v0.1.6

• Fixed compatibility with SeuratWrappers and bioc versions

v0.1.5

• Cluster label smoothing
• Parallelism for clustering using foreach
• Filtering out samples with NAs in their features on initialisation
• Seed setting for clustering
• Version dependency on leidenAlg (>1.1.0) for compatibility with igraph
• Neighborhood-sampling (see arguments sample_size and sample_renorm for function ComputeBanksy)
• Replacing M with compute_agf and use_agf as arguments for specifying which harmonics to compute

v0.1.4

This release implements azimuthal Gabor filters as additional features of a cell's neighborhood.

• Azimuthal Gabor filters implemented in ComputeBanksy, with the number of harmonics determined by the M argument. To obtain similar results as version 0.1.3, use M=0
• Default size factor for NormalizeBanksy is set to the median total count
• RunPCA and RunUMAP renamed to RunBanksyPCA and RunBanksyUMAP respectively to avoid namespace collisions with other packages
• The following argument names have been modified for style:
  • NormalizeBanksy: normFactor to norm_factor
  • NormalizeBanksy: logNorm to log_norm
  • ComputeBanksy: spatialMode to spatial_mode
  • ComputeBanksy: kspatial to k_spatial

v.0.1.3.33

Implements minor fixes and updated documentation from release v.0.1.3.

v.0.1.3

First public release.

Changes from v0.0.9:

• Passing Bioc and R CMD checks
• Implemented: asBanksyObject for interop. with SingleCellExperiment
• Implemented: RunPCA and RunUMAP
• Implemented: plotReduction for generalised plotting
• Implemented: plotARI and getARI for ARI computation and plotting
• Changed: ConnectClusters returns BanksyObject
• Changed: BanksyObject slot dim.reduction to reduction

v0.0.9

Legacy version of BANKSY.

Main differences between v0.0.9 and v0.1.x:

• BanksyObject: dimensionality reduction slot name dim.reduction (changed to reduction in v0.1.x)
• BanksyObject: no clust.names method
• Dimensionality reduction steps (PCA / UMAP) included in ClusterBanksy now removed as separate functions in v0.1.x
• Plotting is generalised in v0.1.x (plotReduction instead of plotUMAP / plotPCA)
• ConnectClusters implementation improved in v0.1.x and returns only BanksyObject in v0.1.x (instead of list in v.0.0.9)
• ARI computation and plotting is included in v0.1.x (getARI / plotARI)
• Data moved from inst/extdata (v0.0.9) to /data (v.0.1.x)