rphylopic

The idea here is to create modular bits and pieces to allow you to add silhouettes to not only ggplot2 plots, but base plots as well.

• Phylopic website: http://phylopic.org/
• Phylopic development documentation: http://phylopic.org/api/

Install

CRAN version

install.packages("rphylopic")

Development version

install.packages("remotes")
remotes::install_github("sckott/rphylopic")

library('rphylopic')

Work with names

Find the taxa in Phylopic whose names match some text

person <- name_search(text = "Homo sapiens", options = "namebankID")[[1]]

Get info on a name

# no options just returns the UUID (aka: self)
name_get(uuid = person$uid[1])
#> $uid
#> [1] "1ee65cf3-53db-4a52-9960-a9f7093d845d"
# specify fields to return with the `options` parameter
name_get(uuid = person$uid[1], options = c('citationStart', 'html'))
#> $html
#> [1] "<span class=\"nomen\"><span class=\"scientific\">Homo sapiens</span> <span class=\"citation\">Linnaeus, 1758</span></span>"
#> 
#> $citationStart
#> [1] 13
#> 
#> $uid
#> [1] "1ee65cf3-53db-4a52-9960-a9f7093d845d"

Searches for images for a taxonomic name.

name_images(uuid = person$uid[1])
#> $other
#> list()
#> 
#> $supertaxa
#> list()
#> 
#> $subtaxa
#> list()
#> 
#> $same
#> $same[[1]]
#> $same[[1]]$uid
#> [1] "c089caae-43ef-4e4e-bf26-973dd4cb65c5"
#> 
#> 
#> $same[[2]]
#> $same[[2]]$uid
#> [1] "ad736445-7147-46f0-9932-d69243dea8f0"
#> 
#> 
#> $same[[3]]
#> $same[[3]]$uid
#> [1] "a146bf1b-c94d-46e1-9cd8-a0ac52a1e0a9"

Find the minimal common supertaxa for a list of names.

insect <- name_search('Orussus abietinus')[[1]]
bird <- name_search('Malacoptila panamensis')[[1]]
(x <- name_minsuptaxa(uuid = c(person$uid[1], insect$uid, bird$uid))[[1]])
#> $canonicalName
#> $canonicalName$uid
#> [1] "68226175-f88d-4ea8-8228-3204c49bfda0"
name_get(x$canonicalName$uid, options = c('string'))
#> $uid
#> [1] "68226175-f88d-4ea8-8228-3204c49bfda0"
#> 
#> $string
#> [1] "Nephrozoa Jondelius & al. 2002"

Collect taxonomic data for a name.

name_taxonomy(uuid = "f3254fbd-284f-46c1-ae0f-685549a6a373", 
  options = "string", as = "list")
#> $taxa
#> $taxa[[1]]
#> $taxa[[1]]$canonicalName
#> $taxa[[1]]$canonicalName$uid
#> [1] "f3254fbd-284f-46c1-ae0f-685549a6a373"
#> 
#> $taxa[[1]]$canonicalName$string
#> [1] "Macrauchenia patachonica Owen 1838"
#> 
#> 
#> 
#> 
#> $uBioCommands
#> [1] FALSE
#> 
#> $inclusions
#> list()

Work with name sets

Retrieves information on a set of taxonomic names.

id <- "8d9a9ea3-95cc-414d-1000-4b683ce04be2"
nameset_get(uuid = id, options = c('names', 'string'))
#> $uid
#> [1] "8d9a9ea3-95cc-414d-1000-4b683ce04be2"
#> 
#> $names
#> $names[[1]]
#> $names[[1]]$uid
#> [1] "105d17a4-9706-4fd5-85d7-becffaf6250a"
#> 
#> $names[[1]]$string
#> [1] "Homo sapiens sapiens Linnaeus 1758"
#> 
#> 
#> $names[[2]]
#> $names[[2]]$uid
#> [1] "9dc78907-02ca-4e98-95d7-f5a7c6166ee8"
#> 
#> $names[[2]]$string
#> [1] "Canis familiaris familiaris"

Collects taxonomic data for a name.

nameset_taxonomy(uuid = "8d9a9ea3-95cc-414d-1000-4b683ce04be2", options = "string")$taxa[1:2]
#> [[1]]
#> [[1]]$canonicalName
#> [[1]]$canonicalName$uid
#> [1] "2265ff9d-cfcf-4bf4-9f3e-fb4dd9e90261"
#> 
#> [[1]]$canonicalName$string
#> [1] "Choanozoa"
#> 
#> 
#> 
#> [[2]]
#> [[2]]$canonicalName
#> [[2]]$canonicalName$uid
#> [1] "b909eda2-4a6d-4d87-a463-87cbe3d20c5f"
#> 
#> [[2]]$canonicalName$string
#> [1] "Coelomata"

Work with images

Get info on an image

id <- "9fae30cd-fb59-4a81-a39c-e1826a35f612"
image_get(uuid = id)
#> $uid
#> [1] "9fae30cd-fb59-4a81-a39c-e1826a35f612"

Count images in Phylopic database

image_count()
#> [1] 4101

Lists images in chronological order, from most to least recently modified

image_list(start=1, length=2)
#> [[1]]
#> [[1]]$uid
#> [1] "d3a78afb-1b9e-45e0-b6f4-144d79f399f0"
#> 
#> 
#> [[2]]
#> [[2]]$uid
#> [1] "c7fbe213-1eac-4f81-80d0-674c3bd2d6b0"

Lists images within a given time range, from most to least recent

image_timerange(from="2013-05-11", to="2013-05-12", options='credit')[1:2]
#> [[1]]
#> [[1]]$credit
#> [1] "Emily Willoughby"
#> 
#> [[1]]$uid
#> [1] "58daaa49-e699-448d-9553-ceedd1fc98a4"
#> 
#> 
#> [[2]]
#> [[2]]$credit
#> [1] "Gareth Monger"
#> 
#> [[2]]$uid
#> [1] "303ddff0-6a51-4f70-adf7-69bb22385d6d"

Work with uBio data

ubio_get(namebankID = 109086)
#> $uid
#> [1] "1ee65cf3-53db-4a52-9960-a9f7093d845d"

Plot a silhouette behind a plot

library('ggplot2')
img <- image_data("27356f15-3cf8-47e8-ab41-71c6260b2724", size = "512")[[1]]
qplot(x = Sepal.Length, y = Sepal.Width, data = iris, geom = "point") +
  add_phylopic(img)

Plot images as points in a plot

For ggplot2 graphics...

library('ggplot2')
img <- image_data("c089caae-43ef-4e4e-bf26-973dd4cb65c5", size = "64")[[1]]
p <- ggplot(mtcars, aes(drat, wt)) +
      geom_blank() +
      theme_grey(base_size = 18)
for (i in 1:nrow(mtcars)) {
  p <- p + add_phylopic(img, 1, mtcars$drat[i], mtcars$wt[i], ysize = 0.3)
}
p

and the same plot in base R graphics:

cat <- image_data("23cd6aa4-9587-4a2e-8e26-de42885004c9", size = 128)[[1]]
posx <- runif(50, 0, 1)
posy <- runif(50, 0, 1)
size <- runif(50, 0.01, 0.2)
plot(posx, posy, type = "n", main = "A cat herd")
for (i in 1:50) {
  add_phylopic_base(cat, posx[i], posy[i], size[i])
}

Save png to disk

cat <- image_data("23cd6aa4-9587-4a2e-8e26-de42885004c9", size = 128)[[1]]
out <- save_png(cat)
identical(png::readPNG(out), cat)
#> TRUE

Use silhouettes as icons in Leaflet plots

There's nothing baked into rphylopic for this, but here's an example of how to do it.

library(leaflet)
data(quakes)

# get an image
cat <- image_data("23cd6aa4-9587-4a2e-8e26-de42885004c9", size = 128)[[1]]
# save to disk
file <- save_png(cat)
# make an icon. this one is super simple, see `makeIcon` docs for more options
sil_icon <- makeIcon(iconUrl = file)

# make the plot
leaflet(data = quakes[1:4,]) %>% addTiles() %>%
  addMarkers(~long, ~lat, icon = sil_icon)

Meta

• Please report any issues or bugs.
• License: MIT
• Get citation information for rphylopic in R doing citation(package = 'rphylopic')
• Please note that this project is released with a Contributor Code of Conduct.

By participating in this project you agree to abide by its terms.