Changes in version 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 Changes in version 1.5.0 New Bioconductor devel (3.15) - Version numbering change with Bioconductor version bump Changes in version 1.4.0 New Bioconductor release (3.14) - Version numbering change with Bioconductor version bump Changes in version 1.3.1 Minor improvements and fixes - Update documentation for getRDS(), mcmcChain(), and spatialEnhance(). Changes in version 1.3.0 Minor improvements and fixes - Added information to documentation. - getRDS() updated with new URL. Changes in version 1.2.0 New Bioconductor release (3.12) - Version numbering change with Bioconductor version bump Changes in version 1.1.2 Minor improvements and fixes - clusterPlot() accepts character vectors and factors as arguments to label. Changes in version 1.1.1 Minor improvements and fixes - spatialPreprocess() uses exact rather than approximate PCA by default. Changes in version 1.1.0 New Bioconductor devel (3.13) - Version numbering change with Bioconductor version bump Changes in version 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%. Changes in version 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(). Changes in version 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. Changes in version 0.99.5 Minor improvements and fixes - In spatialCluster() and spatialEnhance(), setting burn.in equal to nrep now raises an error. Changes in version 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. Changes in version 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. Changes in version 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. Changes in version 0.99.1 Minor improvements and fixes - Removed Maintainer field from DESCRIPTION to adhere to Bioconductor guidelines. Changes in version 0.99.0 New features - Initial Bioconductor submission