feat: in-browser dimensional reduction with KNN backend param controls#38
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Lets users re-run dimensional reduction on an imported .h5ad without an upstream pipeline. A "Recompute" button in the projection selector opens a dialog to pick a dense layers/ matrix as the vote matrix, choose an algorithm (UMAP/PaCMAP/LocalMAP) and parameters, and run the reduction in a web worker. The result is added as a new selectable projection and auto-selected. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Use DruidJS generator API to step through iterations and post progress messages from the worker. The dialog shows a 0-100% progress bar while computing instead of just a spinner. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
While status is running but no progress tick has arrived yet, the dialog shows "Building KNN graph…" with a pulse animation. Once the first progress message lands the bar replaces it. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Column means of observed values replace any NaN entries so DruidJS never sees missing data. Falls back to 0 for all-NaN columns. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Removes range sliders in favour of number inputs laid out in a 2-column grid. Both Select dropdowns get w-full so their width stays stable across selected options. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Adds a "Column mask" select left of the Algorithm select that zeros out var columns whose value is truthy before running reduction. The only current option is "moderated". App.tsx applies the mask using the varNames array (original h5ad var order) to map column indices to statement metadata. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
All layers share the same shape, so display rows×cols once next to the label rather than repeating it inside every dropdown item. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Progress bar and KNN phase text now appear to the left of the Cancel/Run buttons in the footer row, freeing up space in the main content area. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…backend controls Adds a collapsible Advanced section exposing all remaining DruidJS parameters (seed, epochs, learning rate, UMAP internals) and a KNN backend select (Annoy / HNSW) for PaCMAP and LocalMAP. All params are merged into a single Record before being sent to the worker. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Updates DruidJS to the latest add-pacmap-support branch commit (which added knn_params passthrough to PaCMAP and LocalMAP). Wires knn_params through ReducerRequest → useDruidWorker → worker, and adds ef/ ef_construction inputs to the Advanced section of the recompute dialog, shown only when the HNSW backend is selected. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Extracts types, config, and a pure `runReducer()` generator from the app into the reddwarf-ts library package, enabling the polis pipeline to run in JavaScript outside the browser (e.g. Node.js scripts). The app worker and React hook become thin shells; no consuming files needed import changes. `@saehrimnir/druidjs` added as a reddwarf-ts runtime dependency. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Pure statistical functions stay in stats.ts; DB types (VoteConnection, VoteQueryResult) and getGroupVoteMatrices move to new db.ts - Collapse analyzeLabeledGroups + calculateRepresentativeStatements into one function in representative-statements.ts; stats.ts is now DB-free - Unified AnalysisOptions covers all options incl. commentTextMap; removes two divergent options shapes across the package - App adapter updated: commentTextMap folds into options object Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
The class was never instantiated — App.tsx owns isCalculatingRepStatements state directly via useState. Removes both the package class and the app adapter's wrapper, flattening the delegation chain. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…ld listing Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Add KNN_PARAM_DEFS and defaultKnnParamsFor() mirroring the reducer param pattern. Annoy now exposes numTrees/maxPointsPerLeaf/seed; HNSW gains m and seed alongside its existing ef/ef_construction. The dialog shows whichever backend's params are active and always forwards them as knn_params. HNSW_PARAM_DEFS/defaultHnswParams() kept as deprecated aliases. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Summary
.h5adfile, a Recompute button opens a dialog to pick a vote matrix layer, choose UMAP/PaCMAP/LocalMAP and its parameters, and run the reduction in a web worker; result is added as a selectable projectionrunReducer, types, param defs) intoreddwarf-ts; also extractszeroMaskedColumns,imputeColumnMeans, and refactors the stats/DB split andAnalysisOptionsunificationKNN_PARAM_DEFS/defaultKnnParamsFor()mirroring the reducer pattern — Annoy now exposesnumTrees/maxPointsPerLeaf/seed; HNSW exposesef/ef_construction/m/seed; HNSW defaults match the voyager (Spotify) library used by pacmap-pythonTest plan
.h5adfile and open the Recompute dialog🤖 Generated with Claude Code (code and ~150 words of PR description from ~60 words of human prompts across this session)