viscose

Scientific plots that are pieces of art.
Pick a palette. It brings its own colors, type, axes, and special effects.

pip install viscose              # numpy and glycorender are all it needs
pip install "viscose[cluster]"   # adds scipy for clustermaps

One word changes everything

import viscose as vc

fig, ax = vc.subplots(palette = 'aura')
fig.suptitle('Differential abundance', 'Tumor vs. healthy tissue, 412 glycans')
ax.scatter(x, y, hue = direction)
ax.axhline(2)
ax.set_xlabel('log_{2} fold change')
ax.set_ylabel('-log_{10} adjusted p')
fig.save('volcano.pdf')

Same data, same code, and only palette changes. Spheres become rings, gradients become solid shapes, hairline axes become heavy rounded ones, and titles go from light and wide to bold and tight. No styling code, no rcParams, and no theme files.

Four palettes, four personalities

Each palette has two hues in four shades, and effects to match. Few colors, in shades of those few colors, on white: figures that look composed in a paper and striking on a slide.

lumen: peacock and marigold

Gradients run through the marks, points are glossy spheres, lines glow, and everything rests on soft shadows.

couture: plum and gold

Hairline axes held away from the data, slender needle bars, large light titles, and spaced capitals.

poster: forest and vermilion

Heavy rounded axes, big bold type, and thick solid marks cut apart by crisp white gaps.

aura: burgundy and teal

Marks float on soft shadows in their own color, above rounded heatmap cells, with no axis lines at all.

Out of the box

The same data and the same labels, with no styling on either side: matplotlib and seaborn on the left, viscose on the right.

Glycans in your plots

viscose shares its renderer with glycowork's GlycoDraw, so a plot can carry real SNFG drawings as sharp as the rest of the figure, in PNG, PDF, and SVG.

from glycowork.motif.draw import annotate_figure

ax.annotate('Neu5Ac(a2-6)Gal(b1-4)GlcNAc', (x, y), offset = (12, 0), svg_label = True)
fig.save('volcano.svg')
annotate_figure('volcano.svg', filepath = 'volcano.pdf', compact = True)

Everything you reach for

hue, style, and size take one value per point and build the legend for you, as seaborn does.

ax.scatter(x, y, hue = stage, style = source, size = abundance,
           hue_label = 'Stage', style_label = 'Source', size_label = 'Abundance')
ax.text(0.02, 0.98, 'F = 4.2\np = 0.003', axes_fraction = True, va = 'top')

Clustermaps come with both dendrograms and a color bar. Hand over a DataFrame and it brings its own labels.

fig, heat = vc.clustermap(df, palette = 'aura', title = 'Glycan abundance by tissue', colorbar_label = 'z-score')

Light and quick

No compiled plotting stack, no backends, and no font cache. For vector output, viscose is often many times faster than matplotlib and seaborn, and its files can be far smaller. At 300 dpi, in Poster:

matplotlib's compiled rasterizer is still about twice as fast on most PNGs, and the soft shadows of Lumen and Aura add about half a second. To rerun the full comparison, wins and losses alike, use benchmarks/compare_matplotlib.py.

Make it yours

vc.set_palette('aura') changes the default for every figure. A library that builds on viscose calls vc.default_palette('aura') instead, which gives way to the choice of whoever uses it. In any palette, refer to its shades as a0 to a3 and b0 to b3, dark to pale, or as ink, muted, faint, and paper; hex and CSS color names work too. fig.pal.groups(3, 2) gives categories grouped by hue, here three shades of one and two of the other, and fig.pal.contrast(n) alternates between the hues for categories that have to stand apart, as scatter(hue = ...) does.

A palette of your own is two hues, three text colors, and whichever effects you like:

vc.register_palette(vc.Palette('midnight', ['#14213D', '#27477E', '#5C85C5', '#C4D5EE'], ['#8F5B00', '#D08C00', '#F2B83B', '#FBE5B0'],
                               '#14213D', '#5A6478', '#E6EAF1', point = 'sphere', bar = 'deep', shadow = 0.4))
fig, ax = vc.subplots(palette = 'midnight')

A palette's paper is the color of its page, white unless you say otherwise, and every format draws on it. For a dark page, give it a light ink and order its shades from the strongest against the page to the faintest, so that rings, halos, and scales follow.

Century Gothic is used where it is installed, and glycorender's bundled Comfortaa elsewhere.

More

examples/gallery.py draws seven standard figures in every palette, examples/features.py draws one sheet of features per palette, and examples/readme_figures.py draws every image on this page.