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@epurdom epurdom released this 28 Jun 11:16
· 631 commits to master since this release
2.1.5
b38fa98

Changes in version 2.1.5 ( Release date: 2018-06-28)

Changes:

  • Add functionality to getBestFeatures to allow edgeR for DE, as well as weights used with edgeR for zinbwave compatability. As part of this change:
    • Removed isCount argument and replaced with more fine-grained DEMethod argument in getBestFeatures, mergeClusters; or mergeDEMethod in RSEC.
    • Change to class definition: added slot merge_demethod to keep track of the DE method used in merging
  • Change function names (old function name is now depricated):
    • combineMany -> makeConsensus
    • removeUnclustered -> removeUnassigned
  • Arguments to functions changed:
    • combineProportion -> consensusProportion in RSEC
    • combineMinSize -> consensusMinSize in RSEC
    • sampleData -> colData to match SummarizedExperiment syntax (in many plotting functions).
      • alignSampleData -> alignColData in plotHeatmap
    • ignoreUnassignedVar -> filterIgnoresUnassigned in mergeClusters (and other functions) for clarity.
      • removeNegative -> removeUnassigned in getBestFeatures for uniformity
      • Removed largeDataset option to subsampleClustering because no longer provides advantage.
      • nBlank -> nBlankFeatures in makeBlankData to allow for samples
  • Created functions:
    • primaryClusterLabel and primaryClusterType
    • getReducedData
    • assignUnassigned: assigns unassigned samples to nearest cluster
      • renameClusters and recolorClusters: assign new names/colors to clusters within a particular clustering
    • clusterMatrixColors: wrapper to convertClusterLegend to return matrix like clusterMatrix only with colors in place of the internal cluster ids (like existing clusterMatrixNamed)
      • plotClustersTable for plotting a heatmap showing the results of tableClusters
      • subsetByCluster for subsetting CE object to only those samples in a particular cluster(s) of a clustering.
      • plotFeatureScatter for a scatter plot of 2+ features (genes) colored by cluster
      • addToColData and colDataClusters adding clustering information to colData of object. addToColData returns object with colData augmented, while colDataClusters just returns the DataFrame with clusterings added.
      • updateObject to update historical object created from previous versions to the current class definitions.
  • Added arguments:
    • whichAssay to all functions to allow the user to select the assay on which the operations will be performed.
    • stopOnErrors to RSEC
    • nColLegend to plotReducedDims
    • subsample and sequential to RSEC to allow for opting out of those options (but default is TRUE unlike clusterMany)
    • nBlankSamples and groupsOfSamples to makeBlankData to allow for separating samples (columns)
    • add and location to plotClusterLegend
  • makeBlankData will now allow for making blank columns to separate groups of samples.
  • plotDendrogram now allows for plotting of colData (previously sampleData) like plotHeatmap or plotClusters
  • clusterMany now allows user-defined ClusterFunction objects to argument clusterFunction.
  • Removed restriction in plotClustersWorkflow that only clusterType="clusterMany" allowed.
  • Allow getClusterManyParams to search old clusterMany runs as well.
  • Added table method to plotHeatmap (for plotting heatmap of results of table function)
  • Added error catch if try to give argument whichCluster to mergeCluster.
  • Added error catch if give param whichClusters to functions that only take whichCluster (singular) as an argument
  • plotFeatureBoxplot now returns (invisibly) the colors and clusterIds along with the boxplot information.

Bugs:

  • Add check for merge_nodeMerge table that mergeClusterId column can't be NA for entries where isMerged=TRUE
  • Fix internal .makeIntegerClusters so that if given values 1:K for input clustering will retain these same values (Issue #227)
  • mergeClusters now returned object saves the merge information (and deletes old info and updates clusterType/clusterLabel of existing merge clusters), even if mergeMethod="none".
  • Fix removeClusterings so doesn't loose merge info unless deleting relevant clusterings.
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