STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
GeneNMF vs gghighlight
A side-by-side editorial comparison of GeneNMF and gghighlight — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-package
GeneNMF vs gghighlight: at a glance
What is GeneNMF?
GeneNMF rebuilt how it derives meta-programs, changing every result it had produced.
GeneNMF applies non-negative matrix factorization to single-cell expression data to find gene programs, then consolidates programs recurring across samples into meta-programs. Version 0.6.0 replaced the consolidation method: instead of reducing each program to a gene set and taking a consensus, it retains full gene weight vectors and compares them by cosine similarity. Later releases have built reporting and control around that core — a metaprogram composition matrix showing which samples contributed, custom signature databases for enrichment testing, and the ability to drop meta-programs from results.
What is gghighlight?
A single-purpose ggplot2 extension that has spent six years tracking ggplot2 instead of growing.
gghighlight adds one verb to ggplot2: highlight the series matching a predicate and grey out the rest, with unhighlighted_params controlling how the shadowed layer renders and calculate_per_facet deciding whether the predicate evaluates within facets. The API settled at 0.2.0; the 0.5.0 release supports ggplot2 v4.0 including its ink and paper theme elements, and finally deletes gghighlight_point() and gghighlight_line().
GeneNMF vs gghighlight: editorial side-by-side
GeneNMF
0.0ANALYTICS
GeneNMF rebuilt how it derives meta-programs, changing every result it had produced.
◆ Current state
GeneNMF applies non-negative matrix factorization to single-cell expression data to find gene programs, then consolidates programs recurring across samples into meta-programs. Version 0.6.0 replaced the consolidation method: instead of reducing each program to a gene set and taking a consensus, it retains full gene weight vectors and compares them by cosine similarity. Later releases have built reporting and control around that core — a metaprogram composition matrix showing which samples contributed, custom signature databases for enrichment testing, and the ability to drop meta-programs from results.
◆ Where it's heading
The package is moving from producing meta-programs to letting users interrogate and constrain how they were formed. Composition matrices, the drop function and downsampled similarity heatmaps all serve inspection rather than derivation. The parameters added alongside the 0.6.0 rewrite — specificity weighting, cumulative weight thresholds, confidence defined as the fraction of programs containing a gene — turn what were fixed internal choices into stated, tunable ones.
◆ Prediction
Recent releases have been fixes and compatibility work rather than method changes, so the core approach appears settled. The dependency on an RcppML version not on CRAN is the loose end most likely to force the next release.
gghighlight
0.0ANALYTICS
A single-purpose ggplot2 extension that has spent six years tracking ggplot2 instead of growing.
◆ Current state
gghighlight adds one verb to ggplot2: highlight the series matching a predicate and grey out the rest, with unhighlighted_params controlling how the shadowed layer renders and calculate_per_facet deciding whether the predicate evaluates within facets. The API settled at 0.2.0; the 0.5.0 release supports ggplot2 v4.0 including its ink and paper theme elements, and finally deletes gghighlight_point() and gghighlight_line().
◆ Where it's heading
Two threads run through the history. One is a slow deprecation, from soft-deprecating the geom-specific functions at 0.1.0, to defunct at 0.3.0, to removed at 0.5.0 — a five-year removal cycle. The other is compatibility work: purrr 1.0.0, dplyr's across() deprecation, ggplot2 3.4.0, then 4.0. Genuine feature additions are rare and small, with line_label_type at 0.4.0 the last one. Note that 0.3.2's notes restate 0.3.1's n() item, so adjacent tags here overlap rather than each describing distinct work.
◆ Prediction
The next release most likely absorbs further ggplot2 4.x changes, given that is what triggered the last three. Nothing in the entries points to a new highlighting capability.
Alternatives to GeneNMF and gghighlight
Other Analytics products tracked by Sparkpulse, ranked by recent ship velocity. Each card links to a full editorial trajectory and lets you pivot into a head-to-head comparison with either GeneNMF or gghighlight.
ggtrace
A debugger for ggplot2's internals, hardening its grip as the internals it traces keep moving.
kde1d
A univariate density estimator that added zero-inflated data and reopened its C++ API to do it.
svines
Stationary vine copulas for time series, released in lockstep with the rest of Nagler's vine stack.
rtrek
A Star Trek data package that became a Memory Alpha web client and has been patching scrapers ever since.
eiaapi
A thin EIA energy-data client whose whole story is making bulk queries survive the API's limits.
See all GeneNMF alternatives → · See all gghighlight alternatives →
Recent activity from GeneNMF and gghighlight
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 11mo agoGeneNMFSingle-sample runs fixed; gene weight definition refined
- 1y agogghighlightggplot2 v4.0 support; geom-specific functions removed
- 1y agoGeneNMFMetaprogram composition exposed and custom signature DBs supported
- 1y agoGeneNMFSimilarity heatmap downsampling and meta-program removal
- 2y agoGeneNMFMeta-programs rebuilt on gene weight vectors and cosine similarity ⚡
- 2y agoGeneNMFFirst stable release published to CRAN
- 2y agogghighlightTest expectations updated for upcoming ggplot2
- 3y agogghighlightline_label_type adds geomtextpath and second-axis labelling
- 4y agogghighlightDeprecated dplyr::across() usage removed
- 5y agogghighlightExplicit NULL in unhighlighted_params preserved; aesthetic name clash fixed
- 5y agogghighlightDiscrete-scale labels and n() predicates
Frequently asked questions
What is the difference between GeneNMF and gghighlight?
Both compete on the same themes — r-package — within Analytics. GeneNMF and gghighlight are shipping at a similar cadence (velocity 0.0 vs 0.0, both within Sparkpulse's "active" band). See the at-a-glance table above for a side-by-side breakdown of velocity, recent sparks, and editorial themes.
Is GeneNMF better than gghighlight?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. GeneNMF and gghighlight are shipping at a similar cadence (velocity 0.0 vs 0.0, both within Sparkpulse's "active" band). For your specific use case, the alternatives sections above list other Analytics products to evaluate alongside.
What are the best alternatives to GeneNMF?
Top GeneNMF alternatives in Analytics are ranked by recent ship velocity. Browse the "GeneNMF alternatives" section above for the current picks, or visit /alternatives/genenmf for the full list with editorial commentary on each.
What are the best alternatives to gghighlight?
Top gghighlight alternatives in Analytics are ranked by recent ship velocity. Browse the "gghighlight alternatives" section above for the current picks, or visit /alternatives/gghighlight for the full list with editorial commentary on each.