v1.3.2

Changes:

• Default for top.can in seqCluster are changed to be top.can=5.
• makeDendrogram now has the default argument ignoreUnassignedVar=TRUE like in RSEC
• add ClusterFunction class and update all functions to work on this. All built in cluster functions are now given ClusterFunction Objects, so all built in clustering functions can now work for either subsampleClustering or mainClustering. This will also make it easier for a user to define their own ClusterFunction object and have it be used by functions like clusterSingle. This is a major change in how some of the underlying functions work, but should not impact common functions like clusterMany and RSEC. Some of the more notable changes in the arguments for programmers are:
  • clusterD and clusterDArgs have been changed to mainClustering and mainClusterArgs. This change was made to make these arguments more clear as to their role in the clustering workflow (and because the clusterD refered to clustering a dissimilarity but it has clustered either x or D for many versions now. )
  • seqCluster and clusterSingle no longer take the argument clusterFunction. clusterFunction must be given via mainClusterArgs and subsampleArgs to be passed to mainClustering or subsamplingCluster, respectively. Now only the upper-level function clusterMany takes clusterFunction directly as an argument.
  • mainClustering (previously clusterD) and subsampleClustering no longer take k nor alpha as a direct argument. These arguments, like all arguments used directly by the cluster function, now need to be passed to the clustering function in a list via clusterArgs.
  • The list of available built-in clustering routines provided by the package can now be accessed via listBuiltInFunctions(). The functions that are used for these functions are now available to the user via their ClusterFunction object that the user can access with the function getBuiltInFunction. (see ?listBuiltInFunctions)
• hiearchical01 clustering now has a different default, namely to apply as.dist to the input diss in order to get a dist object, rather than dist(1-diss) which was previously the default for historical reasons. This is controlled by argument whichHierDist, and can be set to the previous version by passing whichHierDist="dist" to the clusterArgs argument in either subsampleArgs or mainClusterArgs, depending on where hierarchical01 is being used.
• Spectral clustering is now available ("spectral") via the specc function of kernlab.
• clusterSingle now only returns the dissimilarity matrix in the coClustering slot if subsample=TRUE in the call. Furthermore, for the resulting dissimilarity to replace an existing coClustering slot value, the user must request it by setting replaceCoClustering=TRUE in the call to clusterSingle.
• Removed default value for argument proportion in combineMany. The previous default was proportion=1 but didn't match most common use cases and was accidentally called by upper functions like RSEC.
• If the clusterFunction argument is not given to subsampleArgs by the user explicitly, and the clusterFunction of mainClusterArgs is appropriate, it will be used for subsampleClustering; if the clusterFunction in mainClusterArgs is not appropriate (e.g. subsampleClustering needs a type K because sequential=TRUE), then the default for the subsampleClustering will be 'pam'. This changes the previous behavior of subsampleClustering where the default was 'pam' in all cases where not explicitly given by the user. This change should have no impact on RSEC: since the clusterFunction for the mainClustering terms is a '01' type in RSEC and the subsampleClustering has to be type 'K' when sequential=TRUE, it will revert to the default "pam" as before.

Bugs:

• Fixed error so where if clusterSingle was called on existing clusterExperiment object it would overwrite the information of the existing clusterExperiment object.
• Fixed RSEC so now if rerun on existing clusterExperiment object, it will grab defaults from the matrix version (previously defaults were those of the underlying function, which were not always the same, e.g. combineProportion default was previously 1)
• Fixed clusterMany so now it explicitly sets dimReduce="none" in call to clusterSingle. Before, might have been calling all of the dimReduce defaults (i.e. all of them!).
• Fixed so gives error if whichClusters in plotBarplot doesn't match anything.