# ggplot2
ggplot2::theme_set(ggplot2::theme_gray(base_size = 16))
# set seed
set.seed(1234)
# fontawesome
htmltools::tagList(rmarkdown::html_dependency_font_awesome())
# conflicted
library(conflicted)
conflict_prefer("filter", "dplyr")


## ----packages, echo=FALSE, message=FALSE, warning=FALSE---------
library(tidyverse)
library(Tmisc) # quartet

install.packages("remotes")
remotes::install_github("rstudio-education/dsbox")
library(dsbox) # dataset: student_survey


glimpse(starwars)


## ----mass-height, fig.width = 8, out.width = "52%", warning=T----
ggplot(data = starwars, mapping = aes(x = height, y = mass)) +
  geom_point() +
  labs(title = "Mass vs. height of Starwars characters",
       x = "Height (cm)", y = "Weight (kg)")


## ----ref.label="mass-height", fig.show = "hide"-----------------


## ----fig.width = 8, out.width = "52%"---------------------------
plot(starwars$height, starwars$mass,
main = "Mass vs. height of Starwars characters", xlab = "Height (cm)", ylab = "Weight (kg)")


## ---------------------------------------------------------------
library(tidyverse)


## ----quartet-for-show, eval = FALSE, echo = FALSE---------------
## library(Tmisc)
## quartet


## ----quartet-view1, echo = FALSE--------------------------------
quartet[1:22,]


## ----quartet-view2, echo = FALSE--------------------------------
quartet[23:44,]


## ----quartet-summary--------------------------------------------
quartet %>%
  group_by(set) %>%
  summarise(
    mean_x = mean(x), 
    mean_y = mean(y),
    sd_x = sd(x),
    sd_y = sd(y),
    r = cor(x, y)
  )


## ----quartet-plot, echo = T, out.width = "80%", fig.asp = 0.5----
ggplot(quartet, aes(x = x, y = y)) +
  geom_point() +
  facet_wrap(~ set, ncol = 4)


## ----quartet-R, fig.show='hide'---------------------------------
str(quartet)

attach(quartet)

par(mfrow=c(1,4))

for(j in levels(set)) 
  plot(x[set==j], y[set==j], main=j)

detach(quartet)


## ----ref.label="quartet-R", out.width = "80%", fig.asp = 0.5, echo=F, results='hide'----



## ----out.width = "80%", fig.asp = 0.5---------------------------
coplot(y ~ x | set, data = quartet)


## ---------------------------------------------------------------
str(student_survey)


## ----echo = FALSE, warning = FALSE------------------------------
ggplot(student_survey, aes(x = first_kiss)) +
  geom_histogram(binwidth = 1) +
  labs(
    title = "How old were you when you had your first kiss?", 
    x = "Age (years)", y = NULL
    )


## ----echo = FALSE, warning = FALSE------------------------------
ggplot(student_survey, aes(x = fb_visits_per_day)) +
  geom_histogram(binwidth = 1) +
  labs(
    title = "How many times do you go on Facebook per day?", 
    x = "Number of times", y = NULL
    )


## ---------------------------------------------------------------
library(palmerpenguins)
glimpse(penguins)


## ----ref.label = "penguins", echo = FALSE, warning = FALSE, out.width = "70%", fig.width = 8----


## ----penguins, fig.show = "hide"--------------------------------
ggplot(data = penguins, 
       mapping = aes(x = bill_depth_mm, y = bill_length_mm,
                     colour = species)) +
  geom_point() +
  labs(title = "Bill depth and length",
       subtitle = "Dimensions for Adelie, Chinstrap, and Gentoo Penguins",
       x = "Bill depth (mm)", y = "Bill length (mm)",
       colour = "Species")


## ----penguins-0, fig.show = "hide", warning = FALSE-------------
ggplot(data = penguins) #<<


## ----ref.label = "penguins-0", echo = FALSE, warning = FALSE, out.width = "100%", fig.width = 8----


## ----penguins-1, fig.show = "hide", warning = FALSE-------------
ggplot(data = penguins,
       mapping = aes(x = bill_depth_mm)) #<<


## ----ref.label = "penguins-1", echo = FALSE, warning = FALSE, out.width = "100%", fig.width = 8----


## ----penguins-2, fig.show = "hide", warning = FALSE-------------
ggplot(data = penguins,
       mapping = aes(x = bill_depth_mm,
                     y = bill_length_mm)) #<<


## ----ref.label = "penguins-2", echo = FALSE, warning = FALSE, out.width = "100%", fig.width = 8----


## ----penguins-3, fig.show = "hide", warning = FALSE-------------
ggplot(data = penguins,
       mapping = aes(x = bill_depth_mm,
                     y = bill_length_mm)) + 
  geom_point() #<<


## ----ref.label = "penguins-3", echo = FALSE, warning = FALSE, out.width = "100%", fig.width = 8----


## ----penguins-4, fig.show = "hide", warning = FALSE-------------
ggplot(data = penguins,
       mapping = aes(x = bill_depth_mm,
                     y = bill_length_mm,
                     colour = species)) + #<<
  geom_point()


## ----ref.label = "penguins-4", echo = FALSE, warning = FALSE, out.width = "100%", fig.width = 8----


## ----penguins-5, fig.show = "hide", warning = FALSE-------------
ggplot(data = penguins,
       mapping = aes(x = bill_depth_mm,
                     y = bill_length_mm,
                     colour = species)) +
  geom_point() +
  labs(title = "Bill depth and length") #<<


## ----ref.label = "penguins-5", echo = FALSE, warning = FALSE, out.width = "100%", fig.width = 8----


## ----penguins-6, fig.show = "hide", warning = FALSE-------------
ggplot(data = penguins,
       mapping = aes(x = bill_depth_mm,
                     y = bill_length_mm,
                     colour = species)) +
  geom_point() +
  labs(title = "Bill depth and length",
       subtitle = "Dimensions for Adelie, Chinstrap, and Gentoo Penguins") #<<


## ----ref.label = "penguins-6", echo = FALSE, warning = FALSE, out.width = "100%", fig.width = 8----


## ----penguins-7, fig.show = "hide", warning = FALSE-------------
ggplot(data = penguins,
       mapping = aes(x = bill_depth_mm,
                     y = bill_length_mm,
                     colour = species)) +
  geom_point() +
  labs(title = "Bill depth and length",
       subtitle = "Dimensions for Adelie, Chinstrap, and Gentoo Penguins",
       x = "Bill depth (mm)", y = "Bill length (mm)") #<<


## ----ref.label = "penguins-7", echo = FALSE, warning = FALSE, out.width = "100%", fig.width = 8----


## ----penguins-8, fig.show = "hide", warning = FALSE-------------
ggplot(data = penguins,
       mapping = aes(x = bill_depth_mm,
                     y = bill_length_mm,
                     colour = species)) +
  geom_point() +
  labs(title = "Bill depth and length",
       subtitle = "Dimensions for Adelie, Chinstrap, and Gentoo Penguins",
       x = "Bill depth (mm)", y = "Bill length (mm)",
       colour = "Species") #<<


## ----ref.label = "penguins-8", echo = FALSE, warning = FALSE, out.width = "100%", fig.width = 8----


## ----penguins-9, fig.show = "hide", warning = FALSE-------------
ggplot(data = penguins,
       mapping = aes(x = bill_depth_mm,
                     y = bill_length_mm,
                     colour = species)) +
  geom_point() +
  labs(title = "Bill depth and length",
       subtitle = "Dimensions for Adelie, Chinstrap, and Gentoo Penguins",
       x = "Bill depth (mm)", y = "Bill length (mm)",
       colour = "Species",
       caption = "Source: Palmer Station LTER / palmerpenguins package") #<<


## ----ref.label = "penguins-9", echo = FALSE, warning = FALSE, out.width = "100%", fig.width = 8----


## ----penguins-10, fig.show = "hide", warning = FALSE------------
ggplot(data = penguins,
       mapping = aes(x = bill_depth_mm,
                     y = bill_length_mm,
                     colour = species)) +
  geom_point() +
  labs(title = "Bill depth and length",
       subtitle = "Dimensions for Adelie, Chinstrap, and Gentoo Penguins",
       x = "Bill depth (mm)", y = "Bill length (mm)",
       colour = "Species",
       caption = "Source: Palmer Station LTER / palmerpenguins package") +
  scale_colour_viridis_d() #<<


## ----ref.label = "penguins-10", echo = FALSE, warning = FALSE, out.width = "100%", fig.width = 8----


## ----ref.label="penguins-10-nohighlight", echo = FALSE, warning = FALSE, out.width = "70%", fig.width = 8----


## ----penguins-10-nohighlight, fig.show = "hide"-----------------
ggplot(data = penguins,
       mapping = aes(x = bill_depth_mm,
                     y = bill_length_mm,
                     colour = species)) +
  geom_point() +
  labs(title = "Bill depth and length",
       subtitle = "Dimensions for Adelie, Chinstrap, and Gentoo Penguins",
       x = "Bill depth (mm)", y = "Bill length (mm)",
       colour = "Species",
       caption = "Source: Palmer Station LTER / palmerpenguins package") +
  scale_colour_viridis_d()


## ----named-args, eval = FALSE-----------------------------------
## ggplot(data = penguins,
##        mapping = aes(x = bill_depth_mm,
##                      y = bill_length_mm,
##                      colour = species)) +
##   geom_point() +
##   scale_colour_viridis_d()


## ----not-named-args, eval = FALSE-------------------------------
## ggplot(penguins,
##        aes(x = bill_depth_mm,
##            y = bill_length_mm,
##            colour = species)) +
##   geom_point() +
##   scale_colour_viridis_d()


## ----colour, fig.show = "hide", warning = FALSE-----------------
ggplot(penguins,
       aes(x = bill_depth_mm, 
           y = bill_length_mm,
           colour = species)) + #<<
  geom_point() +
  scale_colour_viridis_d()


## ----ref.label = "colour", echo = FALSE, warning = FALSE, out.width = "100%"----


## ----shape-species, fig.show = "hide", warning = FALSE----------
ggplot(penguins,
       aes(x = bill_depth_mm, 
           y = bill_length_mm,
           colour = species,
           shape = species)) + #<<
  geom_point() +
  scale_colour_viridis_d()


## ----ref.label = "shape-species", echo = FALSE, warning = FALSE, out.width = "100%"----


## ----size, fig.show = "hide", warning = FALSE-------------------
ggplot(penguins,
       aes(x = bill_depth_mm, 
           y = bill_length_mm,
           colour = species,
           shape = species,
           size = body_mass_g)) + #<<
  geom_point() +
  scale_colour_viridis_d()


## ----ref.label = "size", echo = FALSE, warning = FALSE, out.width = "100%"----


## ----alpha, fig.show = "hide", warning = FALSE------------------
ggplot(penguins,
       aes(x = bill_depth_mm, 
           y = bill_length_mm,
           colour = species,
           shape = species,
           size = body_mass_g,
           alpha = flipper_length_mm)) + #<<
  geom_point() +
  scale_colour_viridis_d()


## ----ref.label = "alpha", echo = FALSE, warning = FALSE, out.width = "100%"----


## ----warning = FALSE, out.width = "100%"------------------------
ggplot(penguins,
       aes(x = bill_depth_mm,
           y = bill_length_mm,
           size = body_mass_g, #<<
           alpha = flipper_length_mm)) + #<<
  geom_point()


## ----warning = FALSE, out.width = "100%"------------------------
ggplot(penguins,
       aes(x = bill_depth_mm,
           y = bill_length_mm)) + 
  geom_point(size = 2, alpha = 0.5) #<<


## ----ref.label = "facet", echo = FALSE, warning = FALSE, out.width = "70%"----


## ----facet, fig.show = "hide"-----------------------------------
ggplot(penguins, aes(x = bill_depth_mm, y = bill_length_mm)) + 
  geom_point() +
  facet_grid(species ~ island) #<<


## ----warning = FALSE--------------------------------------------
ggplot(penguins, aes(x = bill_depth_mm, y = bill_length_mm)) + 
  geom_point() +
  facet_grid(species ~ sex) #<<


## ----warning = FALSE--------------------------------------------
ggplot(penguins, aes(x = bill_depth_mm, y = bill_length_mm)) + 
  geom_point() +
  facet_grid(sex ~ species) #<<


## ----warning = FALSE, fig.asp = 0.5-----------------------------
ggplot(penguins, aes(x = bill_depth_mm, y = bill_length_mm)) + 
  geom_point() +
  facet_wrap(~ species) #<<


## ----warning = FALSE, fig.asp = 0.5-----------------------------
ggplot(penguins, aes(x = bill_depth_mm, y = bill_length_mm)) + 
  geom_point() +
  facet_grid(. ~ species) #<<


## ----warning = FALSE--------------------------------------------
ggplot(penguins, aes(x = bill_depth_mm, y = bill_length_mm)) + 
  geom_point() +
  facet_wrap(~ species, ncol = 2) #<<


## ----facet-color-legend, fig.show = "hide", warning = FALSE-----
ggplot(
  penguins, 
  aes(x = bill_depth_mm, 
      y = bill_length_mm, 
      color = species)) + #<<
  geom_point() +
  facet_grid(species ~ sex) +
  scale_color_viridis_d() #<<


## ----ref.label = "facet-color-legend", echo = FALSE, warning = FALSE, out.width = "100%"----


## ----facet-color-no-legend, fig.show = "hide", warning = FALSE----
ggplot(
  penguins, 
  aes(x = bill_depth_mm, 
      y = bill_length_mm, 
      color = species)) +
  geom_point() +
  facet_grid(species ~ sex) +
  scale_color_viridis_d() +
  guides(color = "none") #<<


## ----ref.label = "facet-color-no-legend", echo = FALSE, warning = FALSE, out.width = "100%"----