rphylopic

Get Silhouettes of Organisms from PhyloPic

https://github.com/palaeoverse/rphylopic

Science Score: 39.0%

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CITATION.cff file
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Keywords

base-r ggplot2 phylopic rstats silhouette

Last synced: 4 months ago · JSON representation

Repository

Get Silhouettes of Organisms from PhyloPic

Basic Info

Host: GitHub
Owner: palaeoverse
License: gpl-3.0
Language: R
Default Branch: main
Homepage: https://rphylopic.palaeoverse.org
Size: 62 MB

Statistics

Stars: 95
Watchers: 7
Forks: 13
Open Issues: 13
Releases: 11

Topics

base-r ggplot2 phylopic rstats silhouette

Created over 12 years ago · Last pushed 4 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Codemeta

rphylopic

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.

rphylopic was originally developed and maintained by Scott Chamberlain. From ver. 1.0.0, the package is now developed and maintained by William Gearty and Lewis A. Jones from the Palaeoverse team.

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") addphylopicbase(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 <- getuuid(name = "Canis lupus", n = 1) addphylopic_base(uuid = uuid, x = 1, y = 1, height = 0.25)

What about just using the first image linked to the name? Definitely!

addphylopicbase(name = "Canis lupus", x = 0.75, y = 0.75, height = 0.25)

Black is a bit boring? OK...

addphylopicbase(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 addphylopic and geomphylopic instead!

library(ggplot2)

Get image

uuid <- getuuid(name = "Iris", n = 1) img <- getphylopic(uuid = uuid)

Put a silhouette behind a plot

ggplot(iris) + addphylopic(x = 6.1, y = 3.2, img = img, alpha = 0.2) + geompoint(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.

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, 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), 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.

Cheat sheet

Hex logo and cheatsheet by Miranta Kouvari

Owner

Name: Palaeoverse
Login: palaeoverse
Kind: organization
Email: LewisA.Jones@outlook.com

Website: https://palaeoverse.org
Repositories: 1
Profile: https://github.com/palaeoverse

A Resource Hub for Palaeobiologists

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Top Labels

Issue Labels

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Dependencies

DESCRIPTION cran

crul >= 0.5.2 imports
ggplot2 * imports
graphics * imports
grid * imports
gridBase * imports
jsonlite * imports
png * imports
R.rsp * suggests
data.table * suggests
knitr * suggests
parallel * suggests
rmarkdown * suggests
testthat * suggests
vcr >= 0.2.0 suggests

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