Changelog

Source: NEWS.md

CytoMDS 1.9

CytoMDS 1.9.3

• refactored computeMetricMDS to make the automatic selection of number of dimensions more efficient, while also handling non increasing pseudo rsquares, and implementing verbose messages

CytoMDS 1.9.2

(no change - required update of unit tests)

CytoMDS 1.9.1

(no change)

CytoMDS 1.7

CytoMDS 1.7.2

• added ggplotVolcano()

CytoMDS 1.7.1

• fixed unti tests with new version of ggplot2

CytoMDS 1.5

(no devel)

CytoMDS 1.3

CytoMDS 1.3.7

• changed package citation (and in README.md) to peer reviewed journal article

CytoMDS 1.3.6

• ggplotMarginalDensities(): corrected a bug when channels were specified as marker names.

CytoMDS 1.3.5

• removed contraint (max = 3) on nb of plotly tool_tips variables (pDataForAdditionalLabelling)

CytoMDS 1.3.4

• corrected plotly tool_tips (pDataForAdditionalLabelling)

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 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

• 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