# rphylopic <img src="man/figures/logo.png" align="right" alt="" width="120">

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<img src="https://images.phylopic.org/images/c65573fb-2659-46b9-b7a0-065232a2a08b/vector.svg"  width="150" height="150">

The purpose of the `rphylopic` package is to allow users to add silhouettes of organisms to plots generated in base R and `ggplot2`. To do so, it uses silhouettes made available via the [PhyloPic website](http://phylopic.org/).

`rphylopic` was originally developed and maintained by [Scott Chamberlain](https://scottchamberlain.info). From ver. 1.0.0, the package is now developed and maintained by [William Gearty](https://williamgearty.com) and [Lewis A. Jones](https://www.lewisajones.com/) from the [Palaeoverse team](https://palaeoverse.org).

## Installation

The stable version of `rphylopic` can be installed from CRAN using:

```r
install.packages("rphylopic")
```

The development version of `rphylopic` can be installed via GitHub using:

```r
install.packages("remotes")
remotes::install_github("palaeoverse/rphylopic")
```

# How does it work?

## Get an image uuid

```r
# Load rphylopic
library(rphylopic)
# Get a single image uuid for a species
uuid <- get_uuid(name = "Canis lupus", n = 1)
# Get the image for that uuid
img <- get_phylopic(uuid = uuid)
# But multiple silhouettes can exist per species...
uuid <- get_uuid(name = "Canis lupus", n = 5)
```

## Pick an image

```r
# How do I pick?!
# It's difficult without seeing the image itself, let's use:
img <- pick_phylopic(name = "Canis lupus", n = 5)
```

## Plot an image

### Base R

```r
# OK, now we've got the image we want... let's add it to a plot!
plot(x = 1, y = 1, type = "n")
add_phylopic_base(img = img, x = 1.25, y = 1.25, height = 0.25)

# But can't we just add an image straight away using the uuid? Sure!
uuid <- get_uuid(name = "Canis lupus", n = 1)
add_phylopic_base(uuid = uuid, x = 1, y = 1, height = 0.25)

# What about just using the first image linked to the name? Definitely!
add_phylopic_base(name = "Canis lupus", x = 0.75, y = 0.75, height = 0.25)

# Black is a bit boring? OK...
add_phylopic_base(name = "Canis lupus", x = 0.75, y = 1.25, height = 0.25, color = "orange")
```

### ggplot2

```r
# All of this functionality is available for ggplot2 as well...
# But we use add_phylopic and geom_phylopic instead!
library(ggplot2)
# Get image
uuid <- get_uuid(name = "Iris", n = 1)
img <- get_phylopic(uuid = uuid)
# Put a silhouette behind a plot
ggplot(iris) +
  add_phylopic(x = 6.1, y = 3.2, img = img, alpha = 0.2) +
  geom_point(aes(x = Sepal.Length, y = Sepal.Width))
  
# Plot silhouettes as points!
ggplot(iris) + 
  geom_phylopic(aes(x = Sepal.Length, y = Sepal.Width), img = img,
                color = "purple", height = 0.25)
```

## Get attribution

```r
# PhyloPic has a lot of contributors and we should acknowledge 
# their work. You can get data about images using get_attribution

# Get valid uuid
uuid <- get_uuid(name = "Nycticebus")
# Get attribution data for uuid
get_attribution(uuid = uuid)
```

## Save an image

```r
# How do I save an image?
# Get image
img <- pick_phylopic(name = "Phascolarctos cinereus", n = 1)
# Save image
save_phylopic(img = img)
```

# How to contribute?

If you are interested in contributing to the `rphylopic` R package, you can do so by following these [guidelines](https://rphylopic.palaeoverse.org/CONTRIBUTING.html).

# Code of Conduct

As with any community project, society, or meeting we feel it is important to established some expectations of behaviour. Please read our [code of conduct](https://rphylopic.palaeoverse.org/CODE_OF_CONDUCT.html), and reach out if you ever face any issues. Everyone has the right to live and work in a harassment-free environment.

# Attribution

If you use the `rphylopic` package in your work, please acknowledge the contributors responsible for the image, acknowledge the creator of PhyloPic ([Michael Keesey](http://tmkeesey.net)), and cite the following for `rphylopic`:

Gearty, W. and Jones, L.A. 2023. rphylopic: An R package for fetching, transforming, and visualising PhyloPic silhouettes. Methods in Ecology and Evolution, 14(11), 2700-2708. doi: [10.1111/2041-210X.14221](https://doi.org/10.1111/2041-210X.14221).

# Cheat sheet

![](man/figures/cheatsheet.png)

<p align="left">

<img src="man/figures/logo.png" width="120" />

</p>

[Hex logo and cheatsheet by Miranta Kouvari](https://www.mirantakouvari.com)
