## ----child = "../setup.Rmd"----------------------------------------------------

## ----setup, include=FALSE------------------------------------------------------
# R options
options(
  htmltools.dir.version = FALSE,
  dplyr.print_min = 6, 
  dplyr.print_max = 6,
  tibble.width = 65,
  width = 65
  )
# figure height, width, dpi
knitr::opts_chunk$set(echo = TRUE, 
                      fig.width = 8, 
                      fig.asp = 0.618,
                      out.width = "60%",
                      fig.align = "center",
                      dpi = 300,
                      message = FALSE)
# ggplot2
ggplot2::theme_set(ggplot2::theme_gray(base_size = 16))
# set seed
set.seed(1234)
# fontawesome
htmltools::tagList(rmarkdown::html_dependency_font_awesome())
# magick
dev.off <- function(){
  invisible(grDevices::dev.off())
}
# conflicted
library(conflicted)
conflict_prefer("filter", "dplyr")
# xaringanExtra
library(xaringanExtra)
xaringanExtra::use_panelset()
# output number of lines
hook_output <- knitr::knit_hooks$get("output")
knitr::knit_hooks$set(output = function(x, options) {
  lines <- options$output.lines
  if (is.null(lines)) {
    return(hook_output(x, options))  # pass to default hook
  }
  x <- unlist(strsplit(x, "\n"))
  more <- "..."
  if (length(lines)==1) {        # first n lines
    if (length(x) > lines) {
      # truncate the output, but add ....
      x <- c(head(x, lines), more)
    }
  } else {
    x <- c(more, x[lines], more)
  }
  # paste these lines together
  x <- paste(c(x, ""), collapse = "\n")
  hook_output(x, options)
})



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


## ----echo=FALSE, out.width="80%"-----------------------------------------------
knitr::include_graphics("img/ggplot2-part-of-tidyverse.png")


## ----echo=FALSE, out.width="100%"----------------------------------------------
knitr::include_graphics("img/grammar-of-graphics.png")


## ------------------------------------------------------------------------------
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)")


## ----fig.width = 8, warning = FALSE, echo=FALSE, out.width = "50%"-------------
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)") +
  geom_point(data = starwars %>% filter(name == "Jabba Desilijic Tiure"), size = 5, pch = 1, color = "pink", stroke = 3)


## ----echo = FALSE, warning = FALSE, cache = TRUE, out.width = "80%"------------
jabba <- image_read("img/jabba.png")

fig <- image_graph(width = 1600, height = 900, res = 200)
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)") +
  geom_point(data = starwars %>% filter(name == "Jabba Desilijic Tiure"), size = 5, pch = 1, color = "pink", stroke = 3)
dev.off()

out <- fig %>% image_composite(jabba, offset = "+1000+30")

image_write(out, "img/jabbaplot.png", format = "png")
knitr::include_graphics("img/jabbaplot.png")


## ----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)


## ----echo=FALSE, out.width="80%"-----------------------------------------------
knitr::include_graphics("img/penguins.png")


## ------------------------------------------------------------------------------
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%"----