vivarium-reportlisted

Make publication-grade figures (and tables / methods text) from comparative-genomics results, in Python OR R. Use whenever the user wants to plot or visualize genomics analysis output — an ANI/AAI heatmap, a CAZy/COG/KEGG category bar chart, a pangenome or presence/absence matrix, a dN/dS (ω) plot, a phylogenetic tree, a synteny/dot plot — or to turn analysis tables into a journal-ready figure, or draft a methods paragraph with tool versions. Triggers on phrases like "plot the ANI matrix", "make a heatmap of", "bar chart of CAZy/COG categories", "figure for the paper", "make this publication quality", "出个图", "画个热图/柱状图", "把这个表画成图", "出版级/Nature 风格的图", "ANI 热图". Produces editable SVG + PDF + TIFF (600 dpi) with Nature-style conventions (Arial, small fonts, editable text, restrained palette). This skill plots results that already exist — to *compute* ANI/AAI use vivarium-compare, to *build* a tree use vivarium-phylo, to *run* a search use vivarium-search; this one turns their output into the figure. Part of the v
Jason-0409-G/vivarium · ★ 1 · AI & Automation · score 72

Install: claude install-skill Jason-0409-G/vivarium

# vivarium-report — publication-grade figures from comparative-genomics results Turn an analysis table (an ANI matrix, a CAZy/COG count table, a dN/dS summary, a tree) into a figure that defends a claim and survives review — not a pretty plot in isolation. Figures come out journal-ready: Arial, small fonts, editable text, a restrained palette, exported as **SVG (editable) + PDF + TIFF (600 dpi)**. ## Step 0 — figure contract, before any code State these four things first; they decide the plot, not the aesthetics: 1. **Claim**: the one sentence this figure must defend (e.g. "L5 and M7 are conspecific, >95% ANI"). 2. **Figure type / data**: which analysis output feeds it (table below). 3. **Backend**: **Python or R?** This is a blocking choice — if the user has not said which, ask "Python or R?" and stop. Both are bundled; use the chosen one exclusively (don't render an R figure with Python or vice-versa). 4. **Export**: final size + formats. Default SVG + PDF + TIFF (600 dpi), editable text. ## Step 1 — map the result to a figure type | Result (vivarium output) | Figure | Bundled? | |---|---|---| | ANI / AAI matrix (square TSV) | annotated heatmap | ✅ `heatmap` | | CAZy / COG / KEGG category counts per genome (TSV) | grouped or stacked bars | ✅ `bars` | | Gene-family presence/absence, small matrix | heatmap (0/1) | ✅ `heatmap` | | dN/dS (ω) per orthogroup | lollipop / sorted bars | use `bars` (one series) or draw directly | | Phylogenetic tree (Newick + support) | tree |