0.99.3

Changes:

• plot in mergeClusters now uses cluster names and colors from clusterLegend
• plotDendrogram now calls plot.phylo
• add 'clusterLabel' argument to clusterSingle
• add options 'mad' and 'cv' to the dimensionality reduction. Also made option to only use clustered samples for feature reduction for relevant functions (e.g. makeDendrogram).
• clusterSingle now always returns the D matrix to the slot coClustering (previously only did so if D was from subsampling).
• change so that clusterSingle takes dissimilarity matrix, and now clusterMany calculates dissimilarities up front (rather than recalculating each time)
• add RSEC function for wrapper that leads to RSEC algorithm.
• add test for clusterMany to make sure replicable with past results (not unit test because too long to run, so not part of R build)

Bug fixes:

• fix bug in .TypeIntoIndices so that handles mix of clusterType and clusterLabels in whichClusters
• fixed bug in plotCoClustering so handles clusterSamplesData
• D for clusterD is now distance, not similarity, for 0-1, meaning larger values are values that are less similar.
• fix bug in plotClusters that would give clusterLegend entries that were vectors, not matrices.

0.99.0

• Allow 'whichCluster'/'whichClusters' arguments to match to clusterLabels, not just clusterTypes
• Added slot 'dendro_index'
• Added 'whichCluster' argument to makeDendrogram
• Added 'hierarchicalK' clustering
• Added default distance for 0-1 clustering
• Added ability to define distance for clustering
• Added 'setToCurrent' and 'setToFinal' options to update status of a cluster.
• Added unit tests for workflow function (in test_constructor)
• 'getBestFeatures' now calls 'clusterContrasts' internally
• Output for 'clusterContrasts' changed
• Removed 'Index' output for getBestFeatures
• Changed tests for getBestFeatures to run on standard objects (which means now have -2 values to test against)
• User can now give clusterLabel for resulting cluster of combineMany and mergeClusters

v0.1.0

Changes in version 0.1.0 (Release date: 2016-03-04)

Changes:

• Conversion to S4 language for bioConductor submission
• All previous functions have been overhauled, renamed, etc.

v0.0.0.9006

• fixed so that mergeClusters, clusterHclust, and getBestGenes will appropriately convert if the input of clustering vector is a factor rather than numeric (with warning).
• fixed mergeClusters to have option to indicate that input matrix is a count matrix (in which case will create dendrogram with log(counts+1) and will do getBestGenes with the voom correction)
• added more tutoral-oriented vignette (old vignette is now the documentation vignette with more detail about the internal workings of package). Currently is just simulated data, but will be updated to real single-cell sequencing dataset.

v0.0.0.9005

• added functionality to find proportion of significant null hypotheses for merging clusters (mergeClusters)
• getBestGenes now can use voom in limma package to deal with count data input (and doesn't require that it is integer counts -- can be normalized data)
• getBestGenes has option "OneAgainstAll"
• findSharedClusters adapted to better find a consensus cluster; added plotting of proportion shared
• Changed simulated data so load all with data(simData) rather than separate calls for simData and simCount. Also added 'trueCluster' vector to give true cluster assignments of simulated data
• added dendro example to getBestGenes
• added example to clusterHclust
• added single function for converting to phylobase tree (used internally by package)
• fixed clusterD so that handles the 'wrong' arguments being passed to it (i.e. arguments that don't match the clustering being done); this avoids errors in compareChoices
• added documentation to findSharedClusters

v0.0.0.9002

Fixed bug in findSharedClusters: before would give error if there was a pair of samples that didn't have any clusters in which they were both assigned to a cluster (i.e. not "-1")

v0.0.0.9003

• Introduced option for "one vs all" DE testing of clusters in getBestGenes
• Fixes numerous errors in examples that didn't run in documentation
• Fixes major error in behavior of plotTracking: error was not long-standing, but introduced when removed function 'clusterTrackingPlot' and instead made it an option in plotTracking (labels no longer printed)
• Fixed showHeatmapPalettes
• Now R CMD CHECK runs without errors/warnings