Merge pull request #21 from cct-datascience/session3-eric

Session 3 slides for intro and patchwork

Author: Aariq

2024/03-extensions/index.qmd

@@ -16,3 +16,7 @@ There are over 100 packages that extend the functionality of ggplot2 to allow yo
 -   Install R, RStudio, and `ggplot2`
 
 -   Some previous usage of `ggplot2`
+
+**Materials:**
+
+- {{< revealjs slides.html >}}

2024/03-extensions/slides.qmd

@@ -0,0 +1,219 @@
+---
+title: "Exploring the Wide World of ggplot2 Extensions"
+author: 
+  - "Eric R. Scott"
+  - "Kristina Riemer"
+  - "Renata Diaz"
+date: 2024-06-20
+format: 
+  uaz-revealjs: default
+execute: 
+  echo: true
+editor: visual
+---
+
+## Learning Objectives
+
+-   Understand where to find packages that extend `ggplot2`
+-   Assemble multi-panel figures with `patchwork`
+-   Make animated plots with `gganimate`
+-   Visualize distributions with `ggdist`
+-   Plot network data with `ggraph`
+
+## Packages
+
+```{r}
+library(ggplot2)
+library(palmerpenguins) #for example dataset
+library(patchwork) #for multi-panel figures
+library(gridGraphics) #for combining ggplot2 and base R figures
+library(gganimate) #for animated plots
+```
+
+# Extensions to `ggplot2`
+
+There are many kinds of extensions to `ggplot2`, ranging from simple to complex, from familiar to transformative.
+
+## General-use and modular
+
+```{r}
+#| code-line-numbers: "|1,4|2,5"
+#| fig-align: center
+library(ggbeeswarm)
+library(ggthemes)
+ggplot(penguins, aes(x = species, y = body_mass_g)) +
+  geom_beeswarm() +
+  theme_economist()
+
+```
+
+::: notes
+`geom_beeswarm()` can easily be combined with other `geom_`s
+:::
+
+## "All-in-one" functions
+
+```{r}
+#| code-line-numbers: "|1,2|3"
+#| fig-align: center
+library(ggstatsplot)
+ggbetweenstats(penguins, species, body_mass_g) +
+  scale_y_continuous("Body Mass (g)", n.breaks = 10)
+```
+
+::: notes
+With great power comes great responsibility—make sure you trust these stats!\
+Notice that the output is a ggplot object, so you can continue to add layers to it.
+:::
+
+## Transformative & field-specific
+
+::: {layout-ncol="2"}
+[![ggspectra](https://exts.ggplot2.tidyverse.org/gallery/images/ggspectra.png){width="100%"}](https://docs.r4photobiology.info/ggspectra)
+
+[![gggenes](https://exts.ggplot2.tidyverse.org/gallery/images/gggenes.png){width="100%"}](https://wilkox.org/gggenes)
+:::
+
+## Finding Extensions
+
+-   Browse the `ggplot2` [extensions gallery](https://exts.ggplot2.tidyverse.org/gallery/)
+
+-   Check out the [Awesome `ggplot2`](https://github.com/erikgahner/awesome-ggplot2#readme) list
+
+-   [The R Graph Gallery](https://r-graph-gallery.com/)
+
+-   Google search with "ggplot2" keyword
+
+# Package Demos
+
+## `patchwork`
+
+`patchwork` allows you to compose multi-panel figures with ease
+
+```{r}
+#| echo: false
+#| fig-align: center
+library(patchwork)
+p1 <- ggplot(penguins, aes(x = body_mass_g, y = bill_length_mm, color = species)) +
+  geom_point()
+p2 <- ggplot(penguins, aes(x = bill_depth_mm, y = bill_length_mm, color = species)) +
+  geom_point()
+p3 <- ggplot(penguins, aes(x = body_mass_g)) + 
+  facet_wrap(vars(island)) +
+  geom_histogram() +
+  theme(axis.title.y = element_blank())
+
+(p1 + p2 + plot_layout(guides = "collect")) / p3 +
+  plot_annotation(tag_levels = "A", tag_suffix = ")")
+```
+
+::: notes
+Things to notice:
+
+-   Plots areas are aligned despite one not having a y-axis label
+-   Only one legend
+-   Labels for panels A, B, C
+:::
+
+## Example plots
+
+```{r}
+p1 <- 
+  ggplot(penguins, aes(x = body_mass_g, y = bill_length_mm, color = species)) +
+  geom_point()
+p2 <-
+  ggplot(penguins, aes(x = bill_depth_mm, y = bill_length_mm, color = species)) +
+  geom_point()
+p3 <- 
+  ggplot(penguins, aes(x = body_mass_g)) + 
+  facet_wrap(vars(island)) +
+  geom_histogram()
+```
+
+## Combine plots
+
+::: columns
+::: {.column width="50%"}
+::: nonincremental
+-   `+` wraps plots
+-   `|` combines plots horizontally
+-   `/` combines plots vertically
+-   `()` can be used to nest operations
+:::
+:::
+
+::: {.column width="50%"}
+```{r}
+#| fig-width: 5
+#| fig-height: 5
+(p1 | p2) / p3
+```
+:::
+:::
+
+## Combine guides
+
+If plots have *identical* guides, you can combine them with `plot_layout(guides = "collect")`
+
+```{r}
+p1 + p2 + plot_layout(guides = "collect")
+```
+
+::: notes
+identical means same scale, same title, same glyph
+:::
+
+## Combining axes
+
+As of the most recent version of `patchwork` (v1.2.0) you can also combine identical axes.
+
+```{r}
+p1 + p2 + plot_layout(guides = "collect", axes = "collect")
+```
+
+## Controlling layout
+
+For more options for controlling layout, see the related vignette on the package website.
+
+-   Adding empty areas
+-   Inset plots
+-   Adjusting widths and heights
+
+## Tags
+
+You can add "tags" to each panel with `plot_annotation()`
+
+```{r}
+p1 + p2 + plot_annotation(tag_levels = "A", tag_suffix = ")")
+```
+
+## Modifying all panels
+
+You can use the `&` operator instead of `+` to modify **all** elements of a multi-panel figure.
+
+```{r}
+p1 + p2 & theme_bw() & scale_color_viridis_d()
+```
+
+## Using with base R plots
+
+You can even combine `ggplot2` plots with base R plots with a special syntax
+
+```{r}
+p1 + ~hist(penguins$bill_depth_mm, main = "")
+```
+
+## Getting Help
+
+-   `patchwork`: [Package website](https://patchwork.data-imaginist.com/index.html)
+
+-   `gganimate`: [Getting started guide](https://gganimate.com/articles/gganimate.html), [reference](https://gganimate.com/reference/index.html)
+
+-   Our [drop-in hours](https://datascience.cct.arizona.edu/drop-in-hours)
+
+-   [UA Data Science Slack](https://join.slack.com/t/uadatascience/shared_invite/zt-1xjxht9k0-E489WA6axO_SRVeKQh3cXg)
+
+# Anything we missed?
+
+Got a `ggplot2` question we didn't cover in this workshop series?
+Let's figure it out together!