Grammer of graphics with ggplot

Aesthetic mappings

x, xmin, xmax

y, ymin, ymax

label

group
fill, color

size, alpha
shape, linetype

Code

ggplot(mtcars, aes(factor(carb), mpg)) +
  stat_summary(
    fun.data = mean_se, 
    geom = "pointrange", 
    width = 0.1, 
    color = "firebrick"
  ) +
  labs(
    x = "Number of carborators",
    y = "Mile per gallon"
  ) + 
  geom_point(
    position = position_jitter(width = 0.05), 
    shape = 21, 
    fill = "whitesmoke"
  ) +
  coord_flip() +
  annotate(
    geom = "text",
    y = c(23, 25.5, 27.5),
    x = c(0.8, 0.8, 0.8),
    label = c("xmin", "x", "xmax"),
    family = "consolas",
    color = "blue"
  )

Code

ggplot(mtcars, aes(factor(carb), mpg)) +
  stat_summary(
    fun.data = mean_se, 
    geom = "pointrange", 
    width = 0.1, 
    color = "firebrick"
  ) +
  labs(
    x = "Number of carborators",
    y = "Mile per gallon"
  ) + 
  geom_point(
    position = position_jitter(width = 0.05), 
    shape = 21, 
    fill = "whitesmoke"
  ) +
  annotate(
  geom = "text",
  y = c(23, 25.5, 27.5),
  x = c(0.8, 0.8, 0.8),
  label = c("ymin", "y", "ymax"),
  family = "consolas",
  color = "blue"
)

Code

ggplot(mtcars, aes(factor(carb), mpg)) +
  stat_summary(
    fun.data = mean_se, 
    geom = "pointrange", 
    width = 0.1, 
    color = "firebrick"
  ) +
  labs(
    x = "Number of carborators",
    y = "Mile per gallon"
  ) + 
  geom_point(
    position = position_jitter(width = 0.05), 
    shape = 21, 
    fill = "whitesmoke"
  ) +
  geom_text(
    data = ~subset(.x, carb >= 6),
    aes(label = model),
    check_overlap = TRUE,
    vjust = -1
  )

Code

ggplot(mtcars, aes(factor(carb), mpg, group = am, color = factor(am))) +
  geom_point(
    position = position_jitter(width = 0.05), 
    fill = "whitesmoke"
  ) +
  stat_summary(
    fun = mean,
    geom = "line"
  ) +
  stat_summary(
    fun.data = mean_se, 
    geom = "pointrange", 
    width = 0.1,
    fill = "whitesmoke"
  ) +
  labs(
    x = "Number of carborators",
    y = "Mile per gallon",
    color = "Engine",
    fill = "Engine",
  ) +
  theme(
    legend.position = c(1, 1),
    legend.justification = c(1, 1) + 0.25
  )

Code

ggplot(mtcars, aes(factor(carb), mpg, group = am)) +
  geom_point(
    position = position_jitter(width = 0.05), 
    fill = "whitesmoke",
    aes(shape = factor(am))
  ) +
  stat_summary(
    fun = mean,
    geom = "line",
    aes(linetype = factor(am))
  ) +
  stat_summary(
    fun.data = mean_se, 
    geom = "pointrange", 
    width = 0.1,
    fill = "whitesmoke",
    aes(shape = factor(am), linetype = factor(am))
  ) +
  labs(
    x = "Number of carborators",
    y = "Mile per gallon",
    color = "Engine",
    linetype = "Engine",
    fill = "Engine",
    shape = "Engine"
  ) +
  scale_shape_discrete(solid = FALSE) +
  theme(
    legend.position = c(1, 1),
    legend.justification = c(1, 1) + 0.25
  )

Summary statistics

mean, median
standard error (mean_se)
standard deviation (mean_sdl)

fitted model (geom_smooth)

Code

ggplot(mtcars, aes(factor(carb), mpg, group = am)) +
  geom_point(
    position = position_jitter(width = 0.05), 
    fill = "whitesmoke",
    aes(shape = factor(am))
  ) +
  stat_summary(
    fun = mean,
    geom = "line",
    aes(linetype = factor(am))
  ) +
  stat_summary(
    fun.data = mean_se, 
    geom = "pointrange", 
    width = 0.1,
    fill = "whitesmoke",
    aes(shape = factor(am), linetype = factor(am))
  ) +
  labs(
    x = "Number of carborators",
    y = "Mile per gallon",
    color = "Engine",
    linetype = "Engine",
    fill = "Engine",
    shape = "Engine"
  ) +
  scale_shape_discrete(solid = FALSE) +
  theme(
    legend.position = c(1, 1),
    legend.justification = c(1, 1) + 0.25
  )

Code

ggplot(mtcars, aes(factor(carb), mpg)) +
  geom_point(
    position = position_jitter(width = 0.05), 
    aes(shape = am),
    fill = "whitesmoke",
    size = rel(3)
  ) +
  geom_smooth(
    method = "lm",
    formula = "y ~ x",
    se = FALSE,
    aes(linetype = am, group = am)
  ) +
  labs(
    x = "Number of carborators",
    y = "Mile per gallon",
    color = "Engine",
    linetype = "Engine",
    fill = "Engine",
    shape = "Engine"
  ) +
  scale_shape_discrete(solid = FALSE) +
  theme(
    legend.position = c(1, 1),
    legend.justification = c(1, 1) + 0.25
  )

Faceting

facet_grid

facet_wrap

labeller

Code

ggplot(survival::cancer, aes(time)) +
  geom_histogram(
    aes(y = after_stat(density)), 
    fill = "#afafaf",
    binwidth = 365.241/4, 
    color = "#a0a0a0", 
    na.rm = TRUE
  ) +
  geom_density(na.rm = TRUE) +
  facet_grid(
    cols = vars(sex), 
    rows = vars(status)
  ) +
  labs(title = "Example of facet grid")

Code

cancer <- as.data.table(survival::cancer)
cancer[, age_group := cut(age, seq(35, 85, 10))]
ggplot(cancer, aes(time)) +
  geom_histogram(
    aes(y = after_stat(density)), 
    fill = "#afafaf",
    binwidth = 365.241/4, 
    color = "#a0a0a0", 
    na.rm = TRUE
  ) +
  geom_density(na.rm = TRUE) +
  facet_wrap(
    facets = vars(age_group),
  ) +
  labs(title = "Example of facet wrap")

Code

cancer <- as.data.table(survival::cancer)
cancer[, age_group := cut(age, seq(35, 85, 10))]
ggplot(cancer, aes(time)) +
  geom_histogram(
    aes(y = after_stat(density)), 
    fill = "#afafaf",
    binwidth = 365.241/4, 
    color = "#a0a0a0", 
    na.rm = TRUE
  ) +
  geom_density(na.rm = TRUE) +
  facet_wrap(
    facets = vars(age_group),
    labeller = labeller(
      age_group = function(x) {
        gsub("\\((.*?),(.*?)\\]", "Age Group: \\1-\\2", x)
      }
    )
  ) +
  labs(title = "Example of facet wrap")

Scale

Function to specify (customize) scales. Usually takes the form scale_<GEOM>_<TYPE>.

Code

cancer <- as.data.table(survival::cancer)
cancer[, age_group := cut(age, seq(35, 85, 10))]
ggplot(cancer, aes(time)) +
  geom_histogram(
    aes(y = after_stat(density)), 
    fill = "#afafaf",
    binwidth = 365.241/4, 
    color = "#a0a0a0", 
    na.rm = TRUE
  ) +
  geom_density(na.rm = TRUE) +
  facet_wrap(
    facets = vars(age_group),
    labeller = labeller(
      age_group = function(x) {
        gsub("\\((.*?),(.*?)\\]", "Age Group: \\1-\\2", x)
      }
    )
  ) +
  labs(title = "Example of facet wrap")

Code

ggplot(cancer, aes(time)) +
  geom_histogram(
    aes(y = after_stat(density)), 
    fill = "#afafaf",
    binwidth = 365.241/4, 
    color = "#a0a0a0", 
    na.rm = TRUE
  ) +
  geom_density(na.rm = TRUE) +
  facet_wrap(
    facets = vars(age_group),
    labeller = labeller(
      age_group = function(x) {
        gsub("\\((.*?),(.*?)\\]", "Age Group: \\1-\\2", x)
      }
    )
  ) +
  labs(title = "Example of facet wrap") +
  scale_x_continuous(
    breaks = seq(0, 3, 0.5) * 365.241,
    labels = function(x) x / 365.241
  )

Code

ggplot(cancer, aes(time)) +
  geom_histogram(
    aes(y = after_stat(density)), 
    fill = "#afafaf",
    binwidth = 365.241/4, 
    color = "#a0a0a0", 
    na.rm = TRUE
  ) +
  geom_density(na.rm = TRUE) +
  facet_wrap(
    facets = vars(age_group),
    labeller = labeller(
      age_group = function(x) {
        gsub("\\((.*?),(.*?)\\]", "Age Group: \\1-\\2", x)
      }
    )
  ) +
  labs(title = "Example of facet wrap") +
  scale_x_continuous(
    breaks = seq(0, 3, 0.5) * 365.241,
    labels = function(x) x / 365.241
  ) +
  scale_y_continuous(
    labels = scales::label_scientific()
  )

Scale

Code

mtcars$gear <- as.factor(mtcars$gear)
ggplot(mtcars, aes(hp, mpg, color = gear)) +
  geom_point(aes(size = wt), alpha = 0.8) +
  scale_size_continuous(breaks = seq(1, 6, 2), limits = c(1, 6)) +
  theme(
    legend.position = c(1, 1),
    legend.justification = c(1.5, 1.5),
    legend.direction = "horizontal"
  ) +
  labs(
    x = "Horse power", 
    y = "Mile per gallon",
    color = "Gear",
    size = "Weight"
  )

Theming `ggplot2`

axis: title, text, ticks, line
legend: background, margin, spacing, key, title,; position, direction justification, box
panel: spacing, grid, background
plot: title, subtitle, caption, tag, margin
strip: background, text

Code

mtcars$gear <- as.factor(mtcars$gear)
plt <- ggplot(mtcars, aes(hp, mpg, color = gear)) +
  geom_point(aes(size = wt), alpha = 0.8) +
  scale_size_continuous(breaks = seq(1, 6, 2), limits = c(1, 6)) +
  facet_grid(rows = vars(am)) +
  theme(
    legend.position = c(1, 1),
    legend.justification = c(1.5, 1.5),
    legend.direction = "horizontal"
  ) +
  labs(
    title = "Power vs Consumption",
    x = "Horse power", 
    y = "Mile per gallon",
    color = "Gear",
    size = "Weight"
  )
plt

Helpers:

element_text
element_line
element_rect
element_blank
margin
unit

Sourcehttps://github.com/isabellabenabaye/ggplot2-reference/blob/master/ggplot2-theme-elements-reference.pdf

Annotations

Use geom to add custom elements
geom can be point, line, segment, rect and more
Add custom grob using annotation_custom

Code

plt +
  annotate(
    geom = "rect",
    xmin = 150, xmax = 250,
    ymin = 10, ymax = 20,
    fill = "ghostwhite",
    alpha = 0.25,
    color = "grey"
  ) +
  annotate(
    geom = "text",
    x = 200,
    y = 20,
    label = "heavy vehicle and\nlow fuel efficint",
    vjust = -0.5,
    family = "mono"
  )

Extensions

patchwork, cowplot: Composing multiple ggplot plots
gganimate: Grammar of animated graphics with ggpolot2
ggstatsplot and ggpubr: Enhance ggplot2 with statistics and annotations

ggthemes, ggtech, see, ggsci: Extra themes and schemes for ggplot2
ggraph: Visualize network, graphs and trees
ggrepel, geomtextpath: Manage and direct text in your plot

More: survminer, ggridge, ggh4x

Grammer of graphics with `ggplot`

Introduction

Grammer of graphics

Plotting system in R

Plotting system in R

Plotting system in R

Components of `ggplot2`

Components of `ggplot2`

Customizing `ggplot2`

Aesthetic mappings

Summary statistics

Faceting

Scale

Scale

Theming `ggplot2`

Annotations

Extensions

Demo

Resources