Multivariate analysis rework, dendrogram/sample-correlation QC tools, and cleanup - #8

Merged

robertsamples merged 18 commits into

mainfrom

todo-cleanup

Jun 30, 2026

Commits on Jun 29, 2026

Reword and reprioritize main.py TODO list
robertsamples
committed
Add search-tab run-check, clean up main.py's dead imports

robertsamples
and
claude
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Add GroupSetModel.move() for groupset reordering (model layer only)

robertsamples
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claude
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Clarify stale PCA TODO note

robertsamples
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claude
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Merge remote-tracking branch 'origin/main' into todo-cleanup
robertsamples
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Merge branch 'main' into todo-cleanup
robertsamples
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Add Qt-free multivariate ordination backend (PCA/NMDS/PLS-DA)

robertsamples
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claude
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Rework the mislabeled "PCA" plot into a multivariate ordination tab

robertsamples
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claude
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Fix ordination feedback: scaling, axis limits, NMDS %explained, bar styling

robertsamples
and
claude
committed
Add dendrogram purity coloring: technical/biological replicate QC view

robertsamples
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claude
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Dendrogram: polyphyletic branches in red, add a no-coloring option

robertsamples
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claude
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Replace treemap/upset PNG round-trip with real canvas plots

robertsamples
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claude
committed
Dendrogram: bridge-only red coloring; move bootstrap/collapse checkboxes to per-plot bars

robertsamples
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claude
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Fix dendrogram coloring: red = proven non-monophyly (label-set overlap)

robertsamples
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claude
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Dendrogram: add Use Sample/Group Names labels; fix AU/BP label scaling

robertsamples
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claude
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Docs: update mkdocs guide for ordination rework and dendrogram improvements

robertsamples
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claude
committed

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Multivariate analysis rework, dendrogram/sample-correlation QC tools, and cleanup - #8

Multivariate analysis rework, dendrogram/sample-correlation QC tools, and cleanup#8
robertsamples merged 18 commits into
mainfrom
todo-cleanup

Commits on Jun 29, 2026

Reword and reprioritize main.py TODO list

Add search-tab run-check, clean up main.py's dead imports

Add GroupSetModel.move() for groupset reordering (model layer only)

Clarify stale PCA TODO note

Merge remote-tracking branch 'origin/main' into todo-cleanup

Merge branch 'main' into todo-cleanup

Add Qt-free multivariate ordination backend (PCA/NMDS/PLS-DA)

Rework the mislabeled "PCA" plot into a multivariate ordination tab

Fix ordination feedback: scaling, axis limits, NMDS %explained, bar styling

Add dendrogram purity coloring: technical/biological replicate QC view

Dendrogram: polyphyletic branches in red, add a no-coloring option

Replace treemap/upset PNG round-trip with real canvas plots

Dendrogram: bridge-only red coloring; move bootstrap/collapse checkboxes to per-plot bars

Fix dendrogram coloring: red = proven non-monophyly (label-set overlap)

Dendrogram: add Use Sample/Group Names labels; fix AU/BP label scaling

Docs: update mkdocs guide for ordination rework and dendrogram improvements

Commits on Jun 30, 2026

correlation matrix control improvements

Update tests.yml