simlandr
Potential landscape tooling settling onto standard R generics after two rounds of renaming.
Comparison · Analytics
gghighlight vs qtl2
A side-by-side editorial comparison of gghighlight and qtl2 — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-package
gghighlight vs qtl2: at a glance
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().
What is qtl2?
The standard QTL mapping package in R opened its genome scan to user-supplied likelihood models.
qtl2 is the R toolkit for QTL mapping in experimental crosses, covering genotype probability calculation, genome scans with and without polygenic effects, permutation testing, SNP association, and the plotting that goes with them. The last year of work has pushed hard in two directions: tooling for high-throughput expression and protein QTL studies, and a generalisation of the scan engine itself so the log-likelihood being maximised can be supplied by the user. Note that the release history reached this feed out of order, so feed position is not a reliable guide to which release came first.
gghighlight vs qtl2: editorial side-by-side
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.
qtl2
2.5ANALYTICS
The standard QTL mapping package in R opened its genome scan to user-supplied likelihood models.
◆ Current state
qtl2 is the R toolkit for QTL mapping in experimental crosses, covering genotype probability calculation, genome scans with and without polygenic effects, permutation testing, SNP association, and the plotting that goes with them. The last year of work has pushed hard in two directions: tooling for high-throughput expression and protein QTL studies, and a generalisation of the scan engine itself so the log-likelihood being maximised can be supplied by the user. Note that the release history reached this feed out of order, so feed position is not a reliable guide to which release came first.
◆ Where it's heading
The eQTL and pQTL direction is the clearest thread — cis-trans plots, hotspot counting over a sliding window, multi-trait scan heat maps, and genome-wide genotype plots all arrived together, which is the toolkit an experiment with thousands of traits needs rather than one with a handful. Running underneath it is a steady generalisation of the core: a scan function that accepts an arbitrary likelihood, permutations that work with alternative scan functions, full variance-covariance output from single-position fits. Performance and parallelism get attention each cycle, including a more considerate default that leaves one core free. The rest is the ordinary maintenance of a long-lived package — renames to avoid tidyverse collisions, compiler warnings, and correctness fixes on specific cross types.
◆ Prediction
With scan1gen and permutation support for alternative scan functions in place, the natural next step is more model types built on that hook rather than more special-cased scan functions; the entries do not indicate which models are planned.
Alternatives to gghighlight and qtl2
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 gghighlight or qtl2.
lavaanExtra
SEM reporting helpers converging on APA output, one CRAN resubmission at a time.
ibis.iSDM
A raster-to-terra migration is the only readable change in a feed of merge notes.
anyflights
A nycflights13 generator whose recent work is all about the data being right.
vinereg
Conditional density and log-likelihood fill out a vine copula regression package.
stringx
A drop-in string API for base R, kept alive by upstream check failures.
See all gghighlight alternatives → · See all qtl2 alternatives →
Recent activity from gghighlight and qtl2
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 27d agoqtl2chr_lengths() extended to cross2 objects
- 1mo agoqtl2A genome scan that takes your own likelihood function ⚡
- 2mo agoqtl2Hotspot counting and cis-trans plots for eQTL studies
- 3mo agoqtl2Confidence interval plotting, plus a documentation correction
- 1y agogghighlightggplot2 v4.0 support; geom-specific functions removed
- 1y agoqtl2Finer-grained parallelism for kinship-based scans
- 1y agoqtl2CSV readers renamed to avoid the readr collision
- 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 gghighlight and qtl2?
Both compete on the same themes — r-package — within Analytics. qtl2 is currently shipping more aggressively (velocity 2.5 vs 0.0), with 0 editorial sparks in the last 30 days against 0. See the at-a-glance table above for a side-by-side breakdown of velocity, recent sparks, and editorial themes.
Is gghighlight better than qtl2?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. qtl2 is currently shipping more aggressively (velocity 2.5 vs 0.0), with 0 editorial sparks in the last 30 days against 0. For your specific use case, the alternatives sections above list other Analytics products to evaluate alongside.
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.
What are the best alternatives to qtl2?
Top qtl2 alternatives in Analytics are ranked by recent ship velocity. Browse the "qtl2 alternatives" section above for the current picks, or visit /alternatives/qtl2 for the full list with editorial commentary on each.