docs: refresh the panel-assembly section for the two layout engines - #106
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docs: refresh the panel-assembly section for the two layout engines#106Starlitnightly wants to merge 1 commit into
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Section 8 predated `panel_size=`, `ov.pl.panelflow`, and the helpers that make a plot behave as a panel, and its closing note was by then factually wrong: it told readers `ov.pl.multipanel` "does not express 'panel A is exactly 70 x 70 mm regardless of its neighbours'" and to fall back to `fig.add_axes`. Both engines express exactly that now. Rewritten to cover: - the two engines and when each applies — canvas-fixed vs panel-fixed `multipanel`, and `panelflow` for panels of genuinely different sizes that wrap into rows (`below=` stacking, `units='pt'`, `reserve=`) - making a plot behave as a panel: `roc(aspect='auto')` (a fixed square aspect shrinks the axes inside the rectangle a layout assigned), `boxplot(show_points=False)`, the volcano threshold guides and its ns legend key, and `add_stat_annotation` - text at panel scale: `declutter_ticks` (rotate, stagger, slide apart with leader lines, thin — never resize) and `adjust_text` (clamped inside the axes, which is what makes it safe to call after a layout resized the panel) - a marsilea heatmap as one panel via `rect=`, and why raster-and-imshow is not the alternative - `sankey` and `slopeplot(group=)` Every code cell was executed against the merged library before committing (synthetic AnnData stand-in for pbmc8k): 15 of 15 run clean. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Why
Section 8 (
## 8. Assemble the panels) predatedpanel_size=,ov.pl.panelflow, and the helpers that make a plot behave as a panel. Its closing note had become factually wrong — it told readers thatov.pl.multipanelBoth engines express exactly that now (omicverse#930, omicverse#932).
What the section now covers
The two engines, and when each applies
multipanel(width=)multipanel(panel_size=)panelflowplus
panelflow'sbelow=stacking,units='pt', andreserve='tight'/'axis'.Making a plot behave as a panel —
roc(aspect='auto')(a fixed square aspect makes matplotlib shrink the axes inside the rectangle the layout assigned, so the panel stops filling its cell and its x-axis leaves the row baseline),boxplot(show_points=False), the volcano threshold guides and itsns:legend key,add_stat_annotation.Text at panel scale —
declutter_ticks(rotate → stagger → slide apart with leader lines → thin; font sizes never change) andadjust_text(clamped inside the axes, which is what makes it safe to call after a layout resized the panel).A marsilea heatmap as one panel via
rect=, and why rendering it to a raster is not the alternative — it loses the vector text that made the export editable.sankeyandslopeplot(group=)— two panel types a grid of scatter plots cannot express.Verification
Every code cell in the section was executed against the merged library before committing, using a synthetic AnnData stand-in for
pbmc8k: 15 of 15 run clean. (One pre-existing cell needs a realistic gene count forpd.qcutdeciles to be unique — it passes at 2000 genes, and pbmc8k has ~33k.)Companion to omicverse#930 – omicverse#940.