docs: explain how to read the molecule rank plot - #101
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The Cell recovery section rendered the molecule rank plot without any guidance on how to interpret it. Add a short paragraph covering the log-log ranking, the cell-to-background drop, the component size thresholds and the highlighting of the sample in focus. Co-authored-by: max.karlsson <max.karlsson@pixelgen.com>
Drop the axis-scale detail, the antibody example and the colour and minimum-size notes so the section stays short. Co-authored-by: max.karlsson <max.karlsson@pixelgen.com>
Co-authored-by: max.karlsson <max.karlsson@pixelgen.com>
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🟡 Changes recommended
The new explanation appears to assume sample-only plots, but the underlying reporting component can also render pool-level plots for hashed experiments, so the wording should be made accurate for both cases.
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Pull request overview
This PR updates the amplicon demux Quality metrics Quarto report to include a short explanation of how to interpret the molecule rank plot shown under Cell recovery > Number of components, and records the documentation update in the changelog.
Changes:
- Added explanatory prose describing how to interpret the molecule rank plot and its threshold lines.
- Added an Unreleased changelog entry noting the new explanation.
File summaries
| File | Description |
|---|---|
| inst/quarto/workflows/amplicon_demux/quality_metrics.qmd | Adds a paragraph explaining what the molecule rank plot shows and how to interpret it. |
| CHANGELOG.md | Notes the documentation update under Unreleased. |
Review details
- Files reviewed: 2/2 changed files
- Comments generated: 1
- Review effort level: Lite
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| The molecule rank plot below ranks the components of a sample from the most to the fewest molecules. Cells appear as | ||
| the plateau of large components to the left, and the curve drops where cells give way to background components such as | ||
| debris. A sharp drop means that cells are well separated from background, while a gradual slope means that the two are | ||
| harder to tell apart. The dashed lines mark the minimum and maximum component size thresholds, and only components | ||
| between them are kept as cells. |
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Summary
The Cell recovery section of the Quality metrics report showed the molecule rank plot without explaining how to read it. This adds a short paragraph above the plot describing what the plot ranks, what the shape of the curve means, and what the dashed lines are.
Changes
inst/quarto/workflows/amplicon_demux/quality_metrics.qmd: short description of the molecule rank plot under Cell recovery > Number of components, following the same in-report explanation style used for k-coreness, denoising and the colocalization heatmaps.CHANGELOG.md: entry under Unreleased.Testing
Documentation-only change to report prose; no code paths affected.