NEWS

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BayesSpace 1.5.1

Minor improvements and fixes

• Update readVisium to work properly when feature names include whitespaces
• Fix rounding of w_i sum in MCMC
• Add details to vignette related to spatialEnhance

BayesSpace 1.5.0

New Bioconductor devel (3.15)

• Version numbering change with Bioconductor version bump

BayesSpace 1.4.0

New Bioconductor release (3.14)

• Version numbering change with Bioconductor version bump

BayesSpace 1.3.1

Minor improvements and fixes

• Update documentation for getRDS(), mcmcChain(), and spatialEnhance().

BayesSpace 1.3.0

Minor improvements and fixes

• Added information to documentation.
• getRDS() updated with new URL.

BayesSpace 1.2.0

New Bioconductor release (3.12)

• Version numbering change with Bioconductor version bump

BayesSpace 1.1.2

Minor improvements and fixes

• clusterPlot() accepts character vectors and factors as arguments to label.

BayesSpace 1.1.1

Minor improvements and fixes

• spatialPreprocess() uses exact rather than approximate PCA by default.

BayesSpace 1.1.0

New Bioconductor devel (3.13)

• Version numbering change with Bioconductor version bump

BayesSpace 0.99.8

Minor improvements and fixes

• spatialCluster() and spatialEnhance() now use a faster implementation of the multivariate normal density that reduces runtime by approximately 40%.

BayesSpace 0.99.7

Minor improvements and fixes

• Documentation examples now use fewer iterations in order to reduce the runtime of R CMD check.
• In qTune(), the min_rep and max_rep parameters have been replaced with burn.in and nrep, respectively, to be consistent with spatialCluster().

BayesSpace 0.99.6

New features

• getRDS() gains a cache parameter. When TRUE, the RDS is cached locally using BiocFileCache.

Minor improvements and fixes

• Addressed reviewer concerns (https://github.com/Bioconductor/Contributions/issues/1624)
  • Updated stop/warning/message statements to remove redundancies and unnecessary use of paste().
  • Removed inline conditional statements.
  • Cache downloaded RDS in getRDS() (see above).
• spatialCluster() and spatialEnhance() handle the edge case where only one iteration is kept after excluding burn-in.
• The coda::mcmc object returned by mcmcChain() now specifies the thinning interval used in enhanced objects.
• spatialCluster() and spatialEnhance() now include platform-specific defaults for the gamma parameter.
• Minor internal refactoring.

BayesSpace 0.99.5

Minor improvements and fixes

• In spatialCluster() and spatialEnhance(), setting burn.in equal to nrep now raises an error.

BayesSpace 0.99.4

New features

• enhanceFeatures() now takes an nrounds parameter that corresponds to the same parameter in xgboost. If nrounds is set to 0, we automatically tune the parameter using a train/test split for improved feature prediction.
• spatialCluster() and spatialEnhance() both gain a burn.in parameter specifying the number of MCMC iterations to exclude when aggregating cluster labels and enhanced PCs.
• In clusterPlot(), label now accepts factors and vectors of strings, in addition to numeric vectors or a column name in colData.
• Additional vignettes provided for reproducing the analyses of the melanoma, dorsolateral prefrontal cortex, and squamous cell carcinoma datasets presented in the bioRxiv manuscript.

Minor improvements and fixes

• The internal layout of subspots is now correctly oriented (accounting for vertical flip of spot coordinates) when using spatial plot functions on enhanced Visium data.
• In spatialEnhance(), PCs are now averaged over the MCMC iterations (excluding the burn-in period).
• In enhanceFeatures(), negative expression is now clipped to 0.
• spatialPreprocess() now adds a boolean is.HVG column to rowData.
• In featurePlot(), additional arguments to geom_polygon() are correctly passed through.

BayesSpace 0.99.3

Minor improvements and fixes

• Updated README.md to include system requirements, additional installation details, and link to vignette with demonstration of package functions, per journal guidelines.

BayesSpace 0.99.2

Minor improvements and fixes

• spatialEnhance() incorrectly added row offset to spot column coordinate when generating subspot colData, and vice versa. This resulted in subspots being reflected over y=x in spatial plots, and has been fixed.
• Figures in the demonstration vignette have been updated with this fix.

BayesSpace 0.99.1

Minor improvements and fixes

• Removed Maintainer field from DESCRIPTION to adhere to Bioconductor guidelines.

BayesSpace 0.99.0

New features

• Initial Bioconductor submission