VeloViz: RNA-velocity informed 2D embeddings for visualizing cell state trajectories


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Documentation for package ‘veloviz’ version 1.4.0

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asNNGraph Function to produce idx and dist representation of a VeloViz graph
buildVeloviz Creates VeloViz graph and FDG layout from PC scores of current and projected transcriptional states.
graphViz Visualize as velocity informed force directed graph
normalizeDepth Normalizes counts to CPM
normalizeVariance Identify overdispersed genes by normalizing counts per million (CPM) gene expression variance relative to transcriptome-wide expectations (Modified from SCDE/PAGODA2 code)
pancreas Pancreas scRNA-seq data
plotEmbedding Plot 2D embedding From scde/pagoda2/MUDAN
plotVeloviz Plot function
projectedNeighbors Computes composite distances between all cell pairs and returns k-nearest neighbors and edge weights needed to build VeloViz graph.
reduceDimensions Reduce dimension using Principal Components Analysis via 'svds' from 'RSpectra'
vel MERFISH velocity subset
veloviz veloviz