Appendix E — Figure and Image Generation Guide

This book uses two kinds of visuals, and this appendix explains how to work with both.

E.1 1. Result figures (data plots)

The plots in Chapter 5 are real, code-generated figures. They are produced from the small teaching tables in data/example/, so you can reproduce every one without running the heavy pipeline.

⬇ make_figures.R ⬇ make_figures.py

# From the book root. Figures are written to images/figures/ (Python)
# or visualization/figures/ (R).
python scripts/make_figures.py
Rscript  scripts/make_figures.R

To make publication figures from your own data, point the scripts at your Phase 4 output tables instead of data/example/:

python scripts/make_figures.py  my_results/  my_figures/
Rscript  scripts/make_figures.R my_results/  my_figures/

Figure file	Shows	Input table
fig-checkv-quality.png	CheckV quality tiers	checkv_quality_summary.tsv
fig-contig-length.png	viral contig lengths	checkv_quality_summary.tsv
fig-top-abundance.png	mean abundance per vOTU (TPM)	votu_abundance.tsv
fig-abundance-heatmap.png	vOTU × sample abundance heatmap	votu_abundance.tsv
fig-taxonomy.png	vOTUs by family	taxonomy.tsv
fig-function.png	COG functional categories	functional_summary.tsv
fig-host.png	predicted host phyla	host_prediction.tsv
fig-alpha-diversity.png	observed richness per sample	votu_abundance.tsv

E.2 2. Concept infographics (AI-generated)

Each chapter opens or closes with a concept infographic. These ship as branded placeholder images so the book renders cleanly. To finalize one:

1. Open the chapter’s collapsible “🎨 Generate this figure” note and copy its prompt.
2. Generate the image in your preferred tool (for example an image model or a vector editor).
3. Save it over the placeholder at the same path and filename listed below. No other edits are needed — the book already references it.

Tip

Keep every concept image at 16:9, on a white background, in the Codanics palette (teal #008b8b, navy #05043b), as a clean flat vector infographic with readable labels. Consistency across chapters is what makes the book look designed rather than assembled.

Chapter	Image file	Concept
1. Fundamentals	images/ch01-viromics-ecosystem.png	viruses within a microbial ecosystem feeding a bioinformatics pipeline
2. Experimental design	images/ch02-experimental-design.png	from research question to sequencing design
3. Linux setup	images/ch03-workstation-setup.png	a reproducible conda + database workstation
4. Complete pipeline	images/ch04-pipeline-overview.png	the full assembly-based pipeline, FASTQ to report
5. Visualization	images/ch05-figure-panels.png	a multi-panel publication figure
6. Mini project	images/ch06-wastewater-miniproject.png	mining viruses from a public metagenome
7. Practice	images/ch07-study-map.png	a skills-consolidation map of the workflow
8. Project ideas	images/ch08-project-ideas.png	six research directions in viromics

The full, ready-to-paste prompt for each image lives in that chapter’s “🎨 Generate this figure” note.

E.3 3. Diagrams (Mermaid)

Flowcharts and decision trees in this book are written as Mermaid code blocks (```{mermaid}). They render automatically in the HTML and PDF editions, so you can edit them directly in the chapter text — no image files to manage.