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"