asNNGraph: Function to produce idx and dist representation of a VeloViz...

In JEFworks-Lab/veloviz: VeloViz: RNA-velocity informed 2D embeddings for visualizing cell state trajectories

Function to produce idx and dist representation of a VeloViz graph

Description

Function to produce idx and dist representation of a VeloViz graph

Usage

asNNGraph(vig)

Arguments

vig	output of buildVeloviz

Value

idx numVertices x numNeighbors matrix, where each row i contains indices of vertex i's neighbors

dist numVertices x numNeighbors matrix, where each row i contains distances from vertex i to its neighbors

Examples

data(vel)
curr <- vel$current
proj <- vel$projected

vv <- buildVeloviz(curr = curr, proj = proj, normalize.depth = TRUE,
use.ods.genes = FALSE, alpha = 0.05, pca = TRUE, nPCs = 3, center = TRUE,
scale = TRUE, k = 10, similarity.threshold = -1, distance.weight = 1,
distance.threshold = 1, weighted = TRUE, verbose = FALSE)

asNNGraph(vv)

JEFworks-Lab/veloviz documentation built on Sept. 14, 2022, 4:03 p.m.