Changes in version 1.12.0
o prepareCellData() now returns a List rather than a
half-complete CyData object.
o expandRadius() and neighborDistances() work explicitly on the
List produced by prepareCellData().
o countCells() will compute weighted-median intensities for
unused markers as well. Minor bugfix to avoid stochastic
results due to numerical imprecision when computing medians.
o intensities() has a new mode= argument to return intensities
for unused markers.
Changes in version 1.10.0
o Removed deprecated plotCell* functions.
Changes in version 1.8.0
o Modified the plotSphere*() functions for more flexibility in
colour choice.
o Added fix.zero= option in normalizeBatch() for range-based
normalization.
Changes in version 1.6.0
o Restructured the CyData class for simplicity and internal
fields.
o Deprecated plotCell* functions, renamed them to plotSphere*.
o Added the createColorBar() convenience function.
o Removed the diffIntDist() function.
o Restored option for quantile normalization in normalizeBatch().
Switched to deterministic algorithm for sampling when
mode="warp".
Changes in version 1.4.0
o Bug fix to interpreSpheres() when making additional plots.
o Switched to custom colour calculation in plotCellIntensity().
Changes in version 1.2.0
o Added labelSpheres() function for labelling unannotated
hyperspheres.
o Exported multiIntHist() for plotting multiple intensity
histograms.
o Slight fix to spatialFDR(), which now computes the correct n-th
nearest neighbour.
Changes in version 1.0.0
o
New package cydar, for detecting differential abundance in mass
cytometry data.