TikZ / pgfplots Figure Review

You help the user review TikZ and pgfplots figures in LaTeX documents and fix alignment, label collision, clipping, and legend-over-data issues. This skill captures 11 failure modes learned from reviewing 40+ figures across two real documents, plus the extract-standalone iteration workflow that makes per-figure fixes fast.

1. Workflow

The cheapest iteration loop is: extract → standalone compile → PNG → view → edit → repeat, keeping the main document untouched until the standalone is clean.

1.1 One-time setup (per project)

Create a working directory (e.g.

figures_check/

) with:

• _preamble.tex

  — mirrors the relevant packages, TikZ libraries,

  pgfplots

  compat version, and all custom math commands (

  \grad

  ,

  \Hp

  ,

  \vq

  , etc.) from the main document. Without these the standalone will fail with "undefined control sequence".
• One

  figN_<name>.tex

  per figure, using

  \documentclass[border=8pt]{standalone}

  and

  \input{_preamble}

  . The body is only the

  \begin{tikzpicture} … \end{tikzpicture}

  block — no caption, no

  figure

  environment.

Known pitfall:

pgfplots compat

mismatch. The main document may pin a newer compat level than the local TeX install supports. Set the preamble to the lowest compat that works on the local install (e.g. 1.17) and do not sync that one line back to the main document.

1.2 Per-figure compile / render

cd figures_check
pdflatex -interaction=nonstopmode figN_name.tex > figN_name.log 2>&1
pdftoppm -r 200 -png figN_name.pdf figN_name
# produces figN_name-1.png

200 dpi is enough to read labels; go to 300 dpi only for fine alignment checks.

1.3 Parallel review

Once every standalone compiles and has a fresh PNG, dispatch review subagents. Each subagent gets:

• The PNG path (to view via the Read tool).
• The standalone

  .tex

  path (for fast iteration).
• The line range in the main

  .tex

  (for syncing the fix back).
• Explicit instructions to edit both files and keep the

  tikzpicture

  body identical.
• A re-render command and a "max 3 iterations" cap.
• A pointer to this SKILL file as reference.

Batching: for <10 figures, one subagent per figure is fine. For 20+ figures, dispatch 5–7 subagents each handling 5–6 figures grouped thematically (e.g. "all phase portraits", "all schematic pipelines"). Thirty-plus individual subagents is slow and noisy — batching gives each subagent a coherent context without over-fragmenting.

Cross-references like

\eqref{eq:foo}

and

\ref{prop:bar}

will not resolve inside a standalone. Tell subagents to use placeholders in the standalone and keep the original refs when editing the main file.

1.4 Scaling to many-figure documents (20+ figures)

For large documents, don't hand-extract each tikzpicture — dispatch a dedicated extraction subagent first. Give it:

• The main

  .tex

  path and a grep-verified list of

  \begin{tikzpicture}

  line numbers.
• A naming scheme (

  figNN_semantic_label.tex

  ).
• The shared

  _preamble.tex

  path.
• Instructions to copy each tikzpicture verbatim (preserving indentation, comments, line breaks) into

  \documentclass{standalone}

  wrappers, and to run

  pdflatex

  +

  pdftoppm

  on all of them.

The extraction subagent will also surface compile-blocking bugs that prevent the main document from building at all (see §2.8 for a classic pgfplots

\foreach

bug). Tell it to fix any such bugs in the standalone copy only, and report them so a review subagent can propagate the fix back to the main file.

If figures

\addplot table {...}

from external

.dat

files, symlink the data directory into the scratch dir rather than copying:

cd figures_check && ln -s ../phase-data phase-data

---

2. Common issues and canonical fixes

When reviewing a new figure, scan for these in the order listed in §3. Each subsection gives the failure mode, a real example, and a canonical fix.

2.1 Legend sits on top of data

By far the most common issue.

legend pos=north east

(the pgfplots default) assumes the plot is roughly linearly rising — which is false for convergence plots, curves that cluster near the top, or bar charts whose tallest bar is near the right.

Fix options, in order of preference:

1. Move legend outside the axis — cleanest when there's horizontal room in the figure:

   legend style={font=\small, at={(1.02,1)}, anchor=north west}
   % or shorthand:
   legend pos=outer north east
   

2. Raise

   ymax

   — if the legend must stay inside, give it empty headroom:

   ymin=0, ymax=1.45   % was 1.1 — top bar was 1.0
   

3. Compact the legend — multi-column, smaller font (see

   references/snippets.md

   ).
4. Opaque legend — last resort when the legend has to sit over low-density data (see

   references/snippets.md

   ).

Pick the fix that preserves the most information. Prefer (1) if the figure has room; (2) for bar charts where extra headroom is cheap; (3) when a 4-entry legend is unavoidable; (4) only if nothing else fits.

2.2 Text label clipping a box, line, or marker

Two sub-cases:

(a) A text node sits on the border of a dashed/solid enclosure. Seen in an IDA-PBC figure where the

u=-y_c

label and the energy-balance labels were kissing the closed-loop rectangle.

• Enlarge the enclosure so labels fit fully inside.
• Move the label inward (shift further from the border).
• If the label belongs to an arrow passing through the border, switch the label to the opposite side of the arrow (

  below

  →

  above

  ).
• Move captions/descriptions clearly outside the enclosure with whitespace (don't let them kiss the border).

(b) A text label is hidden by the glyph it's annotating (e.g. "min" on top of a marker dot). This is the single most common failure mode on phase portraits: equilibrium labels (

center

/

saddle

/

source

/

sink

/

equil.

) placed directly on their marker dots. Default

above

/

above right

anchors still draw the text touching the dot. Split into two nodes and anchor the text explicitly:

\fill[black] (0,0) circle (2.5pt);
\node[font=\small, anchor=west] at (axis cs:0.15, 0.35) {min};

The trap: using the

node

option on

\fill

puts the label at the dot's center anchor, so it sits exactly where the glyph is. Make them separate and anchor the text. For a whole row of equilibrium labels,

anchor=west

at

(x_dot + dx, y_dot + dy)

is more consistent than

anchor=south

because it gives uniform horizontal offset regardless of how tall the text is.

2.3 Bidirectional ports between two boxes → label collision

When two arrows run in the same channel between two nodes (e.g. Plant ⇄ Controller with

y

and

u=-y_c

), a single centered arrow with two labels always collides. Split into two parallel arrows with

xshift

offsets and opposite label sides:

\draw[->, blue!70!black, thick]
  ([xshift=-5pt]plant.south) --
  node[left, font=\scriptsize]{$y = G^T\!\grad H_p$}
  ([xshift=-5pt]ctrl.north);
\draw[<-, orange!70!black, thick]
  ([xshift=5pt]plant.south) --
  node[right, font=\scriptsize]{$u = -y_c$}
  ([xshift=5pt]ctrl.north);

Note the second draw uses

<-

to keep the arrowhead semantically at the plant side while the label stays on the right.

2.4 A third arrow crossing the channel between two boxes

A "Task Oracle → Plant" arrow crossed the plant↔ctrl channel and dragged its

g̃

label through the port labels. Two fixes combined:

• Reposition the source node so the crossing arrow enters from a clean edge (e.g. straight

  plant.west

  , not diagonal through the middle).
• Free up the channel for port labels only by moving other labels to the outside (§2.3).

If the source node is conceptually outside one group and the crossing arrow must traverse a separator, give it enough horizontal room; push boxes apart rather than letting an arrow squeeze through.

2.5 Notes beside a stack of boxes clip into the boxes

A column of annotation

\node[note]

entries at

x=5.3

with default

anchor=center

extended from ~

4.3

, but the boxes ended at

x=4.0

. Only 0.3 cm clearance, and the notes overlapped the box edges.

Rule: when placing text nodes next to the edge of another node, always anchor the text on the side facing the reference node:

note/.style={font=\scriptsize, gray, align=left, anchor=west}
\node[note] at (4.25, 0) {…};   % box right edge at 4.0

Default

anchor=center

is correct when the text stands alone in empty space;

anchor=west/east/north/south

is correct when it sits next to an edge.

2.6 Dashed separators crossed by arrows or labels

Overlay/separator lines (e.g. "Classical GD | SHAPE") must be placed so nothing arrow or label touches them. Either:

• Add horizontal slack between the separator and the boxes on each side, and
• Place the separator's own label (e.g. rotated "vs.") in the empty gap, not at the height of any arrow passing through.

2.7

minimum width

is a minimum, not a cap — use

text width

for consistent stacked boxes

Seen twice on stacked pipeline diagrams. Both had

pstep/.style={draw, ..., minimum width=8cm, minimum height=0.75cm,
              align=center, font=\small}

and 5–6 stacked

pstep

nodes. The notes next to each box were positioned at

x = 4.25

(just past the intended box-right-edge at

x=4.0

). At 2cm of slack the layout should have been clean.

It wasn't:

minimum width

only establishes a lower bound. When a node's content is wider than the minimum, the box grows. One long step text forces that row's box wider than 8cm, and the annotation note — positioned relative to the intended right edge — ends up inside the actual box.

Fix: replace

minimum width

with

text width

so the text is forced to wrap into a fixed-width column, making every box the same size:

pstep/.style={draw, rounded corners=4pt, fill=blue!8,
              text width=9.2cm, minimum height=0.75cm, inner sep=4pt,
              align=center, font=\small}

text width

is a hard ceiling — text that would exceed it wraps onto a new line.

inner sep=4pt

adds internal padding so wrapped lines don't touch the box border. Then place notes cleanly past the real right edge (text width + inner sep + a small gap).

For a row of 6 stacked

pstep

nodes at 9.2 cm text width centered at x=0:

• Real box extent:

  x ∈ [-4.6, 4.6]

  + inner sep
• Notes start at:

  x = 5.05

  (clear of right edge)

Also bump the vertical gap between rows if the wrapping turns a box into two lines — otherwise rows collide.

2.8 pgfplots

\foreach

+

\addplot[\var, ...]

— macro not expanded

Compile-blocking bug. This pattern looks reasonable but fails:

\foreach \ra/\rb/\clr in {0.22/0.18/blue!80,
                          0.35/0.28/blue!60,
                          0.48/0.38/blue!40}{
  \addplot[\clr, thick, ...]  % ← \clr here is never expanded
    ({\ra*cos(x) + 0.35}, {\rb*sin(x)});
}

Error:

! Undefined control sequence. \pgfkeyscurrentkey ->\clr

.

The pgfplots key parser sees

\clr

as a literal key, not as a

\foreach

loop variable. TikZ

\foreach

captures the text but pgfplots' own

\pgfkeys

expands inside a different scope that does not see the foreach variable.

Fix: unroll the loop into explicit

\addplot

calls with literal colors:

\addplot[blue!80, thick, ...] ({0.22*cos(x)+0.35}, {0.18*sin(x)});
\addplot[blue!60, thick, ...] ({0.35*cos(x)+0.35}, {0.28*sin(x)});
\addplot[blue!40, thick, ...] ({0.48*cos(x)+0.35}, {0.38*sin(x)});

(An alternative

color=\clr

form also sometimes works, but unrolling is the safe choice — it's explicit and won't regress on pgfplots upgrades.)

Catch this early: when a full-document compile fails with this error, the extraction phase should still produce a standalone for that figure, and the standalone will also fail to compile until the unroll is applied. Fix it in the standalone first, then propagate to the main file.

2.9 3D axes and vectors project into the same screen direction

Seen in a cross-product visualization. The z-axis was drawn at

z=(-0.45cm, 0.18cm)

per unit and the cross-product vector at

(−0.5, 0.2, 2.6)

— both projected to essentially the same upper-left screen direction. Their labels ended up literally touching: the z-axis's

z

glyph fused with the cross-product label's

∇H

to read as

∇H_z

.

This is a projection-space collision: two 3D directions that are geometrically orthogonal can map to parallel screen vectors under the wrong choice of

x

/

y

/

z

base vectors.

Fix: change the projection so each 3D axis maps to a distinct screen direction. For an isometric-ish look:

x={(1.0cm, 0.25cm)},     % right + slightly down
y={(0cm, 1.0cm)},        % straight up
z={(-0.55cm, -0.30cm)}   % lower-left — NOT upper-left

Then the cross product (whichever direction it points geometrically) will project into its own screen region with room for an annotation.

2.10 Labels inside a dashed/shaded enclosure get struck through by interior content

Seen in a cofactor figure — a "flow tangent to {g=0}" annotation was placed inside the family of dashed level curves and got sliced by the innermost contour. Interior content (level sets, grid lines, arrows) creates a field that no in-plane label can live inside without eventually being crossed.

Fix: move explanatory labels outside the content region, below or above the enclosure, so they read as captions-for-the-region rather than as items embedded in it. Use a leader line if you need to point at something specific.

2.11 Arrow paths crossing through other labels or boxes

Seen in a metriplectic ingredients figure. Two arrows (

\dot H = 0

and

\dot S ≥ 0

) were drawn from a central bracket's east edge and passed through a dashed compatibility box on their way to their labels. The fix was to reroute both arrows to exit from a different edge (

node.south

) into empty space below the figure.

Rule: when drawing an arrow out of a node, check the straight-line path to its target against every other box/label on the canvas. If it passes through anything, either (a) route via a polyline that detours around the obstacle, or (b) pick a different edge of the source node so the straight-line path is clear.

---

3. Review checklist

Scan each rendered figure for these, in order. Stop at the first "yes" and fix before moving on — fixes can change what other issues look like.

1. Is any axis label, title, or tick label clipped or cut off?
2. Does the legend box overlap any data curve, bar, or marker?
3. Does any text node sit on top of a marker dot, another node, or on the border of an enclosure (rectangle, ellipse, group)?
4. Phase portrait specific: are equilibrium labels (

   center

   /

   saddle

   /

   source

   /

   sink

   /

   equil.

   ) touching their marker dots? (§2.2b — the single most common phase-portrait failure mode.)
5. In figures with two boxes and a bidirectional port: are the two labels distinguishable, or are they bunched on top of each other?
6. Do crossing arrows drag their labels through other labels?
7. Do annotation notes next to a stack of boxes clip into the stack's edges? (

   anchor=center

   footgun +

   minimum width

   not being a cap.)
8. Are markers at axis extremes (

   xmin

   /

   xmax

   /

   ymin

   /

   ymax

   ) clipped in half?
9. Is there a separator line / region divider that touches any arrow or label?
10. 3D diagrams: do any two 3D vectors project into the same screen direction, causing their labels to fuse?
11. Dashed enclosures: do any interior labels get struck through by content curves/level sets inside the enclosure?
12. Pipelines / stacks: do boxes vary in width because their text exceeds

    minimum width

    ? (§2.7 — switch to

    text width

    for consistent sizing.)

---

4. Copy-paste snippets

A catalog of the code patterns for each failure mode lives in

references/snippets.md

. Load it when you need to grab a specific pattern (parallel port arrows, legend-outside-plot, text-width stacked boxes, 3D projection template, unrolled

\foreach

, etc.) rather than re-deriving each time.

---

5. Pitfalls specific to this workflow

• Custom macros. Don't forget to copy

  \grad

  ,

  \Hp

  ,

  \Hc

  ,

  \vq

  ,

  \R

  ,

  \md

  , and any other user-defined command into the standalone preamble. The failure mode is a cryptic "Undefined control sequence" several seconds into compile.
• pgfplots compat mismatch. The standalone preamble should pin the compat level your local TeX supports. Do not sync that line back to the main document.
• Cross-references (

  \eqref

  ,

  \ref

  ). These will never resolve in a standalone. Use a short placeholder text locally, keep the original macros when editing the main file.
• Subtle sync drift. After editing in the standalone, diff the two

  tikzpicture

  bodies before declaring victory. It's easy to forget one file.
• Don't delete standalone files. Keeping them around means the next reviewer has a working scaffold — they only have to re-run

  pdflatex

  and look.
• Subagents may be blocked from running

  pdflatex

  . In some harness configurations, subagents can

  Read

  /

  Edit

  files but cannot invoke bash commands (even with

  dangerouslyDisableSandbox=true

  ). When this happens, subagents will edit standalone and main files symmetrically but won't be able to verify their fix. The driver must re-render every file each subagent edited and inspect the PNG. Brief the subagents up front that they may be blocked, and that in that case they should still make their best-guess edits and flag them for driver verification.

• text width

  vs

  minimum width

  for stacked boxes.

  minimum width

  is a lower bound, not a cap — use

  text width

  when you need every box in a stack to be the same size regardless of content. Bitten twice (§2.7).

---

6. Minimal re-render recipe

After any edit to a standalone:

cd figures_check
pdflatex -interaction=nonstopmode figN_name.tex > /dev/null \
  && pdftoppm -r 200 -png figN_name.pdf figN_name
# then view figN_name-1.png

Three iterations should be enough for any single figure. If you're on iteration four, step back and reconsider the layout as a whole, not tweak another parameter.