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@farrellja farrellja released this 28 Apr 18:23
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v1.1.1
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1.1.1 - April 28, 2020

This release incorporates fixes to many bugs uncovered by users over the last several months.

Added

  • plotTreeHighlight can be used to plot an URD dendrogram-style plot where particular cells on the tree are highlighted for visualizing their location.
  • A more evenly spaced color scale is now accessible by using the evenly.spaced = T parameter to defaultURDContinuousColors.
  • combineSmoothFit function can be used to put multiple spline curves together into a single spline curve.
  • Additional visualization options for plotDot, including minimum and maximum point sizes, choice of scaling by area or radius, and customizable color scale.
  • Additional visualization options for plotViolin, allowing customization of point size, color, and transparency.
  • treeForceDirectedLayout: cells.minimum.walks parameter can automatically exclude poorly visited cells from the force-directed layout calculation.
  • Calculations that use moving windows in pseudotime (including geneSmoothFit and its related functions) can now support minimum pseudotime and minimum cell numbers simultaneously. If both are set, windows are determined by number of cells, but then windows whose pseudotime is too small are collapsed.

Changed

  • Fixed installation failures for R > 3.4 due to changes in BioConductor's package management (i.e. to use BiocManager for R >= 3.5).
  • markersAUCPR now calculates AUC ratio compared to random classifier and correctly reports cluster labels. auc.factor parameter allows selecting only results that are some factor better than a random classifier.
  • markersAUCPR now correctly takes pseudocount of 1 into account when determining expression fold-change.
  • plotDot now uses a more evenly spaced color scale by default.
  • Removed delta symbol from NMF doublets plots to prevent Unicode failures during installation.
  • buildTree: If tips.use is not specified, will attempt to auto-detect.
  • buildTree: Fixed error where function would fail if a tip was specified that had no member cells as defined by loadTipCells function.
  • buildTree / treeLayoutDendrogram: Fixed bug in related to changes in ggraph 2.0.0 that was creating crazy dendrograms.
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