EVR 628- Intro to Environmental Data Science

Scaling up your data visualizations (Part 1)

Juan Carlos Villaseñor-Derbez (JC)

Learning Objectives

By the end of this week, you should be able to:

Create complex figures
Develop simple documents

This week

Review of dplyr and tidyr
Review of ggplot()
Layering geoms
Subplots with facets
ggplot extensions
- ggridges
- cowplot

Position adjustments
Labels
Summarizing data on the fly
Topics above not covered AND
Quarto markdown

Review of `ggplot()`

Build a plot with three steps

Specify your data in ggplot()
Specify your x (and y) axis aesthetic mappings in aes()
Specify your geometric representation with geom_*

And maybe:

Modify geoms as needed
Modify your labels as needed

1. Specify the Data

ggplot(data = data_lionfish)

2. Specify the `aes`thetics

ggplot(data = data_lionfish,
       mapping = aes(x = depth_m, y = total_length_mm))

3. Specify the `geom`etric Representation

ggplot(data = data_lionfish,
       mapping = aes(x = depth_m, y = total_length_mm)) +
  geom_point()

4-5. Modify geoms and labels

ggplot(data = data_lionfish,
       mapping = aes(x = depth_m, y = total_length_mm)) +
  geom_point(shape = 21, fill = "steelblue", size = 2) +
  labs(x = "Depth (m)",
       y = "Total length (mm)")

Layering geoms

The group aesthetic
non-data geoms
smooth geom
geom-level vs global-level aesthetics

`geom`s on top of `geom`s 1

Code

ggplot(data = data_lionfish,
       mapping = aes(x = total_length_mm, y = total_weight_gr)) +
  geom_smooth(color = "black", linetype = "dashed") +
  geom_vline(xintercept = c(100, 200), linetype = "dashed") +
  geom_point(aes(color = size_class), size = 2) +
  scale_color_manual(values = palette_UM(3)) +
  labs(x = "Total length (mm)",
       y = "Total weight (gr)",
       color = "Size class") +
  theme(legend.position = "inside",
        legend.justification = c(0, 1),
        legend.position.inside = c(0, 1),
        legend.background = element_blank())

`geom`s on top of `geom`s 2

Code

data(data_mhw_ts)

ggplot(data = data_mhw_ts,
       aes(x = date, y = temp)) + 
  geom_line() +
  labs(x = "Date", y = "Temperature (°C)")

`geom`s on top of `geom`s 2

Code

ggplot(data = data_mhw_ts, aes(x = date, y = temp)) + 
  geom_line(aes(y = seas), color = "blue") +
  geom_line() +
  labs(x = "Date", y = "Temperature (°C)")

`geom`s on top of `geom`s 2

Code

ggplot(data = data_mhw_ts, aes(x = date, y = temp)) + 
  geom_line(aes(y = seas), color = "blue") +
  geom_line(aes(y = thresh), color = "red") +
  geom_line() +
  labs(x = "Date", y = "Temperature (°C)")

`geom`s on top of `geom`s 3

Code

data(data_mhw_events)

ggplot(data = data_mhw_events,
       mapping = aes(x = date_peak, y = intensity_max,
                     color = intensity_max)) +
  geom_linerange(mapping = aes(ymin = 0,
                               ymax = intensity_max),
                 linewidth = 1) +
  geom_point(size = 2) +
  scale_color_gradient(low = "gray90", high = "red") +
  labs(x = "Date peak",
       y = "MHW Intensity (°C)",
       color = "MHW Intensity (°C days)") +
  theme(legend.position = "bottom",
        legend.title.position = "top",
        legend.key.width = unit(1, "cm"))

Facetting

Facetting with wrap

When specifying groups and colors is not enough

Code

total_catch_data <- data_fishing |> 
  group_by(year, fishery) |> 
  summarize(total_catch = sum(catch))

ggplot(total_catch_data, aes(x = year, y = total_catch)) +
  geom_line() +
  geom_point() +
  facet_wrap(~fishery, ncol = 1, scales = "free_y") +
  labs(x = "Year", y = "Total catch (Tons)")

Facetting with grid

Code

tidy_kelp <- data_kelp |> 
  filter(genus_species %in% c("Embiotoca jacksoni",
                              "Embiotoca lateralis"),
         location %in% c("ASA", "ERE", "ERO")) |> 
  pivot_longer(cols = starts_with("TL_"),
               names_to = "total_length",
               values_to = "N",
               values_drop_na = T) |> 
  group_by(location, site, transect, genus_species) |> 
  summarize(total_N = sum(N)) |> 
  group_by(location, site, genus_species) |> 
  summarize(mean_N = mean(total_N))

ggplot(data = tidy_kelp,
       mapping = aes(x = site, y = mean_N)) +
  geom_col() +
  facet_grid(location ~ genus_species) +
  labs(x = "Site", y = "Mean (org / tranect)")

`ggplot` extensions

ggplot extension 1: `cowplot`

Code

library(cowplot)

p1 <- ggplot(data = data_mhw_ts, aes(x = date, y = temp)) + 
  geom_line() +
  geom_line(aes(y = seas), color = "blue") +
  geom_line(aes(y = thresh), color = "red") +
  labs(x = "Date", y = "Temperature (°C)")

p2 <- ggplot(data = data_mhw_events,
       mapping = aes(x = date_peak, y = intensity_max,
                     color = intensity_max)) +
  geom_linerange(mapping = aes(ymin = 0,
                               ymax = intensity_max),
                 linewidth = 1) +
  geom_point(size = 2) +
  scale_color_gradient(low = "gray90", high = "red") +
  labs(x = "Date peak",
       y = "MHW Intensity (°C)",
       color = "MHW Intensity (°C days)") +
  theme(legend.position = "bottom",
        legend.title.position = "top",
        legend.key.width = unit(1, "cm"))

plot_grid(p1, p2, ncol = 1, rel_heights = c(0.5, 1))

`ggplot` extension 2: `ggridges`

Visualizing distributions across groups is difficult

Code

library(ggridges)

ggplot(data_lionfish, aes(x = total_length_mm, y = site, fill = site)) +
  geom_density_ridges(alpha = 0.5, show.legend = FALSE) +
  labs(x = "Total Length (mm)",
       y = "Site")

Position adjustments

Each geom has a default position argument
This argument controls how elements are placed on the graph
There are four options:
- identity (allows for overlaps)
- dodge (no overlaps, move elements horizontally)
- stack (no overlaps, move elements vertically)
- fill (no overlaps, move elements vertically and fill all the space)

Position adjustments with points

Code

ggplot(data_lionfish, aes(x = site, y = total_length_mm)) + 
  geom_point() +
  coord_flip()

Position adjustments with points

Code

ggplot(data_lionfish, aes(x = site, y = total_length_mm)) + 
  geom_point(position = position_jitter(width = 0.1, height = 0)) +
  coord_flip()

Position adjustments with bars

Stack (default)

Code

ggplot(mpg, aes(x = drv, fill = class)) + 
  geom_bar()

Position adjustments with bars

Identity

Code

ggplot(mpg, aes(x = drv, fill = class)) + 
  geom_bar(position = "identity")

Position adjustments with bars

Dodge

Code

ggplot(mpg, aes(x = drv, fill = class)) + 
  geom_bar(position = "dodge")

Position adjustments with bars

Fill

Code

ggplot(mpg, aes(x = drv, fill = class)) + 
  geom_bar(position = "fill")

Labels

Special characters in your plots

subindices go inside “[]”
superscripts go after “^”
greek letters are directly typed
Use “~” for spaces
See ?plotmath for a full list

Code

data <- read_csv("https://gml.noaa.gov/webdata/ccgg/trends/co2/co2_daily_mlo.csv",
                 skip = 32, 
                 col_names = c("year", "month", "day", "decimal", "co2_ppm"))

ggplot(data,
       aes(x = decimal, y = co2_ppm)) + 
  geom_line() +
  theme_minimal(base_size = 10) +
  labs(x = "Date",
       y = quote(CO[2]~concentration~(ppm)),
       caption = "Data from the Global Monitoring Laboratory")

Summarizing data on the fly

Sometimes you might not want to group_by and summarize, but you can go straight into a figure

Code

ggplot(data_heatwaves,
       aes(x = year,
           y = temp_mean)) +
  stat_summary(geom = "pointrange", fun.data = "mean_se") +
  stat_summary(geom = "line", fun = "mean") +
  scale_x_continuous(breaks = seq(1985, 2020, by = 10)) +
  facet_wrap(~str_to_sentence(str_replace(fishery, "_", " ")),
             ncol = 2,
             scales = "free_y") +
  labs(x = "Year",
       y = "Mean Temperature (°C)")

Quarto markdown

Allows you to build documents
- slides
- html files
- pdfs
- word documents
- books…
Particularly useful if your document heavily depends on R-generated content

Quarto markdown

Some people use them throughout their analysis
- Pros:
  - You can write tons and tons of explanations as to why you are doing something
  - You can include equations
- Cons:
  - You have to run the entire document, from top to bottom, every time you want to update it
  - Sometimes more is not better

Quarto markdown

Install Quarto markdown here
We’ll building a document from scratch
Then a slide
Finally a website

EVR 628- Intro to Environmental Data Science

Learning Objectives

This week

Review of ggplot()

Review of ggplot()

1. Specify the Data

2. Specify the aesthetics

3. Specify the geometric Representation

4-5. Modify geoms and labels

Layering geoms

Layering geoms

geoms on top of geoms 1

geoms on top of geoms 2

geoms on top of geoms 2

geoms on top of geoms 2

geoms on top of geoms 3

Facetting

Facetting with wrap

Facetting with grid

ggplot extensions

ggplot extension 1: cowplot

ggplot extension 2: ggridges

Position adjustments

Position adjustments

Position adjustments with points

Position adjustments with points

Position adjustments with bars

Position adjustments with bars

Position adjustments with bars

Position adjustments with bars

Labels

Special characters in your plots

Summarizing data on the fly

Summarizing data on the fly

Quarto markdown

Quarto markdown

Quarto markdown

Quarto markdown

Review of `ggplot()`

Review of `ggplot()`

2. Specify the `aes`thetics

3. Specify the `geom`etric Representation

`geom`s on top of `geom`s 1

`geom`s on top of `geom`s 2

`geom`s on top of `geom`s 2

`geom`s on top of `geom`s 2

`geom`s on top of `geom`s 3

`ggplot` extensions

ggplot extension 1: `cowplot`

`ggplot` extension 2: `ggridges`