plot-check

name	plot-check
description	Visual (VLM) and array-completeness check for plots and figure files. Use proactively after savefig or export; before citing a figure in a paper or report. Axis styling and export settings → scientific-plotting; domain physics → physics-check.

Plot check

Inspect the figure file and, when available, the arrays the plotting script used. Do not infer quality from file size, timestamps, or log lines alone.

VLM alone is not enough for curves and scatter plots. A figure can look smooth while regions, bins, or series are missing. Run Step 2 when numeric artefacts exist; never mark OK on visuals only in that case.

When to run

• Right after any script writes a figure (savefig, PDF/PNG/SVG export). PNG: always dpi=300 (see scientific-plotting).
• Before a manuscript section, slide, or report cites the figure.
• When a plot looks suspicious (gaps, saturation, wrong panel count).

Step 1 — visual inspection (VLM)

Open the figure with the Read tool (PNG/PDF at roughly final print size).

Verify:

• Axis labels, units, and tick formatting present and match the caption.
• Scales appropriate (linear vs log obvious; no misleading truncation).
• Dynamic range plausible (no flat lines, all-NaN panels, unexpected saturation).
• Multi-panel: consistent fonts; comparable scaling when panels are compared.
• Legend readable; series distinguishable; no clipped labels or text overlap.
• Model vs data panels labeled and visually comparable.
• No rendering artefacts (ringing, resampling moiré, debug overlays).

Data completeness (VLM): for every line, curve, scatter cloud, or error-bar series:

• Gaps: holes in curves; lines stopping before the axis ends; thinning scatter.
• Truncation: series ends early while x continues; sibling panels disagree on range.
• Dropped series: legend lists N curves but fewer than N visible traces.
• Masking artefacts: stairs, notches, flat segments where density is expected.
• Histograms: empty interior bins; jagged drops to zero vs stated binning.
• Caption vs plot: claims like "all", "full sample", or count N must be supported.

If incomplete or ambiguous → run Step 2. If arrays are unavailable, verdict is at most WARN with "completeness not verified numerically".

Project-specific visual bands (reference curves, expected ranges) → repo CLAUDE.md.

Step 2 — completeness vs arrays (required when data exists)

Load the arrays the plotting script used. Count before concluding the VLM pass.

import numpy as np

x, y = np.asarray(x).ravel(), np.asarray(y).ravel()
assert x.size == y.size, "x and y length mismatch"
n_total = x.size
plottable = np.isfinite(x) & np.isfinite(y)
n_plotted = int(plottable.sum())
n_dropped = n_total - n_plotted

print(f"total={n_total} plottable={n_plotted} dropped(non-finite)={n_dropped}")
assert n_dropped == 0, f"{n_dropped} points dropped — check mask/NaN handling"

Check	Fail when
Expected count	Caption/manifest says N but n_plotted < N
Shared abscissa	Compared curves differ in x length or finite mask
NaNs	Non-finite values not documented in caption
Histogram	Occupied bins ≪ expected without explanation
2D / image	Most pixels non-finite without stated mask
Replot spot-check	Re-plot (x, y) and diff against saved PNG if unsure

Step 1 OK but Step 2 shows drops → BLOCKING. Scientific plot without arrays → WARN unless user confirms completeness.

Step 3 — manifest cross-check (when project has a run log)

Path from CLAUDE.md. Confirm git_hash, data_paths, seed, script/command match what produced the figure.

Step 4 — verdict

Exactly one of:

• OK: <one-line summary>
• WARN: <summary>; <what to investigate>
• BLOCKING: <reason>; <fix>

Record in research-figure-manifest or source comment. Then run physics-check on saved arrays when they exist.

Integration

Skill	Role
scientific-plotting	Export before Step 1
physics-check	Numeric/domain asserts after plot looks complete
vlm-figure-audit	Print-size QA; defer final OK on curves until plot-check passes
research-figure-manifest	Store plot_check verdict
paper-writing-workflow	Manuscript build loop references this category