Changes in version 1.1.2 ( Release date:  2017-04-04 )
==============

Changes:
* RSEC now has option `rerunClusterMany`, which if FALSE will not rerun the clusterMany step if RSEC is called on an existing clusterExperiment object (assuming of course, clusterMany has been run already on the object)
* setBreaks now has option `makeSymmetric` to force symmetric breaks around zero when using the quantile option. 
* setBreaks now has a default for breaks (i.e. for minimal use, the user doesn't have to give the argument, just the data) in which case setBreaks will automatically find equal-spaced breaks of length 52 filling the range of data compatible with aheatmap. The order of the arguments `data` and `breaks` has been switched, however, to better accomodate this usage. 
* plotClusters can now handle NA values in the colData
* plotClusters for `clusterExperiment` object now allows for setting `sampleData=TRUE` to indicate the plotting all of the sampleData in the colData slot.
* nPCADims now allows values between 0,1 to allow for keeping *proportion* of variance explained.
* addClusters now allows for argument `clusterLabel` to assign a clusterLabel when the added cluster is a vector (if matrix, then clusterLabel is just the column names of the matrix of cluster assignments)

Bug fixes:
* fixed bug in clusterExperiment subsetting to deal with orderSamples correctly.
* fixed bug in mergeClusters unable to plot when too big of edge lengths (same as plotDendrogram)
* fixed bug in subsetting, where unable to subset samples by character
* fixed bug in removeClusters so that correctly updates dendro_index and primary_index slots after cluster removed.

Changes in version 1.1.1 (Release date: 2016-10-14 )
==============

Changes:
* Inverted definition of contrast for one-versus-all so now is X-ave(all but X); this means logFC positive -> cluster X greater than average of rest

Bug fixes:
* add check in clusterMany that non-zero dimensions
* changed 'warning' to 'note' in combineMany when no clusters specified.
* fixed bug in plotDendrogram unable to plot when makeDendrogram used dimReduce="mad"
* fixed bug in clusterMany where beta set to NA if clusteringFunction is type K. Added check that beta cannot be NA.
* Added check that alpha and beta in (0,1)

Changes in version 0.99.3 (Release date:  2016-07-26)
==============

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.

Changes in version 0.99.1 (Release date: 2016-05-24 )
==============

Changes:
* changes to pass development version of bioConductor checks.

Changes in version 0.99.0 (Release date: 2016-05-24 )
==============

Changes:
* changed number to indicate bioconductor submission

Changes in version 0.2.0 (Release date: 2016-05-10 )
==============

Changes:

* 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


Changes in version 0.1.0 (Release date: 2016-05-04)
==============

Changes:

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

Changes in version 0.0.0.9006
==============

Changes:

* fixed so that mergeClusters, clusterHclust, and getBestFeatures 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 getBestFeatures 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.

Changes in version 0.0.0.9005
==============

Changes:

* 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 getBestFeatures
* added example to clusterHclust
* added single function for converting to phylobase tree (used internally by package)
* added functionality to find proportion of significant null hypotheses for merging clusters (mergeClusters)

Changes in version 0.0.0.9004
==============

Changes:

* Changed clusterMany.R to only set k<-NA if sequential=FALSE (previously for all where findBestK=TRUE)
* Added to vignette
* fixed bug in plotClusters to correctly plot "-1"