Changes in version 1.3                         

CytoMDS 1.3.3

  - DistSum class to store distance matrices computed as the sum of
    marker contributions
  - ggplotDistFeatureImportance() now can be used to create a stacked
    bar ggplot object, displaying feature importance in a distance
    matrix (extracted from a DistSum object)

CytoMDS 1.3.2

  - added pointSize argument to ggplotSampleMDS()

CytoMDS 1.3.1

  - corrected bug with nPoints() method of MDS class, due to slightly
    modified behaviour of dist S3 class in R4.5.

                         Changes in version 1.1                         

CytoMDS 1.1.4

  - implemented pkgdown customization

CytoMDS 1.1.2 & 1.1.3

  - expression matrices as input to EMD calculation

CytoMDS 1.1.1

  - added citation to bioRxiv pre-print

                        Changes in version 1.0.0                        

(release Bioconductor)

                        Changes in version 0.99                         

CytoMDS 0.99.16

  - added lineWidth parameter in ggplotSampleMDSShepard()
  - running plotly::ggplotly() on ggplotSampleMDSShepard() output now
    displays row and column number for each distance point.
  - added pointLabelSize and arrowLabelSize in ggplotSample()

CytoMDS 0.99.15

  - corrected bug fix (error message) in pwDist() when verbose=TRUE

CytoMDS 0.99.14

  - re-factored code portions to replace, as much as possible, for loops
    by apply() family of functions.

CytoMDS 0.99.13

  - re-factored code portions to avoid growing lists incrementally

CytoMDS 0.99.12

  - removed useBiocParallel parameters from various stats functions (use
    BPPARAM = BiocParallel::SerialParam() as a default)
  - implemented MDS class to store MDS projection results
  - bi-plots now explicitly discard constant external variables
    (+warning) instead of raising an error without producing a plot
  - implemented ggplotMarginalDensities()
  - updated vignette with Bodenmiller2012 dataset and more biological
    interpretation.

CytoMDS 0.99.11

  - re-factored package documentation file

CytoMDS 0.99.10

  - biplot now handles extVariables with missing values

CytoMDS 0.99.9

  - in ggplotSampleMDS() : add label layer after geom_point() (no more
    before)

CytoMDS 0.99.8

  - renamed getChannelSummaryStats() into channelSummaryStats()
  - in channelSummaryStats(), added support for BiocParallel`, and
    allowed for not loading the whole flowSet in memory at once.
  - replaced NULL defaulted parameters with optional parameters
  - added displayPointLabels argument to ggplotSampleMDS()
  - added displayLegend argument to ggplotSampleMDSWrapBiplots()
  - finalized creating vignette

CytoMDS 0.99.7

  - refactored the pairwise distance calculation code, by pre-computing
    the unidimensional histograms and store them instead of
    recalculating them each time a distance between 2 samples is
    calculated. This improves CPU time and memory consumption.

CytoMDS 0.99.6

  - added subset argument in ggplotSampleMDS() and
    ggplotSampleMDSWrapBiplots

CytoMDS 0.99.5

  - renamed getPairwiseEMDDist() into pairwiseEMDDist()
  - in pairwiseEMDDist(), added support for BiocParallel, and allowed
    for not loading the whole flowSet in memory at once.

CytoMDS 0.99.4

  - in getPairwiseEMDDist(), added a second flowSet argument. When the
    two flowSet arguments are non-null, distances are calculated for all
    sample pairs, where the first element comes from fs, and the second
    element comes from fs2.
  - renamed ggplotSamplesMDS into ggplotSampleMDS
  - renamed ggplotSamplesMDSShepard into ggplotSampleMDSShepard
  - renamed getChannelsSummaryStat into getChannelSummaryStats
  - new function ggplotSampleMDSWrapBiplots()

CytoMDS 0.99.3

  - new version of computeMetricMDS() which automatically sets the
    number of dimensions to reach a target pseudo R squared
  - added ggplotly() functionality for output MDS plots
  - in ggplotSampleMDS(), added flipXAxis, flipYAxis to possibly ease
    low dimensional projection comparisons
  - in ggplotSampleMDS(), added displayArrowLabels to discard the arrow
    labels in biplot. Also added arrowThreshold. Moved arrow labels
    toward the end of the arrows.
  - in ggplotSampleMDS() and ggplotSampleMDSShepard(): added
    displayPseudoRSq parameter.

CytoMDS 0.99.2

  - use global Rsquare as an indicator of quality of projection
  - use %Var explained per axis

CytoMDS 0.99.1

  - in ggplotSamplesMDS(), added parameter pDataForAdditionalLabelling