buildVeloviz: Creates VeloViz graph and FDG layout from PC scores of...

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

Creates VeloViz graph and FDG layout from PC scores of current and projected transcriptional states.

Description

Creates VeloViz graph and FDG layout from PC scores of current and projected transcriptional states.

Usage

buildVeloviz(
  curr,
  proj,
  normalize.depth = TRUE,
  depth = 1e+06,
  use.ods.genes = TRUE,
  max.ods.genes = 2000,
  alpha = 0.05,
  pca = TRUE,
  center = TRUE,
  scale = TRUE,
  nPCs = 10,
  k = 10,
  similarity.threshold = 0,
  distance.weight = 1,
  distance.threshold = 1,
  weighted = TRUE,
  remove.unconnected = TRUE,
  verbose = FALSE,
  details = FALSE
)

Arguments

curr	Genes (rows) x cells (columns) matrix of observed current transcriptional state
proj	Genes (rows) x cells (columns) matrix of predicted future transcriptional state
normalize.depth	logical to normalize raw counts to counts per million, default = TRUE
depth	Depth scaling, default = 1e6 for counts per million (CPM)
use.ods.genes	Use only overdispersed genes to create VeloViz graph, default = TRUE
max.ods.genes	number of most highly expressed overdispersed genes to use to create VeloViz graph, default = 2000
alpha	Significance threshold for overdispersed genes, default = 0.05
pca	logical to use PC scores to create VeloViz graph, default = TRUE. FALSE = use gene expression to create VeloViz graph
center	logical to mean center gene expression before PCA, default = TRUE
scale	logical to scale gene expression variance before PCA, default = TRUE
nPCs	number of principal components to use to create VeloViz graph, default = 10
k	Number of nearest neighbors to assign each cell
similarity.threshold	similarity threshold below which to remove edges, default = -1 i.e. no edges removed
distance.weight	Weight of distance component of composite distance, default = 1
distance.threshold	quantile threshold for distance component above which to remove edges, default = 1 i.e. no edges removed
weighted	logical indicating whether to compute VeloViz edges based on composite distance, default = TRUE. FALSE = all edges are of equal weight
remove.unconnected	logical indicating whether to remove cells with no edges in the VeloViz graph from the output embedding, default = TRUE (removed)
verbose	logical for verbosity setting, default = FALSE
details	logical to return detailed data frame or names of genes, default = FALSE

Value

graph igraph object of VeloViz graph

fdg_coords cells (rows) x 2 coordinates of force-directed layout of VeloViz graph

projectedNeighbors output of projectedNeighbors

See Also

projectedNeighbors

Examples

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

buildVeloviz(curr = curr, proj = proj, normalize.depth = TRUE,
use.ods.genes = TRUE, alpha = 0.05, pca = TRUE, nPCs = 20, center = TRUE,
scale = TRUE, k = 5, similarity.threshold = 0.25, distance.weight = 1,
distance.threshold = 0.5, weighted = TRUE, verbose = FALSE)

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