README.Rmd

---
title: "Fishualize"
author:
  - "Nina Schiettekatte"
date: "`r Sys.Date()`"
output:
  md_document:
    variant: markdown_github
    toc: true
    toc_depth: 1
---
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<img src="man/figures/fishualize_logo.png" width = 120 alt="fishflux logo"/>



# 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