NEWS

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

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.

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

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