cell string | site string | modality string | is_primary bool | verdict string | carrying_axis int64 | carrying_axis_var_frac float64 | neg_eig_mass float64 | rho_comp float64 | p_comp float64 | p_comp_bonferroni9 float64 | partial_rho float64 | partial_p float64 | rho_coverage float64 | rho_star_uniq float64 | est_coverage_cor float64 | kw_chem2v4_p float64 | adonis_r2_estimatescore float64 | adonis_p_estimatescore float64 | adonis_r2_coverage float64 | betadisper_coverage_p float64 | betadisper_estimatescore_p float64 | tpm_top2000_sig_overlap int64 | psi_host_overlap_genes int64 | psi_host_overlap_events int64 | excl_rho_comp float64 | excl_partial_rho float64 | excl_n_events_dropped int64 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Ome_PSI | Ome | PSI | true | composition_axis | 1 | 0.239255 | 0 | -0.697442 | 0.000018 | 0.000166 | -0.632966 | 0.000395 | -0.226366 | 0.174638 | 0.135507 | 0.00051 | 0.051061 | 0.0401 | 0.050316 | 0.0776 | 0.5118 | null | 4 | 4 | -0.697442 | -0.632966 | 4 |
Ome_TPM | Ome | TPM | false | composition_axis | 2 | 0.14425 | 0 | -0.759288 | 0.000001 | 0.00001 | -0.758129 | 0.000005 | -0.424157 | -0.114127 | 0.135507 | 0.000043 | 0.070833 | 0.0152 | 0.030537 | 0.2469 | 0.6282 | 43 | null | null | null | null | null |
Asc_PSI | Asc | PSI | true | composition_axis | 1 | 0.172002 | 0 | -0.841157 | 0 | 0 | -0.899036 | 0 | -0.07851 | 0.02158 | -0.218803 | 0.000968 | 0.112837 | 0.0001 | 0.040225 | 0.8712 | 0.6438 | null | 5 | 7 | -0.841157 | -0.899036 | 7 |
Asc_TPM | Asc | TPM | false | composition_axis | 1 | 0.287134 | 0 | -0.958621 | 0 | 0 | -0.948615 | 0 | 0.253151 | 0.135929 | -0.218803 | 0.172625 | 0.219686 | 0.0001 | 0.041465 | 0.6807 | 0.0017 | 169 | null | null | null | null | null |
Per_PSI | Per | PSI | true | composition_axis | 1 | 0.15013 | 0 | -0.734372 | 0.000004 | 0.000035 | -0.699559 | 0.000049 | -0.224254 | 0.182202 | -0.041908 | 0.000042 | 0.073076 | 0.0002 | 0.036497 | 0.7334 | 0.3506 | null | 3 | 3 | -0.734372 | -0.699559 | 3 |
Per_TPM | Per | TPM | false | composition_axis | 2 | 0.136819 | 0 | 0.78198 | 0 | 0.000003 | 0.707298 | 0.000037 | -0.028533 | -0.096774 | -0.041908 | 0.012014 | 0.118785 | 0.0003 | 0.037296 | 0.2367 | 0.9684 | 61 | null | null | null | null | null |
within-site-subtypes-composition-v1
Within-site (Ome/Asc/Per, PDS, n=30/site) continuous-axis-vs-composition test. RESULT (confirmatory, prereg ec64515 + Amendment 1 72da6ff): all 3 PRIMARY PSI cells + all 3 TPM cells = composition_axis. The dominant continuous axis of within-site splicing (PSI) and expression (TPM) variation is a tumor-composition (ESTIMATEScore) gradient: |rho| 0.70-0.84 (PSI), survives partial control for coverage+depth+chemistry, beats coverage (est_cov_cor 0.04-0.22, not collinear), adonis R2_comp>=R2_cov, betadisper clean, and SURVIVES exclusion of the 3-5 ESTIMATE-282-hosted events (non-circular). Explains the parent's exploratory Per/Asc cross-modal concordance.
Dataset Info
- Rows: 6
- Columns: 28
Columns
| Column | Type | Description |
|---|---|---|
| cell | Value('string') | site_modality identifier |
| site | Value('string') | No description provided |
| modality | Value('string') | No description provided |
| is_primary | Value('bool') | True for the 3 PSI cells (least circular; PSI never contains ESTIMATE gene expression) |
| verdict | Value('string') | composition_axis / technical_depth_axis / no_dominant_axis / ambiguous_collinear (locked rule) |
| carrying_axis | Value('int64') | which of the top-3 PCoA axes carries composition (argmax |
| carrying_axis_var_frac | Value('float64') | that axis's eigenvalue fraction (sum |
| neg_eig_mass | Value('float64') | No description provided |
| rho_comp | Value('float64') | Spearman rho(composition axis, ESTIMATEScore) — the primary effect |
| p_comp | Value('float64') | No description provided |
| p_comp_bonferroni9 | Value('float64') | p_comp x 9 (3 axes x 3 scores Bonferroni; sig < 0.05) |
| partial_rho | Value('float64') | partial Spearman rho(axis, ESTIMATEScore |
| partial_p | Value('float64') | No description provided |
| rho_coverage | Value('float64') | rho(axis, psi_median_coverage) — the technical rival |
| rho_star_uniq | Value('float64') | No description provided |
| est_coverage_cor | Value('float64') | Spearman cor(ESTIMATEScore, coverage); |
| kw_chem2v4_p | Value('float64') | No description provided |
| adonis_r2_estimatescore | Value('float64') | vegan::adonis2 marginal R2 for ESTIMATEScore (by=margin) |
| adonis_p_estimatescore | Value('float64') | No description provided |
| adonis_r2_coverage | Value('float64') | vegan::adonis2 marginal R2 for coverage (rival) |
| betadisper_coverage_p | Value('float64') | betadisper permutest p over coverage tertiles; <0.05 caveats the adonis location term |
| betadisper_estimatescore_p | Value('float64') | No description provided |
| tpm_top2000_sig_overlap | Value('int64') | TPM cells: |
| psi_host_overlap_genes | Value('int64') | PSI cells: |
| psi_host_overlap_events | Value('int64') | No description provided |
| excl_rho_comp | Value('float64') | PSI cells: rho_comp after excluding ESTIMATE-282-hosted events (Amendment 1.2 sensitivity) |
| excl_partial_rho | Value('float64') | No description provided |
| excl_n_events_dropped | Value('int64') | No description provided |
Generation Parameters
{
"script_name": "23_composition_association.py (+ 20-22,24,25)",
"model": "N/A \u2014 ESTIMATE (ssGSEA) + PCoA + partial Spearman + vegan::adonis2",
"description": "Within-site (Ome/Asc/Per, PDS, n=30/site) continuous-axis-vs-composition test. RESULT (confirmatory, prereg ec64515 + Amendment 1 72da6ff): all 3 PRIMARY PSI cells + all 3 TPM cells = composition_axis. The dominant continuous axis of within-site splicing (PSI) and expression (TPM) variation is a tumor-composition (ESTIMATEScore) gradient: |rho| 0.70-0.84 (PSI), survives partial control for coverage+depth+chemistry, beats coverage (est_cov_cor 0.04-0.22, not collinear), adonis R2_comp>=R2_cov, betadisper clean, and SURVIVES exclusion of the 3-5 ESTIMATE-282-hosted events (non-circular). Explains the parent's exploratory Per/Asc cross-modal concordance.",
"experiment_name": "within-site-subtypes",
"experiment_id": "within-site-subtypes",
"artifact_type": "analysis_result",
"visualizer_type": "table",
"cluster": "local",
"artifact_status": "final",
"canary": false,
"hyperparameters": {
"estimate_platform": "illumina (relative ESTIMATEScore, no absolute purity)",
"ensg_to_symbol": "org.Hs.eg.db",
"pcoa": "classical MDS top-3 (sum|lambda| denom)",
"association": "Spearman + partial (| coverage,star_uniq,chem2v4)",
"adonis": "vegan::adonis2 by=margin 9999 perm + betadisper",
"seed": 20260713,
"bonferroni": "3 axes x 3 scores = 9",
"rho_floor": 0.5,
"collinearity_downgrade": "|cor(EST,cov)|>=0.6"
},
"input_datasets": []
}
Usage
from datasets import load_dataset
dataset = load_dataset("depinwang/within-site-subtypes-composition-v1", split="train")
print(f"Loaded {len(dataset)} rows")
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