Analysis mode: Quick (automatic composition + stats)#

Audience: everyone (wet lab + computational)
Time: 10–20 minutes
What you’ll learn:

  • What Quick mode summarizes (and what it deliberately does not)

  • How Dynamic vs Manual page selection works

  • How to interpret the two Quick sections: Composition and Statistics

  • Common failure modes (“nothing shows up”, “wrong page”, “missing fields”)

Prerequisites:

  • A dataset loaded

  • At least one highlight page (Quick can follow the active page automatically)

What Quick mode is for (and what it is not)#

Quick mode is the “sanity check / first glance” analysis:

  • Composition: “What labels make up these cells?” (categorical obs)

  • Statistics: “What are typical QC/score values here?” (continuous obs)

Quick mode is intentionally:

  • fast (minimal configuration, no “Run” button),

  • robust (uses approximate statistics for very large pages),

  • obs-focused (cell metadata), not gene-level hypothesis testing.

Quick mode is not for:

Inputs and scope (what cells does it summarize?)#

Quick mode summarizes highlight pages.

Dynamic mode (default): “follow the active page”#

By default, Quick uses Dynamic mode:

  • it always summarizes the currently active highlight page,

  • switching pages in Highlighted Cells updates Quick automatically.

Manual mode: “combine pages intentionally”#

Quick also supports manual selection:

  • you choose one or more pages,

  • Quick summarizes the union of those pages.

Note

Quick mode summarizes across the selected pages as one combined set.

If you want side-by-side per-page comparisons with statistical tests, use Analysis mode: Detailed (variable + plots + statistical tests).

Filtering note (visibility vs membership)#

Quick uses page membership (stored cell indices), not canvas visibility. If you expected filters to affect analysis, see Analysis mental model (Pages, Variables, Scope).

Outputs (what you should see)#

Quick mode renders two sections:

1) Composition (categorical obs)#

For each selected composition field:

  • Quick reports the top 5 categories by count across the selected pages.

  • It renders a stacked bar where segment widths are percent of cells in those top categories.

  • It prints the top 3 categories as short labels for quick scanning.

Interpretation notes:

  • The bar shows only the top categories; the long tail is not shown.

  • Missing values may appear as (missing) when present.

2) Statistics (continuous obs)#

For each selected statistics field, Quick reports:

  • Mean

  • Median

  • Std

For very large selections, median/quantiles may be approximate (sampling-based), but the goal is to stay fast and stable.

Fast path (wet lab / non-technical)#

Goal: “Tell me what this group of cells looks like in 2 minutes.”

  1. Create or select a highlight page

    • Go to Highlighted Cells.

    • If needed, add a page and put a selection into it.

  2. Open Analysis → Quick

    • You should immediately see a header like “<PageName>: X cells”.

  3. In Composition, choose fields you care about

    • Common picks: cell_type, cluster, sample, batch.

  4. In Statistics, choose QC fields

    • Common picks: n_counts, n_genes, pct_mito, or any score field.

  5. Interpret

    • If composition looks wrong: you may be on the wrong page.

    • If statistics look extreme: you may have selected low-quality cells or a biased subset.

What success looks like:

  • the page name matches what you intended,

  • the cell count is plausible,

  • composition and QC metrics match your expectations.

Practical path (computational users)#

Quick is aggregated, not per-page#

Quick does not show a per-page breakdown. It computes summaries over the combined selected cells.

If you need:

  • per-page distributions,

  • plot customization,

  • statistical tests,

use Analysis mode: Detailed (variable + plots + statistical tests).

“Effective n” can differ by field#

  • Composition counts exclude missing values.

  • Statistics exclude non-finite values (NaN/Inf).

So a page with 50,000 cells may effectively contribute fewer values for a field with missingness.

Edge cases and pitfalls#

  • No pages exist → Quick has nothing to summarize. Create a highlight page first.

  • Empty page (0 cells) → header shows 0 cells; sections are empty.

  • No categorical obs fields → Composition has nothing to choose.

  • No continuous obs fields → Statistics has nothing to choose.

  • Huge number of categories → only top categories are shown; use Detailed + Bar Plot for full distribution.

  • Very small pages (< 20–50 cells) → mean/std are unstable; interpret cautiously.

Troubleshooting (Quick mode)#

Symptom: “Quick is blank / says there are no pages”#

Likely causes:

  • no highlight pages exist yet.

How to confirm:

  • open Highlighted Cells and check if page tabs exist.

Fix:

Symptom: “Quick shows the wrong group”#

Likely causes:

  • Quick is in Dynamic mode and a different page is active than you think.

How to confirm:

  • open Quick’s Page Selection collapsible at the bottom and check the mode indicator.

Fix:

  • switch to Manual mode and explicitly pick the page(s) to summarize.

Symptom: “Composition/Statistics says ‘No … fields selected’”#

Fix:

  • use the “Choose … fields” dropdown and select fields.

Screenshot placeholder (you will replace later)#

Placeholder screenshot for Quick mode showing composition and statistics.

Quick mode gives a fast sanity-check view of page composition and QC/statistics without configuring a full plot.#

Next steps#