5.3-Complex_operations.qmd

---
title: "Complex plot operations"
subtitle: "Here are some strange plot things we have done before"
author:
  - Elizabeth King
  - Kevin Middleton
format:
  revealjs:
    theme: [default, custom.scss]
    standalone: true
    self-contained: true
    logo: QMLS_Logo.png
    slide-number: true
    show-slide-number: all
    link-external-newwindow: true
---

## Complex plot operations

```{r}
#| label: setup
#| echo: false
#| warning: false
#| message: false

library(tidyverse)
library(cowplot)
ggplot2::theme_set(theme_cowplot())
library(patchwork)
library(lemon)
```

When at all possible:

- Generate figures with code
  - Even photos/microscopy/gel panels (`annotation_raster()`)
  - Use version tracking (git)
- Avoid post-export editing with Illustrator, Canvas, Inkscape, etc.

Reproducible and ultimately time-saving.


## Images in a grid

```{r}
#| echo: true
#| output-location: slide
library(jpeg)
img <- readJPEG(system.file("img", "Rlogo.jpg", package="jpeg"))

P <- map(.x = 1:4,
         .f = function(ii) {
           ggplot() +
             annotation_raster(img,
                               xmin = 0, xmax = dim(img)[2],
                               ymin = 0, ymax = dim(img)[1]) +
             xlim(c(0, dim(img)[2])) +
             ylim(c(0, dim(img)[1])) +
             coord_equal() +
             ggpubr::theme_transparent()
         })

wrap_plots(P) +
    plot_annotation(tag_levels = 'a', tag_suffix = ".")
```


## Resizing plots in a grid

- `patchwork` automatically handles axis alignment
- `cowplot::plot_grid()` gives fine control over relative plot size

## Data to work with

```{r}
#| echo: true
#| output-location: slide
set.seed(87534579)

M <- tibble(x1 = runif(20),
            x2 = runif(20),
            y1 = rnorm(20),
            y2 = rnorm(20))
p1 <- ggplot(M, aes(x1, y1)) + geom_point()
p2 <- ggplot(M, aes(x2, y1)) + geom_point()
p3 <- ggplot(M, aes(x1, y2)) + geom_point()
p4 <- ggplot(M, aes(x2, y2)) + geom_point()

plot_grid(p1, p2, p3, p4)
```


## Removing axes

```{r}
#| echo: true
#| output-location: slide
p1 <- ggplot(M, aes(x1, y1)) + geom_point() +
  theme(axis.title.x = element_blank(), axis.text.x = element_blank())
p2 <- ggplot(M, aes(x2, y1)) + geom_point() +
    theme(axis.title = element_blank(), axis.text = element_blank())
p3 <- ggplot(M, aes(x1, y2)) + geom_point()
p4 <- ggplot(M, aes(x2, y2)) + geom_point() +
  theme(axis.title.y = element_blank(), axis.text.y = element_blank())

plot_grid(p1, p2, p3, p4)
```


## Aligning axes

```{r}
#| echo: true
#| output-location: slide
plot_grid(p1, p2, p3, p4,
          align = "hv")
```


## Resizing sublots

```{r}
#| echo: true
#| output-location: slide
plot_grid(p1, p2, p3, p4,
          rel_widths = c(1.05, 1),
          rel_heights = c(1, 1.10))
```


## Moving the legend around

- `theme(legend.position = ...)` for basic positioning
- `lemon` package for [more options](https://cran.r-project.org/web/packages/lemon/vignettes/legends.html)


## Legend positioning 1

```{r}
#| echo: true
#| output-location: slide
p <- ggplot(palmerpenguins::penguins |> 
              drop_na(bill_length_mm, bill_depth_mm),
            aes(bill_length_mm, bill_depth_mm, color = species)) +
  geom_point() +
  facet_wrap("species", nrow = 2)
p +
  theme(legend.position = "inside",
        legend.position.inside = c(0.7, 0.1))
```


## Legend positioning with `reposition_legend`

- Can span multiple grid positions

```{r}
#| echo: true
#| output-location: slide
reposition_legend(p, "center", panel = "panel-2-2")
```


## Legend positioning 2

- Extracting the legend and adding manually with `grid.arrange()`

```{r}
#| echo: true
#| output-location: slide
p1 <- ggplot(M, aes(x1, y1, color = y1)) + geom_point()
p2 <- ggplot(M, aes(x2, y1, color = y1)) + geom_point()
p3 <- ggplot(M, aes(x1, y2, color = y1)) + geom_point()

library(gridExtra)
legend <- g_legend(p1 + theme(legend.position = "bottom"))
grid.arrange(p1 + theme(legend.position = "hidden"),
             p2 + theme(legend.position = "hidden"),
             p3 + theme(legend.position = "hidden"),
             legend)
```


## Customizing the legend elements

- `guides()` and `guide_legend()`
- Control fonts, position, layout of legend elements

```{r}
bp <- Data4Ecologists::beepollen |> 
  mutate(Bee_type = if_else(queen == 0, "Worker", "Queen")) |> 
  rename(Prop_removed = removed,
         Duration = duration) |> 
  select(-queen) |> 
  as_tibble()
```

```{r}
#| echo: true
#| output-location: slide
ggplot(bp, aes(x = Duration, y = Prop_removed, color = Bee_type)) +
  geom_path(linewidth = 3, alpha = 0.5, show.legend = FALSE) +
  geom_point(size = 10, alpha = 0.5) +
  guides(color = guide_legend(override.aes = list(size = 3,
                                                  alpha = 1)))
```


## Customizing facets

```{r}
#| echo: true
#| output-location: slide
PP <- palmerpenguins::penguins |> 
  mutate(Penguin_label = paste0(species, "\npenguin"))

ggplot(PP |> drop_na(bill_length_mm, bill_depth_mm),
       aes(bill_length_mm, bill_depth_mm, color = species)) +
  geom_point(show.legend = FALSE) +
  facet_grid(. ~ Penguin_label) +
  cowplot::theme_cowplot(font_size = 10) +
  theme(strip.background = element_blank(),
        strip.text = element_text(face = "bold", size = rel(1.5)))
```