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 |