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name: visualization description: "Render Squidpy plots for spatial overlays, segmentation, graph statistics, ligand-receptor heatmaps, and variation-by-distance results." disable-model-invocation: true metadata: disco-role: operating license: BSD 3-Clause

Squidpy Visualization

Use this sub-skill when a task is about rendering Squidpy figures after the AnnData or SpatialData-like table is already loaded and, when needed, analysis results have already been computed.

Route

• Spatial overlays and segmentation masks: read references/plotting-workflows.md#spatial-overlays and references/api-reference.md#spatial-plotters.
• Neighborhood, centrality, interaction, co-occurrence, Ripley, or ligand-receptor plots: read references/plotting-workflows.md#graph-and-statistic-plots.
• Distance-to-anchor plots and image-feature extraction for plotting: read references/plotting-workflows.md#tool-and-feature-plotting.
• Plotting failures, headless rendering, palette mismatches, saved files, or visual-regression differences: read references/troubleshooting.md.
• Smoke-test a plotting installation without downloads or repository fixtures: run python scripts/plotting_smoke.py --quiet.

Boundaries

• This sub-skill renders figures with squidpy.pl; it does not compute graph statistics, ligand-receptor tests, or distance design matrices.
• Route graph construction and statistic computation to ../graph-analysis/SKILL.md before plotting graph outputs.
• Route design-matrix creation for sq.pl.var_by_distance to ../tools-workflows/SKILL.md.
• Route data loading, Visium metadata repair, missing .obsm['spatial'], or missing .uns['spatial'] image metadata to ../datasets-and-io/SKILL.md.
• Route stable ImageContainer processing to ../image-analysis/SKILL.md and experimental QC or tiling plots to ../experimental-imaging/SKILL.md.

Practical Defaults

• Use matplotlib.use("Agg") before importing pyplot in headless scripts.
• Prefer return_ax=True for sq.pl.spatial_scatter, sq.pl.spatial_segment, and sq.pl.var_by_distance when the caller needs axes.
• For graph/statistic plotters, compute the corresponding sq.gr.* result first and treat plot functions as renderers over stored keys.
• For image overlays, verify library_id, library_key, img_res_key, scalefactors, and segmentation cell IDs before tuning aesthetics.