Run the analysis

Your task

Run these commands from the project root to validate the inputs and generate descriptive summaries and figures.

Rscript scripts/R/01-check-inputs.R
Rscript scripts/R/02-analyse-example.R

The first command should report Input checks passed. The second saves the outputs listed below.

Output	File under results/
Counts, richness, Shannon diversity	tables/alpha-diversity.tsv
Full feature proportions	tables/relative-abundance.tsv
Plotting categories	tables/composition-display.tsv
Group summaries	tables/group-summary.tsv
Composition	figures/composition.png
Diversity	figures/shannon-diversity.png
Count totals versus diversity	figures/depth-diversity.png

Use your own data

Rscript scripts/R/02-analyse-example.R data/my-study results/my-study

Prepare the three input tables as described in Meet the data. Keep the synthetic example intact. This command validates your study inputs before analysis and saves the outputs separately. The script uses your identifiers and group labels.

Full data for calculations; simplified data for display. The composition plot shows the top eight features by mean sample proportion and combines the rest as Other. Diversity uses every feature.

Check before continuing

Check sample counts, proportions summing to one, count totals, and labels. These are descriptive results; no significance tests are performed. For very large studies, review plot readability and computing resources.

View the results in the guide

quarto render
quarto preview

Rendering displays the results; it does not run the analysis scripts.

Continue to 5. Verify and explain.