Updated to use the latest BiocNeighbors, which means that the output of prepareCellData() is no longer serializable.
This is because the precomputed index is now an external pointer to a C++-owned data structure, and cannot be moved between sessions.
(Arguably, it was a mistake to expose these internals in the expected workflow for this package, but that ship has sailed.)
Hopefully, this should not affect most users as they should be primarily interacting with the CyData object.
prepareCellData() now returns a List rather than a half-complete CyData object.
expandRadius() and neighborDistances() work explicitly on the List produced by prepareCellData().
countCells() will compute weighted-median intensities for unused markers as well.
Minor bugfix to avoid stochastic results due to numerical imprecision when computing medians.
intensities() has a new mode= argument to return intensities for unused markers.
Removed deprecated plotCell* functions.
Modified the plotSphere*() functions for more flexibility in colour choice.
Added fix.zero= option in normalizeBatch() for range-based normalization.
Restructured the CyData class for simplicity and internal fields.
Deprecated plotCell* functions, renamed them to plotSphere*.
Added the createColorBar() convenience function.
Removed the diffIntDist() function.
Restored option for quantile normalization in normalizeBatch(). Switched to deterministic algorithm for sampling when mode="warp".
Bug fix to interpreSpheres() when making additional plots.
Switched to custom colour calculation in plotCellIntensity().
Added labelSpheres() function for labelling unannotated hyperspheres.
Exported multiIntHist() for plotting multiple intensity histograms.
Slight fix to spatialFDR(), which now computes the correct n-th nearest neighbour.
New package cydar, for detecting differential abundance in mass cytometry data.