Changes in version 1.2.1                        

Minor improvements and fixes

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

                        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