omics-plotting

# omics-plotting ## Overview When the user wants a figure, **generate it with matplotlib / seaborn**, applying the shared style block below. The user can hand-tune colors, fonts, or spines per plot, but unless they ask for something specific, paste the style block and reuse the palette so a whole analysis reads as one figure system at a glance. This skill is self-contained: everything you need (style, palette, recipes) is in this document. ## When to use - The user asks for a plot / figure / chart / visualization from a results table or an in-memory DataFrame (DEG table, enrichment result, expression matrix, long-form measurements, survival table…). - You are preparing figures for a report, a paper submission or presentation and want a consistent publication style. > Combining several plots into one multi-panel composite, or assembling > user-supplied PNG/PDF panels, is handled by the sibling `multipanel` > skill — use this skill to draw each individual panel. ## Do NOT use for - Interactive dashboards or web charts (this is static matplotlib output). - 3D molecular structure rendering (that is the structure viewer, not a plot). ## Key Concepts ### One consistent figure system The core idea is that every figure from a single analysis should look like it came from the same publication. That is enforced by two shared objects: the `PUB_STYLE` rcParams block (fonts, spines, DPI, editable vector text) and a fixed `PALETTE` / directional color set (`UP`, `DOWN`, `N...