Add themeable plots, self-describing outputs, failure reporting; markers opt-in - #8
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…ers opt-in - Themeable plots: NMFprofileR() gains `custom_theme` (a ggplot2 theme) and `factor_palette` (a colour vector), threaded into generate_rank_plots() and generate_global_plots() in place of the hardcoded theme/palette. - `umap_n_neighbors` parametrizes the sample-coefficient UMAP; the embedding now renders whenever n_samples exceeds it (was hardcoded > 15) and the neighbour count is capped at n_samples - 1 so smaller cohorts also embed. - Self-describing outputs: an optional `run_id` is stamped as a leading Run_ID column in the consolidated summary and recorded in the manifest; the whole nmf_profile is saved as one <prefix>_nmf_profile.rds bundle; and a Summaries/manifest.tsv lists every file a run produced with its type (write_output_manifest / classify_output_file). - Failed ranks are recorded in $failures (Rank + Reason) and surfaced by print(), instead of silently vanishing from the output. - emit_marker_genes now defaults to FALSE (breaking): specificity markers and their enrichment are opt-in, halving g:Profiler calls per default run. The marker_genes and enrichment$markers elements remain present (empty when off). Tests: add test-manifest (manifest helpers, no network) and test-failures (failure path via mocked fit, no network); extend the smoke test to cover run_id, the .rds bundle, the manifest, and empty $failures. Docs regenerated (S3 methods now registered via S3method()); version bumped to 0.3.0.
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Usability improvements to
NMFprofileR(). Everything is additive except one intentional default change (emit_marker_genes).Changes
custom_theme(a ggplot2 theme) andfactor_palette(a colour vector) arguments, threaded intogenerate_rank_plots()/generate_global_plots(), so figures can match a project's house style without editing the package.custom_themealso matches the argument theNMFprofileR_TCGAscripts already pass.umap_n_neighbors— parametrizes the sample-coefficient UMAP. The embedding now renders whenever the cohort has more samples than this value (previously hardcoded> 15), with the neighbour count capped atn_samples - 1so smaller cohorts also embed.run_idis stamped as a leadingRun_IDcolumn in the consolidated summary and recorded in the manifest; the wholenmf_profileresult is saved as a single<prefix>_nmf_profile.rdsbundle; andSummaries/manifest.tsvlists every file a run produced with its type.$failuresdata frame (Rank + Reason) and listed byprint(), instead of silently disappearing.emit_marker_genesnow defaults toFALSE(breaking) — specificity markers and their second enrichment pass are opt-in, halving g:Profiler calls per default run. Themarker_genes/enrichment$markerselements are still always present (empty when off).Testing
test-manifest(manifest helpers) andtest-failures(failure path via a mocked fit) run without a network.run_id, the.rdsbundle, the manifest, and empty$failures.