Data Visualisation with R Workshop Part 1

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</div>

<br>

---

count: false
background-image: url(images/ramakant-sharda-0aFg0U2uPJY-unsplash.jpg)
background-size: cover
class: hide-slide-number title-slide

.item.center[

# <span style="text-shadow: 2px 2px 30px white;">Data Visualisation with R<br>Workshop Part 1</span>

]

.center.shade_black.animated.bounceInUp.slower[
<br><br>
## Scales and color

<br>

Presented by Emi Tanaka

Department of Econometrics and Business Statistics

<img src="images/monash-one-line-reversed.png" style="width:500px"><br>
<span><i class="fas  fa-envelope faa-float animated "></i></span>  emi.tanaka@monash.edu
<span><i class="fab  fa-twitter faa-float animated faa-fast "></i></span>  @statsgen

.bottom_abs.width100.bg-black[
6th Dec 2021 @ Statistical Society of Australia NSW Branch | Zoom
]

]

</div>

---

# .circle-big[3]
# Scales

---

# 💎 Diamonds data

The `diamonds` data is part of `ggplot2` 📦

```r
glimpse(diamonds)
```

```
## Rows: 53,940
## Columns: 10
## $ carat   <dbl> 0.23, 0.21, 0.23, 0.29, 0.31, 0.24, 0.24, 0.26, 0.22, 0.23, 0.…
## $ cut     <ord> Ideal, Premium, Good, Premium, Good, Very Good, Very Good, Ver…
## $ color   <ord> E, E, E, I, J, J, I, H, E, H, J, J, F, J, E, E, I, J, J, J, I,…
## $ clarity <ord> SI2, SI1, VS1, VS2, SI2, VVS2, VVS1, SI1, VS2, VS1, SI1, VS1, …
## $ depth   <dbl> 61.5, 59.8, 56.9, 62.4, 63.3, 62.8, 62.3, 61.9, 65.1, 59.4, 64…
## $ table   <dbl> 55, 61, 65, 58, 58, 57, 57, 55, 61, 61, 55, 56, 61, 54, 62, 58…
## $ price   <int> 326, 326, 327, 334, 335, 336, 336, 337, 337, 338, 339, 340, 34…
## $ x       <dbl> 3.95, 3.89, 4.05, 4.20, 4.34, 3.94, 3.95, 4.07, 3.87, 4.00, 4.…
## $ y       <dbl> 3.98, 3.84, 4.07, 4.23, 4.35, 3.96, 3.98, 4.11, 3.78, 4.05, 4.…
## $ z       <dbl> 2.43, 2.31, 2.31, 2.63, 2.75, 2.48, 2.47, 2.53, 2.49, 2.39, 2.…
```

---

# Scales

* Scales control the mapping from .blue[data] to .blue[aesthetics].

```r
g <- ggplot(diamonds, aes(carat, price) ) + geom_hex()
```
---

.item.border-right[

```r
g + scale_y_continuous() +
  scale_x_continuous()
```

]

.item.border-right[

```r
g + scale_x_reverse() +
  scale_y_continuous(trans="log10")
```

]

```r
g + scale_y_log10() + 
  scale_x_sqrt()
```

]

---

# `scale`

<div id="htmlwidget-a0b552d22f1613b7480c" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-a0b552d22f1613b7480c">{"x":{"filter":"none","vertical":false,"data":[["scale_alpha, scale_alpha_continuous, scale_alpha_binned, scale_alpha_discrete, scale_alpha_ordinal, scale_alpha_datetime, scale_alpha_date","scale_x_binned, scale_y_binned","scale_colour_brewer, scale_fill_brewer, scale_colour_distiller, scale_fill_distiller, scale_colour_fermenter, scale_fill_fermenter, scale_color_brewer, scale_color_distiller, scale_color_fermenter","scale_colour_continuous, scale_fill_continuous, scale_colour_binned, scale_fill_binned, scale_color_continuous, scale_color_binned","scale_colour_discrete, scale_fill_discrete, scale_color_discrete","scale_x_continuous, scale_y_continuous, scale_x_log10, scale_y_log10, scale_x_reverse, scale_y_reverse, scale_x_sqrt, scale_y_sqrt","scale_x_date, scale_y_date, scale_x_datetime, scale_y_datetime, scale_x_time, scale_y_time","scale_x_discrete, scale_y_discrete","scale_colour_gradient, scale_fill_gradient, scale_colour_gradient2, scale_fill_gradient2, scale_colour_gradientn, scale_fill_gradientn, scale_colour_datetime, scale_color_datetime, scale_colour_date, scale_color_date, scale_fill_datetime, scale_fill_date, scale_color_gradient","scale_colour_grey, scale_fill_grey, scale_color_grey","scale_colour_hue, scale_fill_hue, scale_color_hue","scale_colour_identity, scale_fill_identity, scale_shape_identity, scale_linetype_identity, scale_alpha_identity, scale_size_identity, scale_discrete_identity, scale_continuous_identity, scale_color_identity","scale_linetype, scale_linetype_binned, scale_linetype_continuous, scale_linetype_discrete","scale_colour_manual, scale_fill_manual, scale_size_manual, scale_shape_manual, scale_linetype_manual, scale_alpha_manual, scale_discrete_manual, scale_color_manual","scale_shape, scale_shape_binned, scale_shape_discrete, scale_shape_ordinal, scale_shape_continuous","scale_size, scale_size_continuous, scale_radius, scale_size_binned, scale_size_discrete, scale_size_ordinal, scale_size_area, scale_size_binned_area, scale_size_datetime, scale_size_date","scale_colour_steps, scale_colour_steps2, scale_colour_stepsn, scale_fill_steps, scale_fill_steps2, scale_fill_stepsn, scale_color_steps, scale_color_steps2, scale_color_stepsn","scale_type","scale_colour_viridis_d, scale_fill_viridis_d, scale_colour_viridis_c, scale_fill_viridis_c, scale_colour_viridis_b, scale_fill_viridis_b, scale_colour_ordinal, scale_color_ordinal, scale_fill_ordinal, scale_color_viridis_d, scale_color_viridis_c, scale_color_viridis_b"],["Alpha transparency scales","Positional scales for binning continuous data (x & y)","Sequential, diverging and qualitative colour scales from ColorBrewer","Continuous and binned colour scales","Discrete colour scales","Position scales for continuous data (x & y)","Position scales for date/time data","Position scales for discrete data","Gradient colour scales","Sequential grey colour scales","Evenly spaced colours for discrete data","Use values without scaling","Scale for line patterns","Create your own discrete scale","Scales for shapes, aka glyphs","Scales for area or radius","Binned gradient colour scales","Determine default scale type","Viridis colour scales from viridisLite"]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th>scales<\/th>\n      <th>Description<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"dom":"tp","ordering":false,"pageLength":4,"autoWidth":true,"columnDefs":[{"width":"400px","targets":0}],"order":[],"orderClasses":false,"lengthMenu":[4,10,25,50,100]}},"evals":[],"jsHooks":[]}</script>

---
# Guide: an axis or a legend

* The scale creates a .blue[guide]: an .blue[axis] or .blue[legend].
* So to modify these you generally use .blue[`scale_*`] or other handy functions (`guides`, `labs`, `xlab`, `ylab` and so on).

---

# Modify axis

```r
g + 
  scale_y_continuous(name = "Price", 
                     breaks = c(0, 10000),
                     labels = c("0", "More\n than\n 10K")) + 
  geom_hline(yintercept = 10000, color = "red", size = 2)
```

---

# Nicer formatting functions in `scales` 📦

```r
g + 
  scale_y_continuous(
*   label = scales::dollar_format()
  )
```

---

# Modifying legend

```r
g + 
  scale_fill_continuous(
    breaks = c(0, 10, 100, 1000, 4000),
    trans = "log10"
  )
```

---

# Removing legend

```r
g + 
  scale_fill_continuous(
    guide = "none"
  )
```

---

# Alternative control of guides

```r
g + 
  ylab("Price") + # Changes the y axis label
  labs(x = "Carat", # Changes the x axis label
       fill = "Count") # Changes the legend name 
```

```r
g + guides(fill = "none") # remove the legend
```

---

# .circle-big[4]
# Color space

.footnote.monash-bg-blue[
Zeileis, Fisher, Hornik, Ihaka, McWhite,
Murrell, Stauffer, Wilke (2019). colorspace: A
Toolbox for Manipulating and Assessing Colors and
Palettes. *arXiv 1903.06490*

Zeileis, Hornik, Murrell (2009). Escaping RGBland:
Selecting Colors for Statistical Graphics.
_Computational Statistics & Data Analysis_ 53(9)
3259-3270
]

---

# Qualitative palettes

designed for categorical variable with no particular ordering

```r
colorspace::hcl_palettes("Qualitative", plot = "TRUE", n = 7)
```

---

# Sequential palettes

designed for ordered categorical variable or number going from low to high (or vice-versa)

```r
colorspace::hcl_palettes("Sequential", plot = "TRUE", n = 7)
```

---

# Diverging palettes

designed for ordered categorical variable or number going from low to high (or vice-versa) with a neutral value in between

```r
colorspace::hcl_palettes("Diverging", plot = "TRUE", n = 7)
```

---

# RGB color space

made for screen projection

<br><br>
  <div class="col-sliders">
      <div>
          <label for="red">Red</label>
          <input type="number" id="redNum">
          <input value="0" type="range" min="0" max="255" id="red">
      </div>
      <div>
          <label for="green">Green</label>
          <input type="number" id="greenNum">
          <input value="109" type="range" min="0" max="255" id="green">
      </div>
      <div>
          <label for="blue">Blue</label>
          <input type="number" id="blueNum">
          <input  value="174" type="range" min="0" max="255" id="blue">
      </div>
  </div>

.footnote.bg-transparent[
Code adapted from https://github.com/Golobro/rgbcolorslider
]

---

# HCL color space

made for human visual system

<br><br>
  <div class="col-sliders">
      <div>
          <label for="hue">Hue</label>
          <input type="number" id="hueNum">
          <input value="268" type="range" min="0" max="360" id="hue">
      </div>
      <div>
          <label for="chroma">Chroma</label>
          <input type="number" id="chromaNum">
          <input value="42" type="range" min="0" max="180" id="chroma">
      </div>
      <div>
          <label for="luminance">Luminance</label>
          <input type="number" id="luminanceNum">
          <input  value="44" type="range" min="0" max="100" id="luminance">
      </div>
  </div>

.footnote.bg-transparent[
Color conversion using https://github.com/gka/chroma.js
]

---

# `colorspace` 📦

<br>

```r
library(colorspace)
hcl_wizard() # OR choose_palette()
```
<br>
.center.animated.rubberBand[
.tag[LIVE DEMO]
<br>
]

]
.item[

]
]

---

# `hcl_wizard`

Choose your palette > Export > R > Copy the command

</center>

---

# Registering your own palette

```r
library(colorspace)
# register your palette
sequential_hcl(n = 7, 
               h = c(300, 200), 
               c = c(60, 0), 
               l = c(25, 95), 
               power = c(2.1, 0.8), 
               register = "my-set")
# now generate from your palette
sequential_hcl(n = 3, 
               palette = "my-set")
```

```
## [1] "#6B0077" "#7C8393" "#F1F1F1"
```

]
.item[

]
]

```r
hcl_palettes(n = 5, palette = "my-set", plot = T)
```

<img src="images/part1-session3/unnamed-chunk-17-1.png" style="display: block; margin: auto;" />
<br>
Combining with `ggplot`:

```r
ggplot(penguins, 
       aes(bill_length_mm, fill = species)) + 
 geom_density(alpha = 0.6) + 
  # notice here you don't need to specify the n!
 scale_fill_discrete_sequential(palette = "my-set")
```

---

# Manually selecting colors
<center>
<img src="images/lter_penguins.png" width = "250px"/>
</center>

```r
g <- ggplot(penguins, 
       aes(bill_length_mm, fill = species)) + 
 geom_density(alpha = 0.6) + 
 scale_fill_manual(
   breaks = c("Adelie", "Chinstrap", "Gentoo"), # optional but makes it more robust
   values = c("darkorange", "purple", "cyan4"))
g
```

---

# Check that it's colour blind friendly!

```r
cols <- c("darkorange", "purple", "cyan4")
```

```r
g # original
```

```r
g + scale_fill_manual(values = deutan(cols))
```

]
.item50[

```r
g + scale_fill_manual(values = protan(cols))
```

```r
g + scale_fill_manual(values = tritan(cols))
```

<img src="images/part1-session3/unnamed-chunk-22-2.png" style="display: block; margin: auto;" />
]

]

---

# <i class="fas fa-code"></i> Open `part1-exercise-03.Rmd`

---

# Session Information

```r
devtools::session_info()
```

```
## ─ Session info  🎡  👉🏻  🙅🏻   ─────────────────────────────────────────────────
##  hash: ferris wheel, backhand index pointing right: light skin tone, person gesturing NO: light skin tone
## 
##  setting  value
##  version  R version 4.1.2 (2021-11-01)
##  os       macOS Big Sur 10.16
##  system   x86_64, darwin17.0
##  ui       X11
##  language (EN)
##  collate  en_AU.UTF-8
##  ctype    en_AU.UTF-8
##  tz       Australia/Melbourne
##  date     2021-12-06
##  pandoc   2.11.4 @ /Applications/RStudio.app/Contents/MacOS/pandoc/ (via rmarkdown)
## 
## ─ Packages ───────────────────────────────────────────────────────────────────
##  package        * version date (UTC) lib source
##  anicon           0.1.0   2021-11-30 [1] Github (emitanaka/anicon@0b756df)
##  assertthat       0.2.1   2019-03-21 [1] CRAN (R 4.1.0)
##  backports        1.3.0   2021-10-27 [1] CRAN (R 4.1.0)
##  broom            0.7.10  2021-10-31 [1] CRAN (R 4.1.0)
##  bslib            0.3.1   2021-10-06 [1] CRAN (R 4.1.0)
##  cachem           1.0.6   2021-08-19 [1] CRAN (R 4.1.0)
##  callr            3.7.0   2021-04-20 [1] CRAN (R 4.1.0)
##  cellranger       1.1.0   2016-07-27 [1] CRAN (R 4.1.0)
##  cli              3.1.0   2021-10-27 [1] CRAN (R 4.1.0)
##  colorspace     * 2.0-2   2021-06-24 [1] CRAN (R 4.1.0)
##  countdown        0.3.5   2021-11-30 [1] Github (gadenbuie/countdown@a544fa4)
##  crayon           1.4.2   2021-10-29 [1] CRAN (R 4.1.0)
##  crosstalk        1.2.0   2021-11-04 [1] CRAN (R 4.1.0)
##  DBI              1.1.1   2021-01-15 [1] CRAN (R 4.1.0)
##  dbplyr           2.1.1   2021-04-06 [1] CRAN (R 4.1.0)
##  desc             1.4.0   2021-09-28 [1] CRAN (R 4.1.0)
##  devtools         2.4.2   2021-06-07 [1] CRAN (R 4.1.0)
##  digest           0.6.28  2021-09-23 [1] CRAN (R 4.1.0)
##  dplyr          * 1.0.7   2021-06-18 [1] CRAN (R 4.1.0)
##  DT               0.20    2021-11-15 [1] CRAN (R 4.1.0)
##  ellipsis         0.3.2   2021-04-29 [1] CRAN (R 4.1.0)
##  evaluate         0.14    2019-05-28 [1] CRAN (R 4.1.0)
##  fansi            0.5.0   2021-05-25 [1] CRAN (R 4.1.0)
##  farver           2.1.0   2021-02-28 [1] CRAN (R 4.1.0)
##  fastmap          1.1.0   2021-01-25 [1] CRAN (R 4.1.0)
##  forcats        * 0.5.1   2021-01-27 [1] CRAN (R 4.1.0)
##  fs               1.5.0   2020-07-31 [1] CRAN (R 4.1.0)
##  generics         0.1.1   2021-10-25 [1] CRAN (R 4.1.0)
##  ggplot2        * 3.3.5   2021-06-25 [1] CRAN (R 4.1.0)
##  glue             1.5.0   2021-11-07 [1] CRAN (R 4.1.0)
##  gtable           0.3.0   2019-03-25 [1] CRAN (R 4.1.0)
##  haven            2.4.3   2021-08-04 [1] CRAN (R 4.1.0)
##  hexbin           1.28.2  2021-01-08 [1] CRAN (R 4.1.0)
##  highr            0.9     2021-04-16 [1] CRAN (R 4.1.0)
##  hms              1.1.1   2021-09-26 [1] CRAN (R 4.1.0)
##  htmltools        0.5.2   2021-08-25 [1] CRAN (R 4.1.0)
##  htmlwidgets      1.5.4   2021-09-08 [1] CRAN (R 4.1.0)
##  httr             1.4.2   2020-07-20 [1] CRAN (R 4.1.0)
##  icon             0.1.0   2021-11-30 [1] Github (emitanaka/icon@8458546)
##  jquerylib        0.1.4   2021-04-26 [1] CRAN (R 4.1.0)
##  jsonlite         1.7.2   2020-12-09 [1] CRAN (R 4.1.0)
##  knitr            1.36    2021-09-29 [1] CRAN (R 4.1.0)
##  labeling         0.4.2   2020-10-20 [1] CRAN (R 4.1.0)
##  lattice          0.20-45 2021-09-22 [1] CRAN (R 4.1.2)
##  lifecycle        1.0.1   2021-09-24 [1] CRAN (R 4.1.0)
##  lubridate        1.8.0   2021-10-07 [1] CRAN (R 4.1.0)
##  magrittr         2.0.1   2020-11-17 [1] CRAN (R 4.1.0)
##  memoise          2.0.0   2021-01-26 [1] CRAN (R 4.1.0)
##  modelr           0.1.8   2020-05-19 [1] CRAN (R 4.1.0)
##  munsell          0.5.0   2018-06-12 [1] CRAN (R 4.1.0)
##  palmerpenguins * 0.1.0   2020-07-23 [1] CRAN (R 4.1.0)
##  pillar           1.6.4   2021-10-18 [1] CRAN (R 4.1.0)
##  pkgbuild         1.2.0   2020-12-15 [1] CRAN (R 4.1.0)
##  pkgconfig        2.0.3   2019-09-22 [1] CRAN (R 4.1.0)
##  pkgload          1.2.3   2021-10-13 [1] CRAN (R 4.1.0)
##  prettyunits      1.1.1   2020-01-24 [1] CRAN (R 4.1.0)
##  processx         3.5.2   2021-04-30 [1] CRAN (R 4.1.0)
##  ps               1.6.0   2021-02-28 [1] CRAN (R 4.1.0)
##  purrr          * 0.3.4   2020-04-17 [1] CRAN (R 4.1.0)
##  R6               2.5.1   2021-08-19 [1] CRAN (R 4.1.0)
##  Rcpp             1.0.7   2021-07-07 [1] CRAN (R 4.1.0)
##  readr          * 2.1.0   2021-11-11 [1] CRAN (R 4.1.0)
##  readxl           1.3.1   2019-03-13 [1] CRAN (R 4.1.0)
##  remotes          2.4.1   2021-09-29 [1] CRAN (R 4.1.0)
##  reprex           2.0.1   2021-08-05 [1] CRAN (R 4.1.0)
##  rlang            0.4.12  2021-10-18 [1] CRAN (R 4.1.0)
##  rmarkdown        2.11    2021-09-14 [1] CRAN (R 4.1.0)
##  rprojroot        2.0.2   2020-11-15 [1] CRAN (R 4.1.0)
##  rstudioapi       0.13    2020-11-12 [1] CRAN (R 4.1.0)
##  rvest            1.0.2   2021-10-16 [1] CRAN (R 4.1.0)
##  sass             0.4.0   2021-05-12 [1] CRAN (R 4.1.0)
##  scales           1.1.1   2020-05-11 [1] CRAN (R 4.1.0)
##  sessioninfo      1.2.1   2021-11-02 [1] CRAN (R 4.1.0)
##  stringi          1.7.5   2021-10-04 [1] CRAN (R 4.1.0)
##  stringr        * 1.4.0   2019-02-10 [1] CRAN (R 4.1.0)
##  testthat         3.1.0   2021-10-04 [1] CRAN (R 4.1.0)
##  tibble         * 3.1.6   2021-11-07 [1] CRAN (R 4.1.0)
##  tidyr          * 1.1.4   2021-09-27 [1] CRAN (R 4.1.0)
##  tidyselect       1.1.1   2021-04-30 [1] CRAN (R 4.1.0)
##  tidyverse      * 1.3.1   2021-04-15 [1] CRAN (R 4.1.0)
##  tzdb             0.2.0   2021-10-27 [1] CRAN (R 4.1.0)
##  usethis          2.1.3   2021-10-27 [1] CRAN (R 4.1.0)
##  utf8             1.2.2   2021-07-24 [1] CRAN (R 4.1.0)
##  vctrs            0.3.8   2021-04-29 [1] CRAN (R 4.1.0)
##  whisker          0.4     2019-08-28 [1] CRAN (R 4.1.0)
##  withr            2.4.2   2021-04-18 [1] CRAN (R 4.1.0)
##  xaringan         0.22    2021-06-23 [1] CRAN (R 4.1.0)
##  xfun             0.28    2021-11-04 [1] CRAN (R 4.1.0)
##  xml2             1.3.2   2020-04-23 [1] CRAN (R 4.1.0)
##  yaml             2.2.1   2020-02-01 [1] CRAN (R 4.1.0)
## 
##  [1] /Library/Frameworks/R.framework/Versions/4.1/Resources/library
## 
## ──────────────────────────────────────────────────────────────────────────────
```
]

These slides are licensed under <br><center><a href="https://creativecommons.org/licenses/by-sa/3.0/au/"><img src="images/cc.svg" style="height:2em;"/><img src="images/by.svg" style="height:2em;"/><img src="images/sa.svg" style="height:2em;"/></a></center>