EVOLUTION-MANAGER

Edit File: introduction.R

## ----warning = FALSE, message = FALSE-----------------------------------------
library(ggplot2)
library(ggridges)

data <- data.frame(x = 1:5, y = rep(1, 5), height = c(0, 1, 3, 4, 2))
ggplot(data, aes(x, y, height = height)) + geom_ridgeline()

## ----message = FALSE, fig.width=9, fig.height=3-------------------------------
library(patchwork) # for side-by-side plotting

data <- data.frame(x = 1:5, y = rep(1, 5), height = c(0, 1, -1, 3, 2))
plot_base <- ggplot(data, aes(x, y, height = height))

plot_base + geom_ridgeline() | plot_base + geom_ridgeline(min_height = -2)

## ----message = FALSE----------------------------------------------------------
d <- data.frame(
  x = rep(1:5, 3),
  y = c(rep(0, 5), rep(1, 5), rep(2, 5)),
  height = c(0, 1, 3, 4, 0, 1, 2, 3, 5, 4, 0, 5, 4, 4, 1)
)

ggplot(d, aes(x, y, height = height, group = y)) + 
  geom_ridgeline(fill = "lightblue")

## ----message = FALSE----------------------------------------------------------
ggplot(d, aes(x, y, height = height, group = y)) + 
  geom_density_ridges(stat = "identity", scale = 1)

## ----message=FALSE------------------------------------------------------------
ggplot(iris, aes(x = Sepal.Length, y = Species)) + geom_density_ridges()

## ----message=FALSE------------------------------------------------------------
ggplot(iris, aes(x = Sepal.Length, y = Species)) + geom_density_ridges2()

## ----message=FALSE------------------------------------------------------------
# modified dataset that represents species as a number
iris_num <- transform(iris, Species_num = as.numeric(Species))

# does not work, causes error
# ggplot(iris_num, aes(x = Sepal.Length, y = Species)) + geom_density_ridges()

# works 
ggplot(iris_num, aes(x = Sepal.Length, y = Species_num, group = Species_num)) + 
  geom_density_ridges()

## ----message=FALSE------------------------------------------------------------
ggplot(iris, aes(x = Sepal.Length, y = Species)) + 
  geom_density_ridges(rel_min_height = 0.01)

## ----message=FALSE------------------------------------------------------------
# scale = 0.9, not quite touching
ggplot(iris, aes(x = Sepal.Length, y = Species)) + geom_density_ridges(scale = 0.9)
# scale = 1, exactly touching
ggplot(iris, aes(x = Sepal.Length, y = Species)) + geom_density_ridges(scale = 1)
# scale = 5, substantial overlap
ggplot(iris, aes(x = Sepal.Length, y = Species)) + geom_density_ridges(scale = 5)

## ----message=FALSE------------------------------------------------------------
ggplot(iris, aes(x = Sepal.Length, y = Species)) + 
  geom_density_ridges(scale = 1) + facet_wrap(~Species)

## ----message = FALSE----------------------------------------------------------
d <- data.frame(
  x = rep(1:5, 3) + c(rep(0, 5), rep(0.3, 5), rep(0.6, 5)),
  y = c(rep(0, 5), rep(1, 5), rep(3, 5)),
  height = c(0, 1, 3, 4, 0, 1, 2, 3, 5, 4, 0, 5, 4, 4, 1))

ggplot(d, aes(x, y, height = height, group = y, fill = factor(x+y))) +
  geom_ridgeline_gradient() +
  scale_fill_viridis_d(direction = -1, guide = "none")

## ----message = FALSE----------------------------------------------------------
ggplot(lincoln_weather, aes(x = `Mean Temperature [F]`, y = Month, fill = stat(x))) +
  geom_density_ridges_gradient(scale = 3, rel_min_height = 0.01) +
  scale_fill_viridis_c(name = "Temp. [F]", option = "C") +
  labs(title = 'Temperatures in Lincoln NE in 2016')

## ----message = FALSE----------------------------------------------------------
ggplot(iris, aes(x = Sepal.Length, y = Species)) +
  stat_density_ridges(quantile_lines = TRUE)

## ----message = FALSE----------------------------------------------------------
ggplot(iris, aes(x = Sepal.Length, y = Species)) +
  stat_density_ridges(quantile_lines = TRUE, quantiles = 2)

## ----message = FALSE----------------------------------------------------------
ggplot(iris, aes(x = Sepal.Length, y = Species)) +
  stat_density_ridges(quantile_lines = TRUE, quantiles = c(0.025, 0.975), alpha = 0.7)

## ----message = FALSE----------------------------------------------------------
ggplot(iris, aes(x=Sepal.Length, y=Species, fill = factor(stat(quantile)))) +
  stat_density_ridges(
    geom = "density_ridges_gradient", calc_ecdf = TRUE,
    quantiles = 4, quantile_lines = TRUE
  ) +
  scale_fill_viridis_d(name = "Quartiles")

## ----message = FALSE----------------------------------------------------------
ggplot(iris, aes(x = Sepal.Length, y = Species, fill = factor(stat(quantile)))) +
  stat_density_ridges(
    geom = "density_ridges_gradient",
    calc_ecdf = TRUE,
    quantiles = c(0.025, 0.975)
  ) +
  scale_fill_manual(
    name = "Probability", values = c("#FF0000A0", "#A0A0A0A0", "#0000FFA0"),
    labels = c("(0, 0.025]", "(0.025, 0.975]", "(0.975, 1]")
  )

## ----message = FALSE----------------------------------------------------------
ggplot(iris, aes(x = Sepal.Length, y = Species, fill = 0.5 - abs(0.5 - stat(ecdf)))) +
  stat_density_ridges(geom = "density_ridges_gradient", calc_ecdf = TRUE) +
  scale_fill_viridis_c(name = "Tail probability", direction = -1)

## ----message = FALSE----------------------------------------------------------
ggplot(iris, aes(x = Sepal.Length, y = Species)) +
  geom_density_ridges(jittered_points = TRUE)

## ----message = FALSE----------------------------------------------------------
ggplot(iris, aes(x = Sepal.Length, y = Species)) +
  geom_density_ridges(
    jittered_points = TRUE,
    position = position_points_jitter(width = 0.05, height = 0),
    point_shape = '|', point_size = 3, point_alpha = 1, alpha = 0.7,
  )

## ----message = FALSE----------------------------------------------------------
ggplot(iris, aes(x = Sepal.Length, y = Species, fill = Species)) +
  geom_density_ridges(
    aes(point_color = Species, point_fill = Species, point_shape = Species),
    alpha = .2, point_alpha = 1, jittered_points = TRUE
  ) +
  scale_point_color_hue(l = 40) +
  scale_discrete_manual(aesthetics = "point_shape", values = c(21, 22, 23))

## ----message = FALSE, fig.width = 6, fig.height = 6---------------------------
ggplot(iris, aes(x = Sepal.Length, y = Species, fill = Species)) +
  geom_density_ridges(
    aes(point_shape = Species, point_fill = Species, point_size = Petal.Length), 
    alpha = .2, point_alpha = 1, jittered_points = TRUE
  ) +
  scale_point_color_hue(l = 40) + scale_point_size_continuous(range = c(0.5, 4)) +
  scale_discrete_manual(aesthetics = "point_shape", values = c(21, 22, 23))

## ----message = FALSE----------------------------------------------------------
ggplot(iris, aes(x = Sepal.Length, y = Species)) +
  geom_density_ridges(
    jittered_points = TRUE, quantile_lines = TRUE, scale = 0.9, alpha = 0.7,
    vline_size = 1, vline_color = "red",
    point_size = 0.4, point_alpha = 1,
    position = position_raincloud(adjust_vlines = TRUE)
  )

## ----message=FALSE------------------------------------------------------------
ggplot(iris, aes(x = Sepal.Length, y = Species, height = stat(density))) + 
  geom_density_ridges(stat = "density")

## ----message=FALSE------------------------------------------------------------
library(dplyr)

iris_densities <- iris %>%
  group_by(Species) %>%
  group_modify(~ ggplot2:::compute_density(.x$Sepal.Length, NULL)) %>%
  rename(Sepal.Length = x)

iris_densities

## ----message=FALSE------------------------------------------------------------
ggplot(iris_densities, aes(x = Sepal.Length, y = Species, height = density)) + 
  geom_density_ridges(stat = "identity")

## ----message=FALSE------------------------------------------------------------
ggplot(iris, aes(x = Sepal.Length, y = Species, height = stat(density))) + 
  geom_density_ridges(stat = "binline", bins = 20, scale = 0.95, draw_baseline = FALSE)

## ----message=FALSE------------------------------------------------------------
ggplot(iris, aes(x = Sepal.Length, y = Species)) + 
  geom_density_ridges() + 
  theme_ridges()

## ----message=FALSE, warning=FALSE---------------------------------------------
ggplot(iris, aes(x = Sepal.Length, y = Species)) + 
  geom_density_ridges() + 
  scale_x_continuous(expand = c(0, 0)) +
  scale_y_discrete(expand = expand_scale(mult = c(0.01, .7))) +
  theme_ridges()

## ----message=FALSE------------------------------------------------------------
ggplot(iris, aes(x = Sepal.Length, y = Species)) + 
  geom_density_ridges() +
  scale_x_continuous(expand = c(0, 0)) +
  scale_y_discrete(expand = c(0, 0)) +
  coord_cartesian(clip = "off") +
  theme_ridges()

## ----message=FALSE------------------------------------------------------------
 ggplot(iris, aes(x = Sepal.Length, y = Species)) + 
   geom_density_ridges() + 
   scale_x_continuous(expand = c(0, 0)) +
   scale_y_discrete(expand = c(0, 0)) +
   coord_cartesian(clip = "off") +
   theme_minimal(base_size = 14) + 
   theme(axis.text.y = element_text(vjust = 0))

## ----message=FALSE------------------------------------------------------------
 ggplot(diamonds, aes(x = price, y = cut, fill = cut)) + 
   geom_density_ridges(scale = 4) + 
   scale_fill_cyclical(values = c("blue", "green"))

## ----message=FALSE, fig.width = 5.5-------------------------------------------
 ggplot(diamonds, aes(x = price, y = cut, fill = cut)) + 
   geom_density_ridges(scale = 4) + 
   scale_fill_cyclical(values = c("blue", "green"), guide = "legend")

## ----message=FALSE, fig.width = 6.5-------------------------------------------
 ggplot(diamonds, aes(x = price, y = cut, fill = cut, color = cut)) + 
   geom_density_ridges(scale = 4, size = 1) + 
   scale_fill_cyclical(
     name = "Color scheme",
     values = c("blue", "green"), guide = "legend",
     labels = c("Fair" = "blue w/ black outline", "Good" = "green w/ yellow outline")
    ) +
   scale_color_cyclical(
     name = "Color scheme",
     values = c("black", "yellow"), guide = "legend",
     labels = c("Fair" = "blue w/ black outline", "Good" = "green w/ yellow outline")
   )

## ----message=FALSE, fig.width = 6.5-------------------------------------------
ggplot(mpg, aes(x = class, fill = class, color = class)) + 
  geom_bar(size = 1.5) +
  scale_fill_cyclical(
    name = "Color scheme",
    values = c("blue", "green"), guide = "legend",
    labels = c("blue w/ black outline", "green w/ yellow outline")
  ) +
  scale_color_cyclical(
    name = "Color scheme",
    values = c("black", "yellow"), guide = "legend",
    labels = c("blue w/ black outline", "green w/ yellow outline")
  )

## ----message=FALSE, fig.width=5.5---------------------------------------------
mpg %>% group_by(class) %>% 
  tally() %>% 
  arrange(desc(n)) %>%
  mutate(class = factor(class, levels = class)) %>%
  ggplot(aes(x = class, y = n, fill = class)) + 
  geom_col() +
  scale_fill_cyclical(values = c("#4040B0", "#9090F0")) +
  scale_y_continuous(expand = c(0, 0)) + 
  theme_minimal()