Description Creating an URD object Basic data analysis Calculate diffusion map Calculate pseudotime Find developmental trajectories Build developmental tree Plot with abandon
URD reconstructs transcriptional trajectories underlying specification or differentiation
processes in the form of a branching tree from single-cell RNAseq data. The URD
object class is documented under URDclass
. There are many functions
in the package, but a starting guide to help you get started is:
createURD
- Create an URD object
seuratToURD
- Import an object from Seurat
findVariableGenes
- Find highly variable genes
calcKNN
- Calculate a k-nearest neighbor graph
knnOutliers
- Find outliers based on k-NN distance
calcPCA
- Principal Components Analysis
calcTsne
- tSNE project of data
graphClustering
- Graph-based clustering of cells
calcDM
- Calculate a diffusion map
floodPseudotime
- Perform 'flood' breadth-first graph search
floodPseudotimeProcess
- Convert 'floods' into cell pseudotime
pseudotimePlotStabilityOverall
- Verify that enough 'flood' simulations were performed
pseudotimeDetermineLogistic
- Determine parameters of logistic for biasing transition probabilities
pseudotimeWeightTransitionMatrix
- Bias transition probabilities according to pseudotime
simulateRandomWalksFromTips
- Perform biased random walks starting at each 'tip'
processRandomWalksFromTips
- Convert biased random walks into visitation frequencies
loadTipCells
- Load cells belonging to each tip into the URD object
buildTree
- Find branching tree structure from trajectory data
treeForceDirectedLayout
- Generate a force-directed layout of the tree
plotDim
- Plot data on dimensionality reduction (tSNE, PCA, or diffusion map)
plotDimDual
- Plot multiple data on dimensionality reduction
plotDimArray
- Plot the same data on many pairs of dimensions
plotDim3D
- Plot dimensionality reduction in 3D
plotDim3DStoreView
- Store a plotDim3D orientation for making many similar plots
plotTree
- Plot data on dendrogram representation of tree
plotTreeForce
- Plot data on 3D force-directed layout representation of tree
plotTreeForceStore3DView
- Store a plotTreeForce orientation for making many similar plots
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