TidyTuesday 2020 Week31
Palmer Penguins
Preparations
library(tidyverse)
library(palmerpenguins)
library(ggalluvial)
library(ggpubr)
library(magick)
library(patchwork)
library(munsell)
library(colorspace)
library(flair) #Highlight, Annotate, and Format your R Source CodeTidy & Transform
(
penguins_lodes <-
penguins %>%
count(species, island, year, sex, name = "freq") %>%
rowid_to_column("alluvium") %>%
mutate(year = factor(year)) %>%
pivot_longer(
-c(alluvium, freq, species),
names_to = "variable", values_to = "stratum"
)
)
## # A tibble: 105 x 5
## alluvium species freq variable stratum
## <int> <fct> <int> <chr> <fct>
## 1 1 Adelie 5 island Biscoe
## 2 1 Adelie 5 year 2007
## 3 1 Adelie 5 sex female
## 4 2 Adelie 5 island Biscoe
## 5 2 Adelie 5 year 2007
## 6 2 Adelie 5 sex male
## 7 3 Adelie 9 island Biscoe
## 8 3 Adelie 9 year 2008
## 9 3 Adelie 9 sex female
## 10 4 Adelie 9 island Biscoe
## # … with 95 more rows
Visualise
scale_fill_manual()3- Layered Grammar for Alluvial Plots(Brunson 2020b)
- Art for teaching with palmerpenguins
alluvial_plot <-
penguins_lodes %>%
ggplot(
aes(
x = variable, y = freq,
stratum = stratum, alluvium = alluvium, label = stratum
)
) +
geom_alluvium(
aes(fill = species),
aes.bind = "alluvia", colour = "darkgray", reverse = FALSE
) +
geom_stratum(aes(fill = stratum), reverse = FALSE) +
geom_text(stat = "stratum", reverse = FALSE) +
scale_x_discrete(expand = expansion(mult = .1)) +
scale_fill_manual(
values = c(
Adelie = "darkorange", Chinstrap = "purple", Gentoo = "cyan4",
`2007` = munsell::mnsl("5Y 9/2"), `2008` = munsell::mnsl("5Y 9/4"), `2009` = munsell::mnsl("5Y 9/6"),
female = 'aliceblue', male = 'honeydew',
Biscoe = '#FCDAE0', Dream = '#D4E8CE', Torgersen = '#D3E4F7'
),
guide = FALSE,
na.value = "red"
) +
coord_flip()
penguins_png <- image_read("penguins.png")
img <- ggplot() + background_image(penguins_png)
(alluvial_plot / img) +
plot_annotation(
title = 'Palmer Penguins species by year, sex and island',
caption = 'Artwork by @allison_horst | #TidyTuesday | @mstkolf',
theme = theme(
plot.title = element_text(face = "bold", size = 20, family = "serif"),
plot.caption = element_text(size = 10)
)
)
References
Brunson, Jason Cory. 2020a. Ggalluvial: Alluvial Plots in ’Ggplot2’. https://CRAN.R-project.org/package=ggalluvial.
———. 2020b. “ggalluvial: Layered Grammar for Alluvial Plots.” Journal of Open Source Software 5 (49): 2017. https://doi.org/10.21105/joss.02017.
Horst, Allison, Alison Hill, and Kristen Gorman. 2020. Palmerpenguins: Palmer Archipelago (Antarctica) Penguin Data. https://CRAN.R-project.org/package=palmerpenguins.
Ihaka, Ross, Paul Murrell, Kurt Hornik, Jason C. Fisher, Reto Stauffer, Claus O. Wilke, Claire D. McWhite, and Achim Zeileis. 2019. Colorspace: A Toolbox for Manipulating and Assessing Colors and Palettes. https://CRAN.R-project.org/package=colorspace.
Wickham, Charlotte. 2018. Munsell: Utilities for Using Munsell Colours. https://CRAN.R-project.org/package=munsell.
Reproducibility
## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 4.0.0 (2020-04-24)
## os macOS Catalina 10.15.5
## system x86_64, darwin17.0
## ui X11
## language (EN)
## collate ja_JP.UTF-8
## ctype ja_JP.UTF-8
## tz Asia/Tokyo
## date 2020-08-22
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## package * version date lib source
## abind 1.4-5 2016-07-21 [1] CRAN (R 4.0.2)
## assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0)
## backports 1.1.7 2020-05-13 [1] CRAN (R 4.0.0)
## blob 1.2.1 2020-01-20 [1] CRAN (R 4.0.0)
## blogdown 0.20 2020-06-23 [1] CRAN (R 4.0.2)
## bookdown 0.20 2020-06-23 [1] CRAN (R 4.0.2)
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## data.table 1.13.0 2020-07-24 [1] CRAN (R 4.0.2)
## DBI 1.1.0 2019-12-15 [1] CRAN (R 4.0.0)
## dbplyr 1.4.4 2020-05-27 [1] CRAN (R 4.0.0)
## digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.0)
## dplyr * 1.0.0 2020-05-29 [1] CRAN (R 4.0.0)
## ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.0)
## evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.0)
## fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0)
## farver 2.0.3 2020-01-16 [1] CRAN (R 4.0.0)
## flair * 0.0.2 2020-04-23 [1] CRAN (R 4.0.2)
## forcats * 0.5.0 2020-03-01 [1] CRAN (R 4.0.0)
## foreign 0.8-78 2020-04-13 [1] CRAN (R 4.0.0)
## fs 1.4.1 2020-04-04 [1] CRAN (R 4.0.0)
## generics 0.0.2 2018-11-29 [1] CRAN (R 4.0.0)
## ggalluvial * 0.12.0 2020-07-14 [1] CRAN (R 4.0.2)
## ggplot2 * 3.3.2 2020-06-19 [1] CRAN (R 4.0.2)
## ggpubr * 0.4.0 2020-06-27 [1] CRAN (R 4.0.2)
## ggsignif 0.6.0 2019-08-08 [1] CRAN (R 4.0.2)
## glue 1.4.1 2020-05-13 [1] CRAN (R 4.0.0)
## gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.0)
## haven 2.3.0 2020-05-24 [1] CRAN (R 4.0.0)
## here 0.1 2017-05-28 [1] CRAN (R 4.0.2)
## hms 0.5.3 2020-01-08 [1] CRAN (R 4.0.0)
## htmltools 0.5.0 2020-06-16 [1] CRAN (R 4.0.2)
## httr 1.4.1 2019-08-05 [1] CRAN (R 4.0.0)
## jsonlite 1.6.1 2020-02-02 [1] CRAN (R 4.0.0)
## knitr 1.28 2020-02-06 [1] CRAN (R 4.0.0)
## labeling 0.3 2014-08-23 [1] CRAN (R 4.0.0)
## lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.0)
## lubridate 1.7.8 2020-04-06 [1] CRAN (R 4.0.0)
## magick * 2.4.0 2020-06-23 [1] CRAN (R 4.0.2)
## magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.0)
## modelr 0.1.8 2020-05-19 [1] CRAN (R 4.0.0)
## munsell * 0.5.0 2018-06-12 [1] CRAN (R 4.0.0)
## openxlsx 4.1.5 2020-05-06 [1] CRAN (R 4.0.2)
## palmerpenguins * 0.1.0 2020-07-23 [1] CRAN (R 4.0.2)
## patchwork * 1.0.1 2020-06-22 [1] CRAN (R 4.0.2)
## pillar 1.4.4 2020-05-05 [1] CRAN (R 4.0.0)
## pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.0)
## purrr * 0.3.4 2020-04-17 [1] CRAN (R 4.0.0)
## R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.0)
## Rcpp 1.0.4.6 2020-04-09 [1] CRAN (R 4.0.0)
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## rio 0.5.16 2018-11-26 [1] CRAN (R 4.0.2)
## rlang 0.4.7 2020-07-09 [1] CRAN (R 4.0.2)
## rmarkdown 2.3 2020-06-18 [1] CRAN (R 4.0.2)
## rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.0)
## rstatix 0.6.0 2020-06-18 [1] CRAN (R 4.0.2)
## rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.0)
## rvest 0.3.5 2019-11-08 [1] CRAN (R 4.0.0)
## scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.0)
## sessioninfo * 1.1.1 2018-11-05 [1] CRAN (R 4.0.2)
## stringi 1.4.6 2020-02-17 [1] CRAN (R 4.0.0)
## stringr * 1.4.0 2019-02-10 [1] CRAN (R 4.0.0)
## tibble * 3.0.3 2020-07-10 [1] CRAN (R 4.0.2)
## tidyr * 1.1.0 2020-05-20 [1] CRAN (R 4.0.0)
## tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.0)
## tidyverse * 1.3.0 2019-11-21 [1] CRAN (R 4.0.0)
## utf8 1.1.4 2018-05-24 [1] CRAN (R 4.0.0)
## vctrs 0.3.1 2020-06-05 [1] CRAN (R 4.0.0)
## withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.0)
## xfun 0.14 2020-05-20 [1] CRAN (R 4.0.0)
## xml2 1.3.2 2020-04-23 [1] CRAN (R 4.0.0)
## yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.0)
## zip 2.0.4 2019-09-01 [1] CRAN (R 4.0.2)
##
## [1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library