scientific-plotting

name	scientific-plotting
description	Publication-quality plots: vector PDF output, PNG at dpi=300, label and tick font sizes readable at final column width. Use when generating or updating figures for papers, slides, or reports; or when plot text is too small or clipped.

Scientific plotting

Goal: figures that look correct in the compiled paper PDF, not on a large monitor. Do not teach or paste plotting code in chat; change the project's plot script and re-export.

What matters

1. Vector PDF saved under the manuscript figures directory, with a stable filename the paper already references. Prefer PDF for manuscript figures.

2. PNG exports: dpi=300 always — for slides, previews, VLM audit, or when raster is required. Do not rely on matplotlib's default (~100 dpi); text and lines will look soft or pixelated when zoomed or printed.

   fig.savefig("figure.pdf")                    # vector — preferred for LaTeX
   fig.savefig("figure.png", dpi=300)           # raster — always 300
   plt.savefig("figure.png", dpi=300, bbox_inches="tight")
   

3. Font sizes chosen for the width the figure will occupy in the PDF: axis labels, ticks, legend, colorbar, and panel letters should read as roughly 7--9 pt in the printed page. Defaults are usually too small after scaling.

4. Figure dimensions set in the plotting step for that width, not oversized on screen and shrunk only in the manuscript.

5. No clipped or overlapping text at the edges; legend must not hide the data.

Secondary styling: distinguish series with line/marker style and colour, not colour alone (colour-vision deficiency affects up to ~10% of readers; Paper II, Sect. 2.3). Other styling unless the project specifies it.

How to verify

After export, run plot-check, then vlm-figure-audit at publication size. If labels fail, adjust the plot script and regenerate — do not patch readability only in LaTeX.

Workflow

1. Regenerate the figure asset (PDF and/or PNG at dpi=300).
2. plot-check → physics-check on backing arrays.
3. vlm-figure-audit on the standalone figure or compiled PDF page.

Domain-specific units, axis ranges, and science checks belong in the project, not here.