figtools

figtools is a matplotlib style with helpers for the figures of research papers and slides, inspired by Kieran Healy's Data Visualization. It does four things:

• Direct labels. Each series is named at its end, in its own colour, instead of in a legend, and the labels place themselves clear of one another and of the data at whatever size the figure is drawn.
• A check that no label collides with anything. collisions(fig) measures the drawn figure and reports any label on a line, a marker, a shape or another label, and any text cut off at the edge. save refuses to write such a figure, and fig-check checks every figure in a folder of documents.
• Figures at the size of their destination. save writes each figure at the exact width of a paper's text column and of a slide, so its type lands on the page at the point size setup chose.
• Figures a program can read. Every exported figure carries a digest, its plotted data, inside the image file. render-digest reads it back as tables, and after a Quarto render a hook writes each document's figures, tables and printed output as text, so a script or a language model working from a paper's figure files or a rendered document reads the values each figure shows. The digest holds every plotted point, a scatter's raw observations included, so for confidential data turn it off with ft.setup(digest=False).

Synthetic data, drawn by docs/readme_figure.py.

Install

pip install figtools

or, in a uv project, uv add figtools. figtools needs Python 3.11 or later, matplotlib and NumPy. The fig-check command also reads YAML, and the check extra installs PyYAML for it: pip install "figtools[check]".

Pin the version in each project that uses figtools. The library decides sizes, colours and label placement, so a new release can change how a figure is drawn, and a pinned project changes its figures only when it upgrades. A uv project pins the version in uv.lock; with pip, pin it with == in the requirements file. The changelog marks each change that alters figures.

Quick start

import matplotlib.pyplot as plt
import numpy as np

import figtools as ft

ft.setup()                                  # the style, once, before any figure

rng = np.random.default_rng(0)
years = np.arange(2000, 2025)
fig, ax = plt.subplots()
for region, growth in [('North', 1.5), ('Centre', 0.7), ('South', -0.4)]:
    y = 100 + growth * (years - 2000) + rng.normal(0, 1, len(years))
    ax.plot(years, y, label=region)
    ft.band(ax, years, y - 3, y + 3)        # in the colour of the line just drawn
ft.refline(ax, 100, '2000 level')           # a grey rule, named on the line
ax.set_ylabel('Employment (2000 = 100)')
ft.label_lines(ax)                          # each line named at its end
ft.save(fig, 'employment')                  # employment.pdf, employment_slides.pdf

save writes employment.pdf, 5.9 inches wide for a paper, and employment_slides.pdf, 4.1 inches wide for a slide, each carrying the figure's digest. Before writing each one it checks the figure at that size, and it raises an error instead of writing a file in which a label overlaps something. In a notebook the figure also appears below the cell.

python -m figtools prints a short usage guide, and help(ft.label_lines) gives the full reference of any function.

Gallery

Each figure is drawn from synthetic data by the script linked under it. The scripts run with the tests, which fail if any label collides.

Time series with bands and a named reference rule (script)	A period shaded and named in place (script)
Event study with a zero rule and the treatment date (script)	Coefficient plot, ranked (script)
Dumbbell: two measurements per row, told apart by fill (script)	Binned scatter net of a control, with the fitted slope (script)
Scatter in which each name is the mark (script)	A few points named, each label clear of every point (script)
Small multiples with the series named once (script)

Direct labels

A legend makes the reader hold a colour in memory and move back and forth between the key and the data; a name at the end of each line does not. label_lines puts the names in the margin beyond the panel, moves them clear of one another and of the lines, and draws a hairline leader back to a line once its label has moved far enough that the pairing stops being obvious. setup turns on matplotlib's constrained layout, which measures the margin the labels need and shrinks the axes to fit, so the panel ends where the data end and the grid stops with it. A tight_layout() call on such a figure warns and switches the layout engine off. A label wider than a fifth of the figure is broken at spaces into two or three balanced lines, decided again at each output size; a label broken by hand, with a newline, is kept as written.

Where line ends crowd, as in small multiples, key stacks the names in a free corner, each word in its series' colour. label_points names some points of a scatter, each name moved clear of the others, of the points and of the lines; label_scatter prints names as the marks themselves. Reference rules and shaded periods are named in place too: an unlabelled rule at 0 or 1 leaves the reader to work out what it marks, so refline and shade write the name on the rule or the band, where the data leave room.

Checking figures

Direct labelling fails silently: a label on a line or on another label still renders and raises nothing. collisions(fig) draws the figure and measures it. It returns one (panel, kind, description) tuple per problem, and an empty list when the figure is clean. The kinds are 'label/label', 'label/line', 'label/marker', 'label/shape', 'label/outside' (a rule's label outside its panel) and 'text/edge' (text that runs off the figure). It measures every piece of text, a legend or a key built from offset boxes counting as one label, against other text, plotted lines, scatter markers at their drawn size and the outlines of filled shapes such as bars, arrows and bands. Reference rules and shaded periods are furniture that any label may cross. A label may sit inside a shape or clear of it, but not across its edge unless it is pinned in the shape, as a value written at the end of its bar is. The names label_scatter prints may overlap one another, since they are the observations, but any other label over one of them is reported. The placement helpers steer clear of everything the check measures; the check catches what they could not resolve and what was drawn by hand.

In a script, assert not ft.collisions(fig) stops on a bad figure. save runs the check at each size it writes and raises instead of writing a figure whose labels collide or whose text is cut off at the edge, so a bad figure never reaches the disk.

fig-check checks every figure in a folder of documents without rendering them. It runs each document's code as Quarto or Jupyter would (the # %% cells of a percent-format .py, the Python chunks of a .qmd, the code cells of a .ipynb), in the folder Quarto runs it in, and measures each figure at the size an HTML render gives it, read from fig-width and fig-height as Quarto reads them (7 by 5 inches when nothing sets them). A .py file counts as a document when it has a # %% [markdown] or # %% [raw] cell. A figure the document saves with save is measured at each size and not written, so a check leaves the document's figure files as they were. It needs the check extra.

fig-check docs                  # every document in docs/
fig-check docs report           # one document, by stem or file name
fig-check docs --figs figures   # also write each figure as a PNG

Every document is checked, even after one fails. The exit code can gate a commit or a CI job:

• 0: every figure is clean.
• 1: some document has overlaps, and none crashed.
• 2: some document raised an error, whose traceback is printed, or the check could not start (wrong arguments, or PyYAML missing).

The digest

A figure is a picture of data that a program cannot read back. figtools embeds a digest in each figure it exports: the plotted data as compressed JSON in the image's metadata, a PNG's text chunk or a PDF's document information. For each panel it holds the axis titles, scales and kinds; each series with its label, colour and values (lines, markers, bars, scatters, bands, intervals, error bars); the reference rules and shaded periods with their names; named points; and notes. A script or a language model working from a paper's figure files or a rendered document can then read what each figure shows. The image itself is unchanged.

The digest holds the data. It embeds every plotted point, raw observations of a scatter included, up to 5,000 points per series, and anyone who has the file can read them back. A binned or aggregated figure carries only the aggregates it plots. For figures of confidential data, turn the digest off: ft.setup(digest=False) for every figure, or ft.save(fig, path, digest=False) for one figure's files.

The digest is on by default. It goes into every PDF that save writes, and into every figure a notebook kernel (Jupyter, VS Code's interactive window) displays after setup(). Terminal IPython runs no kernel, and there setup leaves the display alone. To read a digest back:

render-digest figure results/fig1.pdf

prints each panel's values as markdown tables. It takes PNGs and PDFs; a PDF that LaTeX built from several figure files carries the digest of each. describe(fig) in figtools.digest returns the digest of a live figure.

With Quarto, a post-render hook collects the digests after each render. In the project's _quarto.yml:

project:
  post-render: python -m figtools.digest post-render

For each rendered document the hook writes a folder holding outputs.md (the headings, each figure's values as tables, the page's tables as markdown and its printed output as code blocks, in document order), one CSV and one PNG per figure, and a manifest with the render time and a hash of the source. A document rendered to PDF yields its figures' digests under pdf/ in the same folder. The folder is ~/.local/share/render-digests/<project folder>/<document path>/, outside the repository; the environment variable FIGTOOLS_DIGEST_DIR, set to an absolute folder, moves the root. The manifest records the project's path, and the hook refuses to overwrite the digest of another project with the same folder name while that project's folder still holds its _quarto.yml; give one of them its own root. The digest of a project that has moved or been deleted is stale, and the next render replaces it.

• render-digest where <document> prints the folder of a document.
• render-digest check <document> exits 0 when the digest matches the source, 1 when the source has changed since the render, and 2 when there is no digest or the digest belongs to another project that still exists.

Both exit 2 with a message when the document lies in no Quarto project.

The hook reads the paths Quarto passes in its environment, so it runs from a Quarto render only. It finds each output's source at the same path under the project folder as the output has under the output folder (output-dir, a website's _site, a book's _book), and reads each figure from the page, embedded in it or linked in the <document>_files folder Quarto writes beside it, so the page need not embed its resources. It skips, with a line saying why, a page made from plain Markdown (.md), which runs no figtools code, and a PDF that no single document made, such as a book's; render-digest figure reads the digests such a PDF carries. It fails the render when an output has two sources among .py, .qmd and .ipynb, or a page has none at all, and, naming the figure, when a figure lost its caption to another output of its cell.

Limits, each stated in the digest itself: a series longer than 5,000 points is thinned evenly; a large image grid is given by its shape and range only; colour or size that varies point by point is not decoded. A markdown table over about 600 cells is thinned to its first, last and extreme rows and says so, while the CSV keeps every row. Calling set_matplotlib_formats after setup() replaces the formatter that adds the digest; call setup() again after it.

Figures at the size of their destination

save renders each file at the physical width of where it goes, 5.9 inches for a paper's text column and 4.1 inches for a slide by default, re-solving the label placement at each size. Include the PDFs in LaTeX at their natural size, with no width= option: the type then lands on the page at the point size setup chose. Scaling a figure when it is included is what changes the size of its type. Each file is written whole, uncropped, so figures built alike come out the same size and subfigures stacked in a paper line up; the usage guide gives the recipe for figures read at one scale. Other destinations are a width away: save(fig, path, widths={'poster': 9.0}) also writes path_poster.pdf.

The style, and what the helpers assume

Each choice below is something the helpers assume. A figure that departs from one still draws, but its labels and its check may not behave as described.

One palette in a fixed order. Paul Tol's vibrant scheme, which readers with colour-blindness can tell apart, with black in place of its grey: seven colours, which series receive in the same order in every figure. Up to four series, the colour alone identifies each; past four, the labels carry the identification. Since a label names its series by colour, label_lines raises an error when two lines it would name cannot be told apart by colour, line style and marker, as happens to the eighth series of an unstyled plot. A key's colours are chosen by hand, and its entries may share a colour when their words tell them apart. Grey is kept for everything that is not data: rules, the grid, shaded periods, notes.

No frame, and a grid on the measured axis only. There are no spines and no tick marks: the grid and the tick labels give the reader every reference needed, and a frame is ink that carries no data. The grid is light, sits behind the data, runs along the axis that carries the measurement only (horizontal lines for a time series, vertical ones for a dot plot), and stops where the data stop.

Ticks at values the data can take. Where everything plotted against an axis is a whole number, so are its ticks. Matplotlib's default steps include 2.5, which labels a sixteen-year axis 2007.5, 2010.0, 2012.5, and whether a panel lands on that step depends on how much margin its labels take, so one longer series name can flip it. An axis of fractional data keeps its fractional ticks; a reference rule at 2020.5 is furniture and does not count as data.

Dots instead of bars. Where a figure compares magnitudes across categories, dotplot draws a Cleveland dot plot. A bar spends ink on the length from zero, which misleads when zero is not a meaningful origin; a dot marks the value alone.

Type from one base size. setup(base=11) puts titles and axis labels at the base size and every other piece of text (ticks, line labels, key entries, notes) half a point below it. The one exception is the names that label_points and label_scatter print at scatter points, two points smaller again so that many of them fit in the panel. Every helper reads its sizes from the base, so sizes cannot drift apart element by element, and a slide deck is setup(base=13) rather than a retouching session. The default of 11 points is ggplot's base size.

The caption carries the quantity. The helpers assume that the caption names the quantity, its unit and its sign convention, and that each reference rule is named on its line, so the axes carry no title that repeats them. A title is kept where the ticks alone would mislead, as on a scatter whose two axes are different variables.

Limits left to autoscale. A helper moves an axis limit only while that limit autoscales: label_lines ends the panel at the data, and a rule's label at the top of the data raises the top to fit. A limit set by hand, such as a scale shared across figures, is never moved. A rule's label that then does not fit on its usual side goes to the other side of the rule, or stays outside the panel for the check to report.

A captioned figure cell shows the figure and nothing else. In a Jupyter or Quarto document, a cell displays the value of its last statement when that statement is an expression. A bare matplotlib call such as ax.set_xlabel(...) returns an object that is then displayed as a second output, and so is a table. Quarto numbers the figure and that output as subfigures (a) and (b), gives the caption to the second output, and leaves the figure without one. The drawing helpers and save return values that a notebook displays as nothing, so a cell may end on one of them; panels and collisions return values a notebook shows. End any other figure cell with plt.show(), and give tables cells of their own. The digest's Quarto hook fails the render and names any figure whose caption another output took over.

setup changes the whole process. It sets matplotlib's rcParams globally, replaces the linear scale with one that applies the whole-number tick rule to every axes created afterwards by any library, and in a notebook kernel wraps the formatters that display figures. Code that shares a process with other plotting can use with ft.style(): instead, which applies the same inside the block and undoes it on leaving.

Data in any array form. The helpers convert their data with np.asarray, so lists, NumPy arrays, pandas Series and Polars columns all work as they are.

Public names

The drawing helpers return what they drew (lines, labels, bands, markers) in a list, so that it can be restyled; rule, label = ft.refline(ax, 0, 'zero') is a typical use. A notebook displays the list as nothing.

Versions and changes

Until version 1.0, a minor release (0.8 to 0.9) may change the interface and how figures are drawn. The changelog lists each release's changes, marks those that alter figures, and gives the steps to upgrade. Read it before upgrading a pinned project, and compare the figures after. CONTRIBUTING.md covers the tests and the release steps.

License

MIT; see LICENSE.