STACAS
Single-cell batch correction that learned to use cell labels, then spent three releases chasing Seurat.
Comparison · Analytics
GeneNMF vs ggmapinset
A side-by-side editorial comparison of GeneNMF and ggmapinset — release velocity, themes, recent moves, and the top alternatives to consider.
GeneNMF vs ggmapinset: 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 ggmapinset?
A ggplot2 inset-map extension that is now infrastructure for other packages
ggmapinset adds magnified inset panels to ggplot2 sf maps, handling the coordinate transformation, the inset frame and the sf-related stat layers that have to follow it. The 0.5.0 release is aimed less at end users than at extension authors: coerce_centre() is a new extension point required by sibling package ggautomap, and the inset parameter drops NA in favour of waiver() as its default. It comes from cidm-ph, alongside nswgeo.
GeneNMF vs ggmapinset: 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.
ggmapinset
0.0ANALYTICS
A ggplot2 inset-map extension that is now infrastructure for other packages
◆ Current state
ggmapinset adds magnified inset panels to ggplot2 sf maps, handling the coordinate transformation, the inset frame and the sf-related stat layers that have to follow it. The 0.5.0 release is aimed less at end users than at extension authors: coerce_centre() is a new extension point required by sibling package ggautomap, and the inset parameter drops NA in favour of waiver() as its default. It comes from cidm-ph, alongside nswgeo.
◆ Where it's heading
The package has moved steadily from feature to foundation. 0.3.0 replaced confusing parameter names and rebuilt everything on stat_sf_inset() so coordinate limits stayed correct, then exposed transform_to_inset() explicitly for extension developers. 0.4.0 generalised inset shapes beyond circles to rectangles and arbitrary sf geometries. 0.5.0 continues in that direction, changing defaults in ways that require downstream extensions to adapt — the cost of being depended upon.
◆ Prediction
Expect further extension points driven by what ggautomap and the other cidm-ph mapping packages need, with the user-facing inset API staying largely settled after the shape generalisation.
Alternatives to GeneNMF and ggmapinset
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 ggmapinset.
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 ggmapinset alternatives →
Recent activity from GeneNMF and ggmapinset
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 4mo agoggmapinsetNew extension point for ggautomap; waiver() replaces NA
- 11mo agoGeneNMFSingle-sample runs fixed; gene weight definition refined
- 1y agoGeneNMFMetaprogram composition exposed and custom signature DBs supported
- 1y agoggmapinsetRectangular and arbitrary sf inset shapes
- 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
- 3y agoggmapinsetRebuilt on stat_sf_inset() with corrected coordinate limits
Frequently asked questions
What is the difference between GeneNMF and ggmapinset?
They serve adjacent needs but don't currently overlap on shipped themes. GeneNMF and ggmapinset 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 ggmapinset?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. GeneNMF and ggmapinset 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 ggmapinset?
Top ggmapinset alternatives in Analytics are ranked by recent ship velocity. Browse the "ggmapinset alternatives" section above for the current picks, or visit /alternatives/ggmapinset for the full list with editorial commentary on each.