NEWS.md

In farrellja/URD: URD

News

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.

1.1.0 - July 25, 2019

This release accompanies the release of our manuscript Stem cell differentiation trajectories in Hydra resolved at single-cell resolution and includes new functions developed during the analysis presented in that work.

Added

• Added functions for using expression of NMF modules to identify cells that are potentially doublets: NMFDoubletsDefineModules, NMFDoubletsPlotModuleThresholds, NMFDoubletsDetermineCells, NMFDoubletsPlotModulesInCell, and NMFDoubletsPlotModuleCombos. The idea is that many NMF modules encode cell type programs; if you identify modules that are not expressed in overlapping gradients (which might represent legitimate developmental transitions), and are strongly expressed in distinct sets of cells, then small numbers of cells that express both modules are likely to represent technical or biological doublets where two distinct cells (which each have their own cell type program expressed) have been detected as a single cell. Removing these can improve trajectory inference, as they often create 'short-circuits' between distinct portions of the developmental process.
• Added new functions for calculating smoothed expression and plotting expression curves: geneSmoothFit, plotSmoothFit, cropSmoothFit, plotSmoothFitMultiCascade. Provides alternative, less parametric options (LOESS smoothing and spline curves) to the previous impulse model
• Added whichCells to help identify cells that match particular criteria for use in plotting, subsetting, and differential expression testing.
• Added plotDimDiscretized and plotTreeDiscretized to allow plotting expression or other metadata in an on/off fashion (based on user-defined thresholds) to improve some visualizations.

Changed

• Changed behavior of pseudotimeWeightTransitionMatrix to allow processing of more than 46,503 cells by processing the matrix in pieces.
• Fixed (another) bug in treeForceDirectedLayout that results from cells with duplicate random walk parameters
• Fixed an issue where createURD would fail because it would not find method::new for some reason.
• Structure of impulse fits has been modified to allow plotting with the original functions, but also the new plotSmoothFit and plotSmoothFitMultiCascade functions.
• Added additional input checking to plotTree, plotTreeDual to help identify bad inputs.
• Fixed bug in plotTreeForce when plotting TRUE/FALSE metadata
• Modified treeForceDirectedLayout to check for graph connectivity prior to calling some FDL routines that require connected graphs
• Fixed bug with segment names in treeForceDirectedLayout.

1.0.3 - May 28, 2019

Added

• Added plotTreeDual function which can plot two labels as red/green on the tree dendrogram layout

Changed

• Fixed bug in processRandomWalks when a cell occurs in in walks that is not in @diff.data
• Fixed bug in plotTree when using color.limits without explicitly setting symmetric.scale.
• Fixed bug in plotTreeForce when plotting discrete values.
• Fixed bugs in treeForceDirectedLayout that result from cells with duplicate random walk parameters or cells assigned NA by force-directed layout.

1.0.2 - October 1, 2018

Added

• Plots now search slot @nmf.c1 as well.
• Additional plotTree plotting options (can plot +/- values, configure limits of color axis, turn off legend).
• Additional options in edgesFromDM for displaying diffusion map transitions in plotDim.
• Can fit onset/offset times against absolute value of curve in impulseFit.
• Added treeForceStretchCoords for additional refinement of force-directed layouts.

Changed

• Changed behavior: Fixed bug where tip cells could end up being assigned to a segment other than the one they define.
• Fixed treeForceDirectedLayout to work without named segments.
• Fixed importing Seurat object when tSNE or PCA not calculated.
• Fixed bug in floodPseudotimeCalc when only one cell is used as the root. (Note: This is still not recommended usage, as in real data it is unlikely that a single cell can be definitely chosen as the starting point.)
• Reduced memory usage of floodBuildTM on large data
• Updated installation instructions with FAQ about udunits on Linux.
• Additional cleanup of documentation.

1.0.1 - May 20, 2018

Added

• Added to repository: Supplementary Analysis

Changed

• Fixed plotTreeForce with discrete labels.
• Fixed outdated references to deprecated @group slot.

farrellja/URD documentation built on June 17, 2020, 4:48 a.m.