OncoPath

The smallest sub-module — four analyses: waterfall, swimmer plot, diagnostic-test meta-analysis, and IHC heterogeneity. The staging and molecular work this page used to claim is in the umbrella.

Purpose

Provide oncology-specific plots and analyses without hand-coding them. In practice, and read from source rather than from the chapter, that means treatment-response visualisation plus two analyses that have nothing to do with staging at all.

Data used

Best-response percent change and time-on-treatment data for the response plots; paired test/reference data for the meta-analysis; multi-region IHC scores for the heterogeneity analysis.

Methods

Package OncoPath, version 1.0.1, 4 analyses, 7 vignettes.

Analysis What it is
waterfall Treatment Response Analysis
swimmerplot Swimmer Plot
diagnosticmeta Diagnostic Test Meta-Analysis for Pathology
ihcheterogeneity IHC Heterogeneity Analysis

Correction: most of what this page claimed is not here

The previous version described AJCC/UICC TNM summaries, stage-migration analyses, grouped-stage comparisons, biomarker cut-point analysis and categorisation, biomarker-by-outcome tables, mutation and co-mutation matrices, oncoprint-style plots, and subgroup forest summaries. None of those is in this repository. Waterfall and swimmer plots are; the rest are in ClinicoPath jamovi Module — stagemigration (“Advanced TNM Stage Migration Analysis”), groomecompare, jjoncoplot, circos, subgroupforest, groupedforest, jforester, optimalcutpoint, categoricaladvanced.

The cut-point claim had propagated into the wiki: Biomarker Cut Points cited this module as implementing cut-point analysis, and has been corrected to point at optimalcutpoint in the umbrella and categorize in ClinicoPathDescriptives.

Two analyses nobody had written down

Both are directly relevant to work already running here, and neither appeared on this page before:

  • ihcheterogeneity — IHC Heterogeneity Analysis. HER2 Intratumoral Heterogeneity is an active project about exactly this, and Intratumoral Heterogeneity is a concept page about exactly this. Whether the project uses this analysis is not recorded anywhere. [unverified]
  • diagnosticmeta — Diagnostic Test Meta-Analysis for Pathology. Nothing in the wiki mentions the group having meta-analysis capability for diagnostic accuracy, which is a different thing from the single-study evaluation in meddecide.

Current state / open questions

Active; last commit 2026-07-16 at version 1.0.1, in step with the other five.

Documented pitfalls carried over from the chapter, with a caveat: AJCC 7 and AJCC 8 disagree on substantial numbers of cases so the edition must be stated in every table; waterfall plots should stay ordered by percent change, not by ID; data-derived biomarker cut-points overfit unless validated. The first and third of those describe umbrella functionality rather than anything in this module — only the waterfall advice applies to what is actually installed here.

  • Does HER2 Intratumoral Heterogeneity use ihcheterogeneity, and if not, why not? It is the most direct overlap between a module and a project in the whole estate. [unverified]
  • Has diagnosticmeta been used for anything? A pathology-specific diagnostic-accuracy meta-analysis tool is a publishable capability sitting unmentioned. [unverified]
  • Four analyses makes this the thinnest sub-module by a wide margin. Is it intended to grow, or is oncology work expected to run from the umbrella? [unverified]

Related: ClinicoPath jamovi Module — the umbrella, where staging, oncoprint, forest and cut-point analyses actually live. Biomarker Cut Points — the concept page whose attribution to this module was wrong and is now corrected.

Derived from: repository working tree read 2026-07-26 — DESCRIPTION, the 4 jamovi/*.a.yaml files, vignettes/, plus git ls-files/git log; and the umbrella’s analysis inventory for the correction. Earlier content derived from jamovi/oncopath.qmd.