OMIX L2P Multi

Run L2P over-representation analysis across several differential-expression contrasts and compare pathway signals in standardized OMIX bubble plots.

This repository is the Code Ocean deployment adapter. The portable scientific implementation, interface schema, and tests are maintained in the canonical OMIX L2P Multi module.

What it does

• selects up- and down-regulated genes for each ordered contrast;
• tests built-in L2P collections and optional custom gene sets;
• exports all pathways meeting the configured hit and significance criteria;
• creates combined, cross-collection, and collection-specific bubble plots; and
• keeps comparison order consistent from the input controls through the plots.

Threshold selection is the default: nominal p-value at most 0.05 and absolute linear fold change at least 1.2. Rank selection remains available as an advanced compatibility method. Shared plots show the top 20 pathways by adjusted p-value by default; the CSV is not truncated to 20 rows.

Input

Provide one wide DEG table in CSV, TSV, TXT, or RDS format. It must contain:

• one gene-symbol column;
• one signed ranking statistic per comparison;
• one p-value or adjusted-p-value column per comparison; and
• one linear- or log-fold-change column per comparison.

For example:

GeneName,B-A_tstat,B-A_pval,B-A_FC,C-A_tstat,C-A_pval,C-A_FC
Gene1,3.2,0.001,2.1,-2.4,0.010,-1.8

Enter comparison IDs in the exact order you want analyzed and plotted. The adapter does not reinterpret or reverse contrasts. C-B therefore requires C-B_* columns; it will not silently substitute B-C_* columns.

When every comparison uses the same alternative naming convention, set the advanced suffix controls instead of listing every column. For example, t_statistic_suffix=_statistic, significance_suffix=_adjpval, and fold_change_suffix=_logFC resolve the ordered columns for every comparison. Exact comma-separated column lists remain available for irregular tables and take precedence over the suffix settings.

The optional custom pathway input may be an L2P-compatible RDS object or a delimited table with one pathway/gene membership per row. The default columns are gene_set_name and gene_symbol.

Code Ocean quick start

1. Open the App Panel.
2. To try the attached demo, leave DEG Table blank and retain Mouse plus B-A,C-A,B-C.
3. For your data, select DEG Table, replace Comparisons, and select the correct species.
4. Leave column overrides blank when names use the comparison prefixes and configured suffixes. For a consistent alternative convention, change the three suffix controls; for irregular tables, provide one exact column per comparison in the same order.
5. Choose built-in collections such as H,REACTOME and optionally select a custom pathway file.
6. Run the capsule and inspect /results.

If DEG Table is blank, the adapter accepts only one unambiguous eligible table from the attached deg_table asset or workflow result. When several candidates exist, it stops and lists them rather than choosing one silently.

The attached mouse demo and its comparison list are the only App Panel default exceptions to the canonical portable interface. All other public and advanced controls use canonical names and defaults. Retired legacy-renderer controls and platform result paths are not shown in the App Panel.

Main controls

Control	Default	Purpose
comparisons	demo: B-A,C-A,B-C	Ordered contrast identifiers.
t_statistic_suffix	_tstat	Suffix used to derive ordered rank columns when exact overrides are blank.
significance_suffix	_pval	Suffix used to derive ordered significance columns when exact overrides are blank.
fold_change_suffix	_FC	Suffix used to derive ordered fold-change columns when exact overrides are blank.
species	demo: Mouse	Species for symbol validation and ortholog mapping.
collections_to_include	H	Comma-separated built-in pathway collections.
select_by_rank	FALSE	Use threshold selection unless explicitly enabled.
significance_threshold	0.05	Gene-list significance threshold.
fold_change_threshold	1.2	Absolute linear fold-change threshold.
number_of_significant_events	1	Comparisons in which a pathway must pass export criteria.
minimum_pathway_hit_count	5	Minimum selected-gene hits for export selection.
p_value_limit	0.05	Pathway export threshold.
pathway_bubble_top_n	20	Rows per standardized plot scope; 0 means all.
pathway_bubble_significance_statistic	padj	padj or pval for shared-plot selection and shapes.

When supplying a custom pathway database alone, clear collections_to_include. The adapter preserves that intentional blank rather than restoring H; blank file selectors remain safely omitted.

All additional supported controls remain available in the App Panel's advanced sections. See the canonical interface schema for exact types, allowed values, and semantics.

Outputs

The adapter writes stable artifacts under /results:

• l2p_multi_results.csv — all pathways meeting export criteria, ordered by requested comparison and then by ascending p-value within each comparison;
• l2p_multi_results_provenance.csv — result provenance, including requested comparison order and aligned input columns;
• L2P-Multi-Pathway-Bubble_*.png — standardized shared plots; and
• L2P-Multi-Pathway-Bubble_manifest.csv — selection, scale, and figure metadata. Comparison order is verified from provenance and rendered axes, not this manifest.

Compatibility

Older saved capsule runs may still use --deg_file, --collections, and --select_top_percentage. The adapter translates these aliases to the canonical controls and warns when they are used. New App Panel runs emit only canonical names.

The optional legacy Table, Filtered DEG, and All DEG values accepted by --deg_file are retained for saved runs but are not new App Panel controls.

Reproducibility and validation

OMIX_MODULE_SOURCE.md records the canonical commit, scientific-file hash, schema hash, runtime tag, platform translations, and release-evidence state. A successful Code Ocean computation is recorded in the validation record. Adapter commit 743acb2ebae0ca4325bf801bb8ef1f59a71ab3cb has a successful attached-demo computation and complete visible output set; its runtime digest, platform release identifier, artifact-content assertions, and remaining validation-plan cases are still pending. Follow the Code Ocean validation plan before release.

For developers

Read AGENTS.md and OMIX_MODULE_SOURCE.md before editing. Scientific changes belong in canonical OMIX and must flow one-way into code/functions/ without modification. Deployment input discovery, App Panel configuration, and /results translation belong here.

References and support

• L2P
• OMIX module contract
• NIDAP Team: NCICCBRNIDAP@mail.nih.gov