library(ggrepel)
set.seed(42)
ggplot(mtcars) +
  geom_point(aes(wt, mpg), color = 'red') +
  geom_text_repel(aes(wt, mpg, label = rownames(mtcars))) +
  theme_classic(base_size = 16)

set.seed(42)
ggplot(mtcars) +
  geom_point(aes(wt, mpg), size = 5, color = 'grey') +
  geom_label_repel(
    aes(wt, mpg, fill = factor(cyl), label = rownames(mtcars)),
    fontface = 'bold', color = 'white',
    box.padding = 0.35, point.padding = 0.5,
    segment.color = 'grey50'
  ) +
  theme_classic(base_size = 16)

set.seed(42)
ggplot(mtcars) +
  geom_point(aes(wt, mpg, color = factor(cyl)), size = 3) +
  geom_text_repel(
    aes(
      wt, mpg,
      color = factor(cyl),
      label = rownames(mtcars),
      # Cars with 4 cylinders are rotated 90 degrees.
      angle = ifelse(mtcars$cyl == 4, 90, 0)
    ),
    size = 4,
    family = 'Times',
    fontface = 'bold',
    # Add extra padding around each text label.
    box.padding = 0.5,
    # Add extra padding around each data point.
    point.padding = 1.6,
    # Color of the line segments.
    segment.color = '#cccccc',
    # Width of the line segments.
    segment.size = 0.5,
    # Draw an arrow from the label to the data point.
    arrow = arrow(length = unit(0.01, 'npc')),
    # Strength of the repulsion force.
    force = 1,
    # Maximum iterations of the naive repulsion algorithm O(n^2).
    max.iter = 3e3,
    # Cars with 6 cylinders are nudged up and to the right.
    nudge_x = ifelse(mtcars$cyl == 6, 2, 0),
    nudge_y = ifelse(mtcars$cyl == 6, 9, 0)
  ) +
  scale_color_discrete(name = 'cyl') +
  scale_x_continuous(expand = c(0.5, 0)) +
  scale_y_continuous(expand = c(0.25, 0)) +
  theme_classic(base_size = 16)

set.seed(42)

mtcars$label <- rownames(mtcars)

ggplot(mtcars, aes(wt, mpg, label = label)) +
  geom_point(color = "red") +
  geom_text_repel(point.padding = NA) +
  theme_bw(base_size = 16)

set.seed(42)

mtcars$label <- rownames(mtcars)
mtcars$label[1:15] <- ""

ggplot(mtcars, aes(wt, mpg)) +
  geom_point(aes(color = factor(cyl)), size = 2) +
  geom_text_repel(
    aes(
      color = factor(cyl),
      size = hp,
      label = label
    ),
    point.padding = 0.25,
    box.padding = 0.25,
    nudge_y = 0.1
  ) +
  theme_bw(base_size = 16)

set.seed(42)
data <- mtcars
mu <- mean(data$wt)

left <- data[data$wt < mu,]
right <- data[data$wt >= mu,]

ggplot() +
  geom_vline(xintercept = mu) +
  geom_point(
    data = data,
    mapping = aes(wt, mpg)
  ) +
  geom_text_repel(
    data = left,
    mapping = aes(wt, mpg, label = rownames(left), colour = 'Left half'),
    # Limit labels to the left of the vertical x=mu line
    xlim = c(NA, mu)
  ) +
  geom_text_repel(
    data = right,
    mapping = aes(wt, mpg, label = rownames(right), colour = 'Right half'),
    # Limit labels to the right of the vertical x=mu line
    xlim = c(mu, NA)
  ) +
  theme_classic(base_size = 16)

set.seed(42)

ggplot(mtcars) +
  geom_point(aes(wt, mpg), color = 'red') +
  geom_text_repel(aes(wt, mpg, label = rownames(mtcars)), direction = "x") +
  theme_classic(base_size = 16) + xlim(1,6)

set.seed(42)

ggplot(mtcars) +
  geom_point(aes(wt, mpg), color = 'red') +
  geom_text_repel(aes(wt, mpg, label = rownames(mtcars)), direction = "y") +
  theme_classic(base_size = 16)

set.seed(42)
ggplot(Orange, aes(age, circumference, color = Tree)) +
  geom_line() +
  coord_cartesian(xlim = c(min(Orange$age), max(Orange$age) + 90)) +
  geom_text_repel(
    data = subset(Orange, age == max(age)),
    aes(label = paste("Tree", Tree)),
    size = 6,
    nudge_x = 45,
    segment.color = NA
  ) +
  theme_classic(base_size = 16) +
  theme(legend.position = "none") +
  labs(title = "Orange Trees", x = "Age (days)", y = "Circumference (mm)")

set.seed(42)

# Read Stephen Turner's data
genes <- read.table("genes.txt.bz2", header = TRUE)
genes$Significant <- ifelse(genes$padj < 0.05, "FDR < 0.05", "Not Sig")

ggplot(genes, aes(x = log2FoldChange, y = -log10(pvalue))) +
  geom_point(aes(color = Significant)) +
  scale_color_manual(values = c("red", "grey")) +
  theme_bw(base_size = 16) +
  geom_text_repel(
    data = subset(genes, padj < 0.05),
    aes(label = Gene),
    size = 5,
    box.padding = 0.25,
    point.padding = 0.3
  )
ggsave("figures/ggrepel/volcano-1.png", width = 12, height = 8, dpi = 84)

set.seed(42)

mtcars$label <- rownames(mtcars)
mtcars$label[mtcars$mpg < 25] <- ""
ggplot(mtcars, aes(x = wt, y = mpg, label = label)) +
  coord_polar(theta = "x") +
  geom_point(aes(color = factor(cyl)), size = 2) +
  geom_text_repel(
    aes(
      color = factor(cyl)
    ),
    point.padding = 0.25,
    box.padding = 0.25,
    nudge_y = 0.1
  ) +
  theme_bw(base_size = 16)

library(gridExtra)

set.seed(0)
d <- data.frame(
  x = runif(30),
  y = runif(30),
  Parameter = c(
    "prod(plain(P)(X == x), x)",
    "integral(f(x) * dx, a, b)",
    "lim(f(x), x %->% 0)",
    rep("", 27)
  )
)

p1 <- ggplot(d, aes(x, y, label = Parameter)) +
  geom_point() +
  geom_text_repel(
    parse = TRUE, size = 8,
    min.segment.length = 0,
    point.padding = 0.5,
    box.padding = 0.5
  ) +
  theme_classic(base_size = 20)

p2 <- ggplot(d, aes(x, y, label = Parameter)) +
  geom_point() +
  geom_label_repel(parse = TRUE, size = 8, alpha = 0.5) +
  theme_classic(base_size = 20)

grid.arrange(p1, p2, ncol = 2)

# This chunk of code will take a minute or two to run.
library(ggrepel)
library(animation)

plot_frame <- function(n) {
  set.seed(42)
  p <- ggplot(mtcars) +
    geom_point(aes(wt, mpg), color = 'red') +
    geom_text_repel(
      aes(wt, mpg, label = rownames(mtcars)),
      size = 5, force = 3, max.iter = n
    ) +
    theme_classic(base_size = 16)
  print(p)
}

saveGIF(
  lapply(ceiling(1.75^(1:12)), function(i) {
    plot_frame(i)
  }),
  interval = 0.20,
  ani.width = 800,
  ani.heigth = 600,
  movie.name = 'animated.gif'
)