This release incorporates fixes to many bugs uncovered by users over the last several months.
plotTreeHighlight
can be used to plot an URD dendrogram-style plot where particular cells on the tree are highlighted for visualizing their location.evenly.spaced = T
parameter to defaultURDContinuousColors
.combineSmoothFit
function can be used to put multiple spline curves together into a single spline curve.plotDot
, including minimum and maximum point sizes, choice of scaling by area or radius, and customizable color scale.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.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.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.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.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.
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.geneSmoothFit
, plotSmoothFit
, cropSmoothFit
, plotSmoothFitMultiCascade
. Provides alternative, less parametric options (LOESS smoothing and spline curves) to the previous impulse modelwhichCells
to help identify cells that match particular criteria for use in plotting, subsetting, and differential expression testing.plotDimDiscretized
and plotTreeDiscretized
to allow plotting expression or other metadata in an on/off fashion (based on user-defined thresholds) to improve some visualizations.pseudotimeWeightTransitionMatrix
to allow processing of more than 46,503 cells by processing the matrix in pieces.treeForceDirectedLayout
that results from cells with duplicate random walk parameterscreateURD
would fail because it would not find method::new
for some reason.plotSmoothFit
and plotSmoothFitMultiCascade
functions.plotTree
, plotTreeDual
to help identify bad inputs.plotTreeForce
when plotting TRUE/FALSE metadatatreeForceDirectedLayout
to check for graph connectivity prior to calling some FDL routines that require connected graphstreeForceDirectedLayout
.plotTreeDual
function which can plot two labels as red/green on the tree dendrogram layoutprocessRandomWalks
when a cell occurs in in walks that is not in @diff.data
plotTree
when using color.limits
without explicitly setting symmetric.scale
.plotTreeForce
when plotting discrete values.treeForceDirectedLayout
that result from cells with duplicate random walk parameters or cells assigned NA by force-directed layout.@nmf.c1
as well.plotTree
plotting options (can plot +/- values, configure limits of color axis, turn off legend).edgesFromDM
for displaying diffusion map transitions in plotDim
.impulseFit
.treeForceStretchCoords
for additional refinement of force-directed layouts.treeForceDirectedLayout
to work without named segments.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.)floodBuildTM
on large dataplotTreeForce
with discrete labels.@group
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