 0.5,
    y = 23.8, yend = 19,
    curvature = -0.15,
    arrow = arrow(length = unit(0.3, "cm"))
  )

Annotate each point

# using geom_text() ----
lob_plot +
  geom_text(aes(label = lobster_id),
            size = 6,
            show.legend = FALSE)

# using geom_label() ----
lob_plot +
  geom_label(aes(label = lobster_id),
             size = 6,
             show.legend = FALSE)

# using ggrepel (text) ----
lob_plot +
  ggrepel::geom_text_repel(aes(label = lobster_id),
                           size = 4,
                           color = "gray10",
                           nudge_x = 0.1, nudge_y = 0.3,
                           arrow = arrow(length = unit(0.25, "cm")))

# using ggrepel (labels) ----
lob_plot +
  ggrepel::geom_label_repel(aes(label = lobster_id),
                           size = 4,
                           color = "gray10",
                           nudge_x = 0.1, nudge_y = 0.3,
                           arrow = arrow(length = unit(0.25, "cm")))

Use `annotate()` to label a few points

ID + arrow

# label 2 points with lobster ID & arrow ----
lob_plot +
  annotate(
    geom = "text",
    x = 0.3, y = 20.1,
    label = "IV10",
    hjust = "left",
    size = 5
    ) +
  annotate(
    geom = "curve",
    x = 0.29, xend = 0.184,
    y = 20, yend = 9.43,
    arrow = arrow(length = unit(0.3, "cm")),
    linewidth = 0.6
    ) +
  annotate(
    geom = "text",
    x = 1.19,
    y = 5.25,
    label = "IV19",
    hjust = "right",
    size = 5
    ) +
  annotate(
    geom = "curve",
    x = 1.2, xend = 1.31,
    y = 5, yend = 14,
    arrow = arrow(length = unit(0.3, "cm")),
    linewidth = 0.6
    )

Mono Lake plot

Setup

#..........................read in data..........................

# read in Google Sheet ----
mono <- googlesheets4::read_sheet("https://docs.google.com/spreadsheets/d/1o0-89RFp2rI2y8hMQWy-kquf_VIzidmhmVDXQ02JjCA/edit#gid=164128885")

# alternatively, read in csv ----
# mono <- read_csv(here::here("week6", "data", "mono.csv"))

Create base plot

# create base plot ----
ggplot(data = mono, aes(x = year, y = lake_level)) +
  geom_line() +
  labs(x = "\nYear",
       y = "Lake surface level\n(feet above sea level)\n",
       title = "Mono Lake levels (1850 - 2017)\n",
       caption = "Data: Mono Basin Clearinghouse") +
  scale_x_continuous(limits = c(1850, 2020),
                     expand = c(0,0),
                     breaks = seq(1850, 2010, by = 20)) +
  scale_y_continuous(limits = c(6350, 6440),
                     breaks = c(6370, 6400, 6430),
                     expand = c(0,0),
                     labels = scales::label_comma()) +
  theme_light() +
  theme(
    plot.title.position = "plot",
    plot.title = element_text(size = 16),
    axis.title = element_text(size = 12),
    axis.text = element_text(size = 10),
    plot.caption = element_text(face = "italic")
    )

Add annotations

order of annotation layers matters!

ggplot(data = mono, aes(x = year, y = lake_level)) +
  annotate(
    geom = "rect",
    xmin = 1941, xmax = 1983,
    ymin = 6350, ymax = 6440,
    fill = "gray90"
  ) +
  geom_line() +
  labs(x = "\nYear",
       y = "Lake surface level\n(feet above sea level)\n",
       title = "Mono Lake levels (1850 - 2017)\n",
       caption = "Data: Mono Basin Clearinghouse") +
  scale_x_continuous(limits = c(1850, 2020),
                     expand = c(0,0),
                     breaks = seq(1850, 2010, by = 20)) +
  scale_y_continuous(limits = c(6350, 6440),
                     breaks = c(6370, 6400, 6430),
                     expand = c(0,0),
                     labels = scales::label_comma()) +
  annotate(
    geom = "text", 
    x = 1962, y = 6425,
    label = "unrestricted diversions\n(1941 - 1983)",
    size = 3
  ) +
  geom_hline(yintercept = 6360, 
             linetype = "dashed") +
  annotate(
    geom = "text",
    x = 1910, y = 6366,
    label = "Decreased shrimp abundance expected\n(6,360 feet above sea level)",
    size = 3
    ) +
  theme_light() +
  theme(
    plot.title.position = "plot",
    plot.title = element_text(size = 16),
    axis.title = element_text(size = 12),
    axis.text = element_text(size = 10),
    plot.caption = element_text(face = "italic")
    )

Lobster plot

Setup

Create base plot

Adding annotations using geom_text() & geom_rect()

Adding annotations using annotate()

Annotate each point

Use annotate() to label a few points

Mono Lake plot

Setup

Create base plot

Add annotations

Adding annotations using `geom_text()` & `geom_rect()`

Adding annotations using `annotate()`

Use `annotate()` to label a few points