STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
GeneNMF vs ggquiver
A side-by-side editorial comparison of GeneNMF and ggquiver — release velocity, themes, recent moves, and the top alternatives to consider.
GeneNMF vs ggquiver: 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 ggquiver?
ggquiver returned after four years to make arrows respect ggplot's own scales.
A small ggplot2 extension for quiver and vector-field plots. The 0.3.x line in late 2021 was about making arrows behave correctly outside plain Cartesian coordinates — non-Cartesian coordinate systems, ggmap backgrounds, arrow sizing and angles. Then nothing for over four years, until 0.4.0 made arrows honour scale transformations on the x and y aesthetics and exposed grid::arrow()'s appearance options.
GeneNMF vs ggquiver: 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.
ggquiver
0.0ANALYTICS
ggquiver returned after four years to make arrows respect ggplot's own scales.
◆ Current state
A small ggplot2 extension for quiver and vector-field plots. The 0.3.x line in late 2021 was about making arrows behave correctly outside plain Cartesian coordinates — non-Cartesian coordinate systems, ggmap backgrounds, arrow sizing and angles. Then nothing for over four years, until 0.4.0 made arrows honour scale transformations on the x and y aesthetics and exposed grid::arrow()'s appearance options.
◆ Where it's heading
The consistent theme across both eras is deferring to ggplot2 rather than drawing on top of it: coordinate systems first, then scale transformations, then arrow styling handed to grid. Development is episodic — years pass, then a release that closes the gap between what the geom does and what a user expects from any other layer. The changelog is entirely correctness and integration work; there is no sign of the package growing new plot types.
◆ Prediction
The entries only support a narrow read: further releases will likely keep closing ggplot2 integration gaps as they are reported, but the four-year gap means cadence is not predictable from this feed.
Alternatives to GeneNMF and ggquiver
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 ggquiver.
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.
gghighlight
A single-purpose ggplot2 extension that has spent six years tracking ggplot2 instead of growing.
rtrek
A Star Trek data package that became a Memory Alpha web client and has been patching scrapers ever since.
See all GeneNMF alternatives → · See all ggquiver alternatives →
Recent activity from GeneNMF and ggquiver
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 6mo agoggquiverArrows respect scale transformations and grid arrow styling
- 11mo agoGeneNMFSingle-sample runs fixed; gene weight definition refined
- 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
- 4y agoggquiverArrow scaling and centered-arrow angle fixes
- 4y agoggquiverFix for resized vectors via vecsize
- 4y agoggquiverNon-Cartesian coordinates and ggmap backgrounds supported
Frequently asked questions
What is the difference between GeneNMF and ggquiver?
They serve adjacent needs but don't currently overlap on shipped themes. GeneNMF and ggquiver 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 ggquiver?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. GeneNMF and ggquiver 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 ggquiver?
Top ggquiver alternatives in Analytics are ranked by recent ship velocity. Browse the "ggquiver alternatives" section above for the current picks, or visit /alternatives/ggquiver for the full list with editorial commentary on each.