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Changelog

Source: NEWS.md

CytoMDS 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

CytoMDS 1.3.1

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

CytoMDS 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

CytoMDS 1.0.0

(release Bioconductor)

CytoMDS 0.99

CytoMDS 0.99.16

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

CytoMDS 0.99.8

  • renamed getChannelSummaryStats() into channelSummaryStats()
  • in channelSummaryStats(), added support forBiocParallel`, 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

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