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@epurdom epurdom released this 23 Oct 22:59
· 1380 commits to master since this release
v1.3.6
aabad67

Changes:

  • MAJOR CHANGE TO DEFINITION OF CLASS: Added slots to ClusterExperiment object so that the object keeps the information about the merging, and added corresponding helper functions (see documentation). This means previous versions made of a ClusterExperiment object will no longer be valid objects! Old, saved objects from previous versions must be manually adapted to have these slots (with NULL or NA values as appropriate).
  • Add function plotClustersWorkflow, see documentation
  • Add function plotDimReduce for plotting low-dim pca with points labeled by cluster.
  • Add function plotContrastHeatmap to plot the significant genes that are result of getBestFeatures
  • getBestFeatures: can now be run on result of mergeClusters without having to call makeDendrogram again for the merged clusters.
  • Change argument to plotClusters and plotBarplot from clusters to object
  • makeDendrogram: default in is now dimReduce="mad" to avoid accidentally calling it with dimReduce="none" (previous default), which can kill interactive R sessions.
  • Changes to plotHeatmap:
    • default in plotHeatmap to clusterSamplesData="dendrogramValue".
    • Changed handling of clusterSamplesData argument in plotHeatmap so that if argument equals dendrogramValue or primaryCluster and gives bad results / errors, will give warning and change argument appropriately.
    • Added arguments to plotHeatmap allowing more user control regarding making blank lines for when have gene groupings.
  • mergeClusters now aligns the colors from mergeClusters and combineMany internally.
  • mergeClusters now suppresses warnings created by the estimation of the percentage non-null unless showWarnings=TRUE.
  • plotDendrogram:
    • has new argument clusterLabelAngle allowing user to change the angle of the clusterLabel printed on top (when plot is of type "colorblock")
    • argument labelType has been changed to plotType

Bugs:

  • Arguments passed to mergeClusters, ClusterExperiment version, via the ... command will now go first to the mergeClusters matrix version and then onto the plotting, as stated in documentation (plotting arguments were being ignored on the clusterExperiment version of the function).
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