TaxonomyMakie — PhyloPic Makie plot integration

PaleobiologyDB.TaxonomyMakie provides PhyloPic silhouette overlays for existing Makie plots. It is a package extension that activates when a Makie backend is loaded.

Installation

pkg> add PaleobiologyDB CairoMakie PhyloPicMakie

Activation

using CairoMakie   # or GLMakie, WGLMakie, …
using PaleobiologyDB
# augment_phylopic!, augment_phylopic_ranges!, phylopic_thumbnail_grid!, etc.
# are now in scope

Stratigraphic range chart — quick start

using CairoMakie
using PaleobiologyDB

taxa      = ["Tyrannosaurus", "Triceratops", "Ankylosaurus",
             "Pachycephalosaurus", "Edmontosaurus"]
first_app = [68.0, 68.0, 70.0, 74.0, 76.0]
last_app  = [66.0, 66.0, 66.0, 66.0, 66.0]

fig = Figure(size = (800, 420))
ax  = Axis(
    fig[1, 1];
    xlabel         = "Age (Ma)",
    title          = "Latest Cretaceous taxa — stratigraphic ranges",
    xreversed      = true,
    yticks         = (1:length(taxa), taxa),
    yticklabelsize = 13,
)

for (i, (fa, la)) in enumerate(zip(first_app, last_app))
    lines!(ax, [fa, la], [i, i]; linewidth = 6, color = :gray30)
end

augment_phylopic_ranges!(
    ax,
    first_app,
    last_app,
    collect(1.0:length(taxa));
    taxon      = taxa,
    at         = :start,
    glyph_size = 0.38,
    placement  = :center,
)

xlims!(ax, 78, 64)
display(fig)

Table-oriented API

When data is in a DataFrame (or any propertynames-compatible structure) the table overloads accept column selectors directly:

using CairoMakie
using PaleobiologyDB
using DataFrames

df = pbdb_occurrences(base_name = "Ursidae"; show = "full", vocab = "pbdb")
df = dropmissing(df, [:genus, :max_ma, :min_ma])
df.midpoint_age = (df.max_ma .+ df.min_ma) ./ 2

appearance_df = combine(
    groupby(df, :genus; sort = true),
    :midpoint_age => maximum => :first_app,
    :midpoint_age => minimum => :last_app,
)
appearance_df = sort(appearance_df, :first_app; rev = true)
appearance_df.row = collect(1.0:nrow(appearance_df))

fig = Figure()
ax  = Axis(
    fig[1, 1];
    xlabel = "Midpoint age (Ma)",
    ylabel = "Genus",
    yticks = (1:nrow(appearance_df), appearance_df.genus),
    xreversed = true,
)

for r in eachrow(appearance_df)
    lines!(ax, [r.first_app, r.last_app], [r.row, r.row])
end

augment_phylopic_ranges!(
    ax, appearance_df;
    xstart    = :first_app,
    xstop     = :last_app,
    y         = :row,
    taxon     = :genus,
    at        = :start,
    glyph_size = 0.4,
)
display(fig)

Supplying a pre-loaded glyph

Pass glyph instead of taxon to bypass the taxon-lookup pipeline and use an image you have already loaded:

using CairoMakie
using PaleobiologyDB
import PhyloPicMakie

rec = acquire_phylopic("Canis lupus")
img = PhyloPicMakie._load_phylopic_image(rec.phylopic_thumbnail)

fig = Figure()
ax  = Axis(fig[1, 1])
scatter!(ax, [1.0, 2.0, 3.0], [1.0, 2.0, 3.0])

# Overlay the same silhouette at every point
augment_phylopic!(ax, [1.0, 2.0, 3.0], [1.0, 2.0, 3.0];
    glyph = img, glyph_size = 0.3)
display(fig)

Downloaded thumbnail images are automatically cached via the same DataCaches.jl infrastructure used by the rest of PaleobiologyDB. Each unique thumbnail URL is downloaded at most once per cache lifetime; subsequent calls for the same URL return the stored matrix without any network activity.

The cache is controlled via PaleobiologyDB.set_autocaching!:

import PhyloPicMakie

# Enable caching for image downloads (default)
PaleobiologyDB.set_autocaching!(true, PhyloPicMakie._load_phylopic_image)

# Disable caching
PaleobiologyDB.set_autocaching!(false, PhyloPicMakie._load_phylopic_image)

This is independent of the taxon-metadata cache (controlled via set_autocaching!(enable, acquire_phylopic)).

Placement and sizing

All augment_phylopic! functions accept the following layout keywords:

Keyword	Default	Description
`placement`	`:center`	Anchor corner/edge on the glyph: `:center`, `:left`, `:right`, `:top`, `:bottom`, `:topleft`, `:topright`, `:bottomleft`, `:bottomright`
`xoffset`	`0.0`	Additional x offset in data units after anchoring
`yoffset`	`0.0`	Additional y offset in data units after anchoring
`glyph_size`	`0.4`	Half-height of the rendered glyph in data units
`aspect`	`:preserve`	Aspect ratio: `:preserve` (original) or `:stretch` (square)
`rotation`	`0.0`	Clockwise rotation: `0`, `90`, `180`, or `270` degrees
`mirror`	`false`	Horizontal flip
`clip`	`true`	Clip to axis bounds (handled automatically by Makie)
`on_missing`	`:skip`	Behaviour when no image is available: `:skip`, `:error`, or `:placeholder`

Range placement

augment_phylopic_ranges! adds the at keyword to control where along the range the glyph is anchored:

Value	Anchor position
`:start` (default)	`xstart`
`:stop`	`xstop`
`:midpoint`	`(xstart + xstop) / 2`

Thumbnail gallery

Use phylopic_thumbnail_grid to build a gallery of silhouettes paired with taxon names. The default layout keeps the number of columns bounded, so larger collections grow downward rather than becoming excessively wide.

using CairoMakie
using PaleobiologyDB

fig = phylopic_thumbnail_grid(
    [
        "Tyrannosaurus",
        "Triceratops",
        "Ankylosaurus",
        "Pachycephalosaurus",
        "Edmontosaurus",
        "Maiasaura",
    ];
    ncols = 3,
    label_fontsize = 18,
    title = "Latest Cretaceous thumbnail gallery",
)
display(fig)