v.1.3.1

Changes in version 1.3.1 ( Release date: 2017-06-14 )

Changes:

• change how plotHeatmap handles visualizeData argument, so not required to have same number of genes as original, only same number of samples.
• Now if color of vectors given in clusterLegend does not have names, plotHeatmap will give them names matching the variable so that they will be used by aheatmap (previously would have left all colors white because do not have matching names).
• Large changes to how dendrograms are plotted by plotDendrogram and mergeClusters. This includes the ability to see the before and after clusterings along side the mergeClusters result, as well as a new slot added to the clusterExperiment class (dendro_outbranch). The names of several arguments to mergeClusters and plotDendrogram were changed for clarity:
  • leaves is now leafType in plotDendrogram.
  • plotType is now plotInfo in mergeClusters
  • doPlot is now plot in mergeClusters
  • leafType is now an option for mergeClusters as well.
  • Now when plotInfo (previously plotType) is set to none, the plot is still drawn, but just no information about the merging is added to the plot. To not plot the dendrogram at all, set plot=FALSE.
  • The option labelType in either plotDendrogram or mergeClusters controls whether names (name) or rectangular color blocks corresponding to the cluster (colorblock) are put at the tips of the dendrogram to label the clusters/samples.
• added dendroClusterIndex that behaves similarly to primaryClusterIndex
• added ability to give dendro as charater option to whichClusters argument
• added transformation<- to be able to assign manually the transformation slot
• Move MAST into 'suggests' pacakge so that not need R 3.4 to run the package.
• Change calculation of PCA dimensionality reduction to use svds from RSpectra package to improve speed

Bugs:

• Fixed bug in RSEC where combineProportion argument was being ignored (set to 1)
• Fixed bug in definition of transform so that extends existing generic rather than masking it.