jaff.plotting

Publication-style plotting in pure matplotlib. A figure is described as data: a grid of axes, each holding a list of series. Themes supply the look; every series can override it.

Functions

Quick start

from jaff import Network
from jaff.plotting import plot, plot_rates, plot_xsecs

net = Network("networks/uclchem_small_gas/uclchem_small_gas_network.jet")
r = list(net.reactions)

plot_rates(r[:3])                                 # one axes, three curves
plot_rates([r[0], [r[1], r[2]]], grid=(1, 2))      # nested list = overlay
plot_rates(r[:4], grid=(2, 2), style="talk", palette="sunset")

photo = [p for p in net.reactions.photo_reactions() if p.xsecs_dict]
plot_xsecs(photo[:4], grid=(2, 2), bands=True, save="xsecs.pdf")

Nesting rule: each top-level item is one panel; a nested list is overlaid on one axes. Without grid everything shares a single axes, unless there are more curves than the style's legend_max (default 12): then the curves are split in order over an automatic grid. Panels fill the grid row by row; leftover cells are hidden (the bottom-right one hosts the shared legend). An axis label common to every panel is drawn once for the whole figure (supxlabel / supylabel) when the panels span two or more columns / rows.

Figures are closed in pyplot after saving / showing (close=True), so loops don't accumulate open figures; the returned (fig, axes) still work. Pass close=False to keep the figure open. After an interactive, non-blocking show (plt.isinteractive()) the figure is left open.

The Reaction.plot_rate_coefficient, Reaction.plot_xsecs, Reactions.plot_rates and Reactions.plot_xsecs methods forward their keyword arguments to these functions.

Look

White surface, black spines on all four sides, inward major and minor ticks on all sides, DejaVu Sans with STIX maths. Panels sit on a tight grid: the same gap (style.gap, inches) between columns and rows, margins sized to the outer labels. In each column the top panel carries its x tick labels on the top spine and the bottom panel at the bottom; a middle panel shows none when it shares the bottom panel's x range, else small labels inside above its bottom spine. Rows and columns without a used panel take no space. Each panel box is style.panel_size, unless figsize fixes the figure.

In the default "paper" style:

• y tick labels are drawn inside the panel, right of the left spine (labels at the top/bottom edge are blanked, and the x range gets an empty strip on the left so no curve runs under a label);
• panel titles sit inside, upper right, with headroom above the data (a title too wide for the panel goes above it);
• log axes are labelled by exponent (−3 for 10⁻³) with at most ~4 labelled decades, minor ticks on decades (at most 4 between labels); axes under 1.5 decades get fractional exponents (1.05); the axis label gains a log₁₀ prefix.

Marker series are hollow markers spaced evenly along the curve on screen; a line+marker style ("-o", "--D") adds sparse markers to a line. A series with "role": "reference" is a thick dark-grey line drawn beneath the rest. See Themes.

Legends

The default legend="auto" (same as "figure") draws one shared legend for the whole figure, de-duplicated by label, in the bottom-right hidden grid cell when the grid is unfinished, else in the right margin. A label keeps one colour and style across every panel, so the shared legend keys them all.

legend="axes" (opt-in, for panels with different labels) draws one legend group per panel, stacked in the right margin and headed by the panel's title, tag or letter (a), (b), … (an untitled panel shows its letter inside). "none" draws no legend; an axes-level legend ("axes" / "none") overrides the figure policy for that panel.

A legend with more than the style's legend_max (default 12) entries is not drawn (with a warning); a shared legend over the cap that keys several panels falls back to per-panel groups. legend_title="Source" adds a bold heading to the shared legend (or above the stack of groups). Panel names are explicit: use the axes title or tag; a lone series is not turned into a tag.