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https://github.com/nschiett/fishualize

The fishualize package provides color scales and silhouettes for plotting in R based on nature’s most stunning and colorful organisms: teleost fishes (with a few chondrichthyan cameos).
https://github.com/nschiett/fishualize

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The fishualize package provides color scales and silhouettes for plotting in R based on nature’s most stunning and colorful organisms: teleost fishes (with a few chondrichthyan cameos).

Host: GitHub
URL: https://github.com/nschiett/fishualize
Owner: nschiett
Created: 2019-09-06T16:12:52.000Z (almost 5 years ago)
Default Branch: master
Last Pushed: 2024-03-08T18:23:01.000Z (4 months ago)
Last Synced: 2024-03-20T18:44:54.262Z (3 months ago)
Language: R
Homepage: https://nschiett.github.io/fishualize/index.html
Size: 29.7 MB
Stars: 152
Watchers: 8
Forks: 9
Open Issues: 6
Metadata Files:
- Readme: README.Rmd

Lists

awesome-r-dataviz - fishualize - Color scales based on nature’s most stunning and colorful organisms: teleost fishes. (ggplot / Palettes 🎨)
awesome-stars - nschiett/fishualize - The fishualize package provides color scales and silhouettes for plotting in R based on nature’s most stunning and colorful organisms: teleost fishes (with a few chondrichthyan cameos). (R)
awesome-stars - fishualize - The fishualize package provides color scales for plotting in R based on nature’s most stunning and colorful organisms: teleost fishes (with a few chondrichthyan cameos). (R)

README

        ---

title: "Fishualize"

author:

  - "Nina Schiettekatte"

date: "`r Sys.Date()`"

output:

  md_document:

    variant: markdown_github

    toc: true

    toc_depth: 1

---

[![Build Status](https://api.travis-ci.org/nschiett/fishualize.png?branch=master)](https://travis-ci.org/nschiett/fishualize)

[![CRAN status](https://www.r-pkg.org/badges/version/fishualize)](https://CRAN.R-project.org/package=fishualize)

[![Downloads](http://cranlogs.r-pkg.org/badges/grand-total/fishualize?color=brightgreen)](https://cran.rstudio.com/package=fishualize)



# Introduction

The [**fishualize**](http:://github.com/nschiett/fishualize) package provides color scales for plotting in R based on nature’s most stunning and colorful organisms: teleost fishes (with a few chondrichthyan cameos). #TeamFish in its colorful glory.

## Installation

```{r, eval = FALSE}

install.packages("fishualize")

library(fishualize)

```

or for the latest development version:

```{r, eval = FALSE}

library(devtools)

devtools::install_github("nschiett/fishualize", force = TRUE)

library(fishualize)

```

```{r setup, include=FALSE}

library(fishualize)

knitr::opts_chunk$set(echo = TRUE, fig.retina=2, fig.width=7, fig.height=5)

```

# The color scales

The package contains one scale per species, defined by five dominant colors. The number of fishualized species will expand over time. For a list of fish species that are currently available, run `fish_palettes()`.  

A visual overview of the color scales can be found [here]( https://nschiett.github.io/fishualize/articles/overview_colors.html).   

To visualize a fish color palette, you can run `fishualize()` and specify your choice.

```{r tldr_vis, message=FALSE}

fishualize()

fishualize(n = 8, option = "Hypsypops_rubicundus", end = 0.9)

```

# Usage

The `fish()` function produces the fish color scale based on your favorite species, which can be specified using ‘option’ = “Your_favorite” or fish_palettes()[] with the number of your species specified.

For base R plots, use the `fish()` function to generate a palette:

```{r tldr_base, message=FALSE}

pal <- fish(256, option = "Trimma_lantana")

image(volcano, col = pal)

pal <- fish(10, option = "Ostracion_cubicus")

image(volcano, col = pal)

```

## ggplot2

The package also contains color scale functions for **ggplot2**

plots: `scale_color_fish()` and `scale_fill_fish()`. 

```{r, tldr_ggplot, message=FALSE}

library(ggplot2)

library(rfishbase)

# load data for plotting 

# 1. Create list of species names currently featured in fishualize

spp <- fishualize::fish_palettes()

# 2. Get data on the included species from FishBase using the rfishbase package

dt <- rfishbase::species(gsub("_"," ", spp))

dt$Importance = factor(dt$Importance, levels = c("highly commercial", "commercial", "minor commercial", "subsistence fisheries", "of no interest"))

# plot bars with discrete colors using color scheme provided by Scarus quoyi

ggplot(dt[!is.na(dt$Importance),]) +

  geom_bar(aes(x = Importance, fill = Importance)) +

  scale_fill_fish_d(option = "Scarus_quoyi") +

  theme_bw() +

  theme(axis.text.x= element_blank() )

# plot points with continuous colors provided by Hypsypops rubicundus

ggplot(dt) +

  geom_point(aes(x = Length, y = Vulnerability, color = Vulnerability), size = 3) +

  scale_color_fish(option = "Hypsypops_rubicundus", direction = -1) +

  theme_bw()

# get ecological information from FishBase

data <- rfishbase::ecology(gsub("_"," ", spp), c("SpecCode","FeedingType", "DietTroph")) %>% 

  dplyr::left_join( rfishbase::species(gsub("_"," ", spp)))

# plot boxplots of length across feeding groups using discrete colors provided by Cirrilabrus solorensis

ggplot(data[!is.na(data$FeedingType),]) +

  geom_boxplot(aes(x = FeedingType, y = log(Length), fill = FeedingType )) +

  scale_fill_fish_d(option = "Cirrhilabrus_solorensis", labels = c("invertivore", "herbivore", "carnivore", "planktivore", "omnivore")) +

  theme_bw() +

  theme(axis.text.x= element_blank() )

# examine relationships between size and trophic level with vulnerability as a continuous color scheme provided by Lepomis megalotis

ggplot(data) +

  geom_point(aes(x = Length, y = DietTroph, color = Vulnerability), size = 6, alpha = 0.9) +

  scale_color_fish(option = "Lepomis_megalotis", direction = -1) +

  theme_bw()

```

Colors can also be used with maps. Here are several examples of discrete and continuous color schemes on a world-map.

```{r, ggplot2}

library(ggplot2)

#get dataset of the world's countries

world <- rnaturalearth::ne_countries(scale = "medium", returnclass = "sf")

#plot worldmap with each country's estimated population as a continuous colors scale based on the reverse colors of Whitley's Boxfish Ostracion whitleyi

ggplot(data = world) +

  geom_sf(aes(fill = pop_est)) +

  scale_fill_fish(option = "Ostracion_whitleyi", direction = -1) +

  theme_bw() +

  theme(legend.position = "top")

#plot worldmap with each country's estimated gdp based on the colors of the Sailfin Tang Zebrasoma velifer

ggplot(data = world) +

  geom_sf(aes(fill = gdp_md_est)) +

  scale_fill_fish(option = "Zebrasoma_velifer", trans = "sqrt") +

  theme_bw()+

  theme(legend.position = "top")

#same example as above but starting at a lighter point of the color scale

ggplot(data = world) +

  geom_sf(aes(fill = gdp_md_est)) +

  scale_fill_fish(option = "Zebrasoma_velifer", trans = "sqrt", begin = 0.3, end = 1) +

  theme_bw()+

  theme(legend.position = "top")

#plot worldmap again, this time with countries colored by their respective regional affiliation using the colors of the Clown coris *Coris gaimard* and 'discrete = TRUE'

ggplot(data = world) +

  geom_sf(aes(fill = region_wb)) +

  scale_fill_fish(option = "Coris_gaimard", discrete = TRUE) +

  theme_bw()+

  theme(legend.position = "top")

##same map with colors reversed

ggplot(data = world) +

  geom_sf(aes(fill = region_wb)) +

  scale_fill_fish(option = "Coris_gaimard", discrete = TRUE, direction = -1) +

  theme_bw()+

  theme(legend.position = "top")

#another map with countries colored by economic status using the colors of the Mandarinfish *Synchiropus splendidus*

ggplot(data = world) +

  geom_sf(aes(fill = income_grp)) +

  scale_fill_fish(option = "Synchiropus_splendidus", discrete = T, alpha = 0.8) +

  theme_bw()+

  theme(legend.position = "top")

#same map as above but with a narrower color palette in discrete values

ggplot(data = world) +

  geom_sf(aes(fill = income_grp)) +

  scale_fill_fish(option = "Synchiropus_splendidus", discrete = T, alpha = 0.8, begin = 0.3, end = 1) +

  theme_bw()+

  theme(legend.position = "top")

```

## Fish shapes  

fishualize 2.0 enables you to add fish silhouettes to a ggplot object with the function `add_fishape()`.

To get an overview of all available silhouettes, run `fishapes()`. 

```{r, shapes}

# Default shape

ggplot() + add_fishape() +

  theme_void()

# Species are specified with family and option

# The color and transparency of the shape is chosen with fill and alpha

# xmin, xmax, ymin, and ymax indicate the position of the fish silhouette

 ggplot(diamonds)+

   geom_bar(aes(cut, fill = cut)) +

   scale_fill_fish_d(option = "Naso_lituratus") +

   add_fishape(family = "Acanthuridae",

               option = "Naso_unicornis",

               xmin = 1, xmax = 3, ymin = 15000, ymax = 20000,

               fill = fish(option = "Naso_lituratus", n = 4)[2],

               alpha = 0.8) +

   theme_bw()

```

 

Alternatively, you can specify the coordinates according to a relative scale 

(between 0 and 1; with scaled = TRUE).

In this case, parameters xlim and ylim indicate the x and y limits of x and y.

This is useful to keep the fish silhouette positioned identically across graphs 

with different scales. 

      

```{r, shapes relative}

 ggplot(diamonds)+

   geom_bar(aes(cut, fill = cut)) +

   scale_fill_fish_d(option = "Naso_lituratus") +

   add_fishape(family = "Acanthuridae",

               option = "Naso_unicornis",

               xmin = 0.3, xmax = 0.7, ymin = 0.8, ymax = 1,

               scaled = TRUE,

               xlim = c(0.5, 5.5), ylim = c(0, 21000) ,

               fill = fish(option = "Naso_lituratus", n = 5)[3],

               alpha = 1) +

   theme_bw()

```

## Contribute

Love it? Missing your favorite species? Check out how you can contribute to this package [here](https://nschiett.github.io/fishualize/articles/contribute.html)

## Citation

To cite package `fishualize` in publications use:

  Nina Schiettekatte, Simon Brandl and Jordan Casey (2019). fishualize:

  Color Palettes Based on Fish Species. R package version 0.1.0.

  https://CRAN.R-project.org/package=fishualize

A BibTeX entry for LaTeX users is

  @Manual{,

    title = {fishualize: Color Palettes Based on Fish Species},

    author = {Nina Schiettekatte and Simon Brandl and Jordan Casey},

    year = {2019},

    note = {R package version 0.1.0},

    url = {https://CRAN.R-project.org/package=fishualize},

  }

## Contributions

JMC, SJB, and NMDS created the color palettes, SJB drew the fish silhouettes, which are freely available [**here**](https://github.com/simonjbrandl/fishape/tree/master/shapes).

NMDS wrote the functions. SJB, JMC, and NMDS wrote the documentation. 

A big thanks to everyone that submitted additional color palettes via GitHub: Jindra Lacko, Andrew Steinkruger, Adam Smit, pomboal, anhsmith, Kent Sorgon, Jean-Pierre Rossi, jdittrich, amedelin, Leonardo Donato Nunes, tesaucier, Thais Araújo, Áthila Bertoncini Andrade

## Credits

The initial structure of this package was inspired by the `harrypotter` package by Alejandro Jiménez: https://github.com/aljrico/harrypotter