Boxplot, violinplot, histogram, stripplot, beeswarm, raincloud

Пакеты

packages <- c("tidyverse", "palmerpenguins", "ggforce", "ggridges",
              "ggbeeswarm", "ggdist")

install.packages(packages)
devtools::install_github('erocoar/gghalves')

library(tidyverse)

Warning: package 'ggplot2' was built under R version 4.4.3

── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
✔ dplyr     1.1.4     ✔ readr     2.1.5
✔ forcats   1.0.0     ✔ stringr   1.5.1
✔ ggplot2   4.0.2     ✔ tibble    3.2.1
✔ lubridate 1.9.3     ✔ tidyr     1.3.1
✔ purrr     1.0.2     
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors

Пингвины

penguins <- palmerpenguins::penguins
my_penguins <- drop_na(penguins)

Квартили

quantile(c(1, 2, 4, 5, 8, 12, 14, 30))

  0%  25%  50%  75% 100% 
 1.0  3.5  6.5 12.5 30.0 

quantile(c(1, 2, 4, 5, 8, 12, 14, 30), type = 2)

  0%  25%  50%  75% 100% 
 1.0  3.0  6.5 13.0 30.0 

Ящик с усами

boxplot(c(1, 2, 4, 5, 8, 12, 14, 30))

boxplot(body_mass_g ~ species, data = my_penguins)

ggplot(my_penguins) +
  geom_boxplot(aes(x = species, y = body_mass_g), width = .5)

Гистограммы

hist(my_penguins$body_mass_g)

hist(my_penguins$body_mass_g,
     breaks = 4)

hist(my_penguins$body_mass_g,
     breaks = 100)

ggplot(my_penguins) +
  geom_histogram(aes(x = body_mass_g, fill = species), bins = 40)

Densityplot

density(c(1, 3, 3, 6)) %>% plot()

density(c(1, 3, 3, 6), kernel = "triangular") %>% plot()

density(c(1, 3, 3, 6), kernel = "rectangular") %>% plot()

density(c(1, 3, 3, 6), kernel = "optcosine") %>% plot()

density(c(1, 3, 3, 6), bw = .1) %>% plot()

density(c(1, 3, 3, 6), bw = 2) %>% plot()

ggplot(my_penguins) +
  geom_density(aes(x = body_mass_g, fill = species))  

ggplot(my_penguins) +
  geom_density(aes(x = body_mass_g, fill = species), adjust = .2)

ggplot(my_penguins) +
  geom_density(aes(x = body_mass_g, fill = species), adjust = 2)

ggplot(my_penguins) +
  geom_density(aes(x = body_mass_g, fill = species), kernel = "triangular")  

Ridgelines (joyplot)

my_penguins %>%
  ggplot(aes(x = body_mass_g, y = species)) +
  ggridges::geom_density_ridges()

Picking joint bandwidth of 153

my_penguins %>%
  ggplot(aes(x = body_mass_g, y = species)) +
  ggridges::geom_density_ridges() +
  scale_y_discrete(expand = c(0, 0)) +     # will generally have to set the `expand` option
  scale_x_continuous(expand = c(0, 0)) +
  coord_cartesian(clip = "off") +
  ggridges::theme_ridges()

Picking joint bandwidth of 153

Violinplot

ggplot(my_penguins) +
  geom_density(aes(y = body_mass_g))  

ggplot(my_penguins) +
  geom_violin(aes(y = body_mass_g, x = ""))

ggplot(my_penguins) +
  geom_violin(aes(y = body_mass_g, x = species))

ggplot(my_penguins) +
  geom_violin(aes(y = body_mass_g, x = species)) +
  coord_flip()

ggplot(my_penguins) +
  geom_violin(aes(y = body_mass_g, x = species),
              quantiles = c(0.25, 0.5, 0.75),
              quantile.linetype = c("solid"))

ggplot(my_penguins) +
  geom_violin(aes(y = body_mass_g, x = species),
              quantiles = c(0.25, 0.5, 0.75),
              quantile.linetype = c("dotted", "dashed", "dotted"))

ggplot(my_penguins) +
  geom_violin(aes(y = body_mass_g, x = species),
              quantiles = seq(0.1, 0.9, by = 0.1),
              quantile.linetype = c("dotted"))

Stripplot

point + position=jitter

ggplot(data = my_penguins) +
  geom_point(aes(x = species, y = body_mass_g))

ggplot(data = my_penguins) +
  geom_point(aes(x = species, y = body_mass_g), alpha = .7)

ggplot(data = my_penguins) +
  geom_point(aes(x = species, y = body_mass_g),
             alpha = .7,
             position = "jitter") +
  geom_point(aes(x = species, y = body_mass_g), alpha = .7, colour = "purple")

ggplot(data = my_penguins) +
  geom_point(aes(x = species, y = body_mass_g),
             alpha = .7,
             position = position_jitter(width = .3, height = 0))

ggplot(data = my_penguins) +
  geom_jitter(aes(x = species, y = body_mass_g),
              width = .3, height = 0)

ggforce::sina() (точке в форме виоланчели)

ggplot(my_penguins) +
  ggforce::geom_sina(aes(y = body_mass_g, x = species), position = "identity")

ggplot(my_penguins) +
  ggforce::geom_sina(aes(y = body_mass_g, x = species, colour = sex), position = "identity")

Beeswarm

ggplot(my_penguins) +
  ggbeeswarm::geom_quasirandom(aes(y = body_mass_g, x = species, fill = species), width = .35)

ggplot(my_penguins) +
  ggbeeswarm::geom_quasirandom(aes(y = body_mass_g, x = species, fill = species), width = .35, method = "smiley")

ggplot(my_penguins) +
  ggbeeswarm::geom_quasirandom(aes(y = body_mass_g, x = species, fill = species), width = .35, method = "frowney")

ggplot(data = my_penguins) +
  ggbeeswarm::geom_beeswarm(aes(y = body_mass_g, x = species))

ggplot(data = my_penguins) +
  ggbeeswarm::geom_beeswarm(aes(y = body_mass_g, x = species), cex = 2)

ggplot(data = my_penguins) +
  ggbeeswarm::geom_beeswarm(aes(y = body_mass_g, x = species), cex = 2, method = "compactswarm")

ggplot(data = my_penguins) +
  ggbeeswarm::geom_beeswarm(aes(y = body_mass_g, x = species), cex = 2, method = "hex")

Warning: In `position_beeswarm`, method `hex` discretizes the data axis (a.k.a the
continuous or non-grouped axis).
This may result in changes to the position of the points along that axis,
proportional to the value of `cex`.
To prevent this behavior, set `preserve.data.axis=TRUE`.
This warning is displayed once per session.

ggplot(data = my_penguins) +
  ggbeeswarm::geom_beeswarm(aes(y = body_mass_g, x = species), cex = 2, method = "hex", side = 1)

ggplot(data = my_penguins) +
  ggbeeswarm::geom_beeswarm(aes(y = body_mass_g, x = species), cex = 2, method = "hex", side = -1)

ggplot(data = my_penguins) +
  ggbeeswarm::geom_beeswarm(aes(y = body_mass_g, x = species), method = "compactswarm", cex = 4)

ggplot(data = my_penguins) +
  ggbeeswarm::geom_beeswarm(aes(y = body_mass_g, x = species), method = "compactswarm", cex = 4, corral = "gutter")

dotplot

ggplot(data = my_penguins) +
  geom_dotplot(aes(x = body_mass_g), binwidth = 40, 
               dotsize = .9,
               stackratio = 1.6)

ggplot(data = my_penguins) +
  geom_dotplot(aes(x = body_mass_g), binwidth = 40, 
               dotsize = .9,
               stackratio = 1.6,
               stackdir = "centerwhole")

ggplot(data = my_penguins) +
  geom_dotplot(aes(y = body_mass_g, x = species), binaxis = "y", stackdir = "center", dotsize = .6, stackratio = 1.2, binwidth = 100)

Объединяем все вместе!

Склеивая разные слоя

ggplot(data = my_penguins) +
  geom_violin(aes(x = species, y = body_mass_g, fill = species)) +
  ggforce::geom_sina(aes(x = species, y = body_mass_g)) +
  geom_boxplot(aes(x = species, y = body_mass_g), width = .1,
               alpha = .8, outliers = FALSE)

ggplot(data = my_penguins, aes(x = species, y = body_mass_g)) +
  geom_violin(aes(fill = species)) +
  ggforce::geom_sina(size = .7) +
  geom_boxplot(width = .1, alpha = .8, outliers = FALSE) +
  scale_fill_brewer(palette = "Set1") +
  hrbrthemes::theme_ipsum()

ggplot(data = my_penguins, aes(x = species, y = body_mass_g)) +
  geom_violin(aes(fill = species)) +
  ggforce::geom_sina(size = .7, shape = 21, colour = "grey35", fill = "#EECCBB") +
  geom_boxplot(width = .1, alpha = .8, outliers = FALSE) +
  scale_fill_brewer(palette = "Set1") +
  hrbrthemes::theme_ipsum()

position_nudge

ggplot(data = my_penguins, aes(x = species, y = body_mass_g)) +
  geom_violin(aes(fill = species), width = .2, position = position_nudge(x = .2)) +
  geom_jitter(width = .1)  +
  geom_boxplot(width = .1, alpha = .8, position = position_nudge(x = -.2))

violinplot + stat_summary()

ggplot(my_penguins, aes(x = species, y = body_mass_g)) +
  geom_violin() +
  stat_summary(fun.data = mean_cl_normal)

ggplot(my_penguins, aes(x = species, y = body_mass_g)) +
  geom_violin() +
  stat_summary(shape = 10, size = .1, fun.data = mean_cl_normal,
               colour = "brown")

ggplot(my_penguins, aes(x = species, y = body_mass_g)) +
  geom_violin() +
  stat_summary(geom = "errorbar", width = .05)

No summary function supplied, defaulting to `mean_se()`

ggplot(my_penguins, aes(x = species, y = body_mass_g)) +
  geom_violin() +
  stat_summary(geom = "linerange", width = .05)

Warning in stat_summary(geom = "linerange", width = 0.05): Ignoring unknown
parameters: `width`

No summary function supplied, defaulting to `mean_se()`

ggridges::geom_density_ridges(): Raincloud plot

ggplot(my_penguins) +
  ggridges::geom_density_ridges(
    aes(
      x = body_mass_g,
      y = species,
      fill = species,
      colour = species
    ),
    jittered_points = TRUE,
    alpha = 0.7
  ) 

Picking joint bandwidth of 153

ggplot(my_penguins) +
  ggridges::geom_density_ridges(
    aes(
      x = body_mass_g,
      y = species,
      fill = species,
      colour = species
    ),
    jittered_points = TRUE,
    position = "raincloud",
    alpha = 0.7
  ) +
  scale_fill_brewer(palette = "Set1") +
  scale_colour_brewer(palette = "Set1") +
  hrbrthemes::theme_ipsum()

Picking joint bandwidth of 153

gghalves: половинки!

ggplot(my_penguins, 
       aes(y = body_mass_g, x = species, colour = species)) +
  gghalves::geom_half_boxplot() 

ggplot(my_penguins, 
       aes(y = body_mass_g, x = species, colour = species)) +
  gghalves::geom_half_boxplot() +
  gghalves::geom_half_violin(position = position_dodge(width = 3), side = "r")

ggplot(my_penguins, 
       aes(y = body_mass_g, x = species, colour = species)) +
  gghalves::geom_half_boxplot() +
  gghalves::geom_half_violin(position = position_dodge(width = 3), side = "r") +
  gghalves::geom_half_dotplot(position = ggridges::position_points_sina(), dotsize = .2, binwidth = 100)