Exporting analysis results#

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

  • What analysis artifacts can be exported (tables, plots)

  • What exports are “stable artifacts” vs ephemeral UI state

  • How analysis exports relate to Figure Export and Sessions

Prerequisites:

  • A dataset loaded

  • At least one analysis result generated (any mode)

What “export” means in Analysis (and what it does not mean)#

Cellucid’s Analysis UI supports exporting two kinds of artifacts:

  1. Plots (PNG / SVG)
    A snapshot of what you see in the analysis result plot at the time you export.

  2. Tables (CSV)
    A machine-readable artifact you can load into R/Python/Excel.

Exports are downloads from your browser:

  • files typically land in your OS/browser “Downloads” location,

  • filenames are generated by the app (you can rename them after download).

Exports are not:

Important

In the current build, most analysis CSVs do not embed full provenance (dataset id, page names, thresholds, etc.).

If you need paper-grade reproducibility, export the CSV and save a session (and/or keep a lab notebook record of settings).

Fast path (save something you can share)#

Goal: export one plot for reporting and one table for re-analysis.

  1. Run the analysis you care about (Detailed / Correlation / DE / Gene Signature / Marker Genes)

  2. Open the expanded view

    • click the plot preview, or click ⤢ Expand (mode-dependent)

  3. In the expanded view, use the export buttons

    • PNG / SVG for plots

    • CSV for tables

  4. Immediately rename the downloaded files (recommended)

    • include dataset name, page names, method, and date, e.g.
      pbmc_demo__DE__T_cells_vs_rest__wilcox__2025-01-02.csv

Tip

For wet lab / reporting workflows:

  • export PNG for slides and lab meeting decks,

  • export SVG only if you need vector editing (Illustrator/Inkscape),

  • export CSV for anything you might re-plot or statistically analyze later.

Where export controls live (UI map)#

Exports are attached to the analysis result view, not to the overall app.

Typical patterns:

  • Detailed Analysis: click the plot preview to open an expanded modal; export from there.

  • DE / Gene Signature / Marker Genes: use ⤢ Expand (or click the preview) to open the expanded modal; export from there.

  • Quick: no formal “export” controls (use it as a summary; screenshot if needed).

In the expanded view you should see an Export: row with buttons:

  • PNG

  • SVG

  • CSV

If you don’t see export controls, it usually means:

  • no result has been computed yet, or

  • the mode does not support export, or

  • you are not in the expanded modal view.

What each mode exports (exact CSV schemas)#

This section is deliberately explicit so you can build downstream tooling.

Detailed Analysis#

  • Plot export: PNG / SVG of the currently selected plot type and options.

  • CSV export: per-cell values for the selected variable.

    • Filename: detailed-analysis-data.csv

    • Columns:

      • page: the page name

      • cell_index: the dataset row index for that value (0-based)

      • <variable>: the exported numeric value

Note

This CSV can be large: it is one row per cell (per selected page). For very large pages, consider exporting summary results instead of per-cell values.

Correlation#

  • Plot export: PNG / SVG of the correlation scatter plot as rendered.

  • CSV export: one row per page with correlation statistics.

    • Filename: correlation_results.csv

    • Columns:

      • page

      • method (pearson or spearman)

      • x_type, x_key (what X is)

      • y_type, y_key (what Y is)

      • r, r_squared

      • p_value

      • n (paired values used)

Note

The exported plot may show a downsampled subset of points for rendering performance. The exported CSV statistics (r, p_value, n) are computed on the full paired data.

Differential Expression (DE)#

  • Plot export: PNG / SVG of the volcano plot with current thresholds/options.

  • CSV export: one row per gene with DE statistics.

    • Filename: differential_expression.csv

    • Columns:

      • gene

      • meanA, meanB

      • log2FoldChange

      • pValue

      • adjustedPValue (BH/FDR)

Important

The DE CSV does not include the compared page names. Record Page A vs Page B yourself (file rename, notes, or session).

Gene Signature#

  • Plot export: PNG / SVG of the signature score plot.

  • CSV export: signature scores as a long table.

    • Filename: gene_signature_scores.csv

    • Columns:

      • page

      • score

Warning

This CSV does not include cell indices. If you need to map scores back to specific cells, export a session and recompute in Python where you can attach indices/obs.

Marker Genes (Genes Panel)#

Marker Genes exports depend on what you’re looking at:

  • Heatmap-style exports (Clustered / Custom Genes)

    • Filename: marker_genes_heatmap.csv

    • Shape: wide matrix

    • Columns:

      • gene (first column)

      • one column per group (column headers are group names)

    • Values: per-group mean expression for each gene, using the current heatmap transform (e.g., z-score/log1p/none).

  • Ranked markers exports (Ranked Genes)

    • Filename: marker_genes_ranked.csv

    • Columns:

      • group, gene, rank

      • log2FoldChange, pValue, adjustedPValue

      • meanInGroup, meanOutGroup

      • percentInGroup, percentOutGroup

Note

If your group labels contain commas, marker_genes_heatmap.csv may be harder to parse in strict CSV readers. If possible, avoid commas in categorical labels used for grouping.

Reproducibility notes (what to record)#

If you need to reproduce an export later, record:

  • dataset identity (dataset name/id, export folder version)

  • active view/snapshot (if relevant to your workflow)

  • selected pages (names + sizes)

  • selected variables (obs key / gene id + how genes are resolved)

  • method settings (Pearson vs Spearman; Wilcoxon vs t-test; signature normalization; performance settings)

  • thresholds and plot options (DE volcano thresholds; log axes; labeling settings)

Recommended workflow:

  1. Save a session: Session Saving, Restoring, and Sharing

  2. Export CSV(s)

  3. Export plot(s) (PNG for sharing; SVG for editing)

  4. Rename files with the important settings

Troubleshooting exports#

Symptom: “Nothing downloads when I click PNG/SVG/CSV”#

Likely causes:

  • browser blocked automatic downloads,

  • you are not in the expanded view (no export toolbar),

  • the analysis did not produce a result yet.

Fix:

  • re-run the analysis and open the expanded view,

  • allow downloads for the site,

  • try a different browser if corporate policies block downloads.

Symptom: “The CSV is empty”#

Likely causes:

  • the analysis returned no valid values (missing data, tiny pages, all-NaN),

  • gene expression is unavailable (expression-based modes),

  • the mode exports a different artifact than you expected (e.g., correlation exports summary statistics, not point-level data).

Fix:

  • confirm you have non-empty pages,

  • confirm gene expression is available,

  • verify the mode’s expected CSV schema above,

  • see Troubleshooting (analysis) for analysis-wide diagnosis.

Screenshot placeholders (you will replace later)#

Placeholder screenshot for analysis export controls.

Analysis results can be exported as tables and/or plots (depending on mode); export tables when you need downstream computation.#

Placeholder screenshot for an exported analysis artifact example.

Open exported CSV/PNG/SVG artifacts outside the app to confirm they are shareable and self-contained.#

Next steps#