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

## Documentation for package ‘veloviz’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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