graphViz: Visualize as velocity informed force directed graph

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

Visualize as velocity informed force directed graph

Description

Visualize as velocity informed force directed graph

Usage

graphViz(
  observed,
  projected,
  k,
  distance_metric = "L2",
  similarity_metric = "cosine",
  distance_weight = 1,
  distance_threshold = 1,
  similarity_threshold = -1,
  weighted = TRUE,
  remove_unconnected = TRUE,
  return_graph = FALSE,
  plot = TRUE,
  cell.colors = NA,
  title = NA
)

Arguments

observed	PCs (rows) x cells (columns) matrix of observed transcriptional state projected into PC space
projected	PCs (rows) x cells (columns) matrix of projected transcriptional states. Cell should be in same order as in observed
k	Number of nearest neighbors to assign each cell
distance_metric	Method to compute distance component of composite distance. "L1" or "L2", default = "L2"
similarity_metric	Method to compute similarity between velocity and cell transition matrices. "cosine" or "pearson", default = "cosine"
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
similarity_threshold	similarity threshold below which to remove edges, default = -1 i.e. no edges removed
weighted	if TRUE, assigns edge weights based on composite distance, if FALSE assigns equal weights to all edges, default = TRUE
remove_unconnected	if TRUE, does not plot cells with no edges, default = TRUE
return_graph	if TRUE, returns igraph object graph, force-directed layout coordinates fdg_coords, and projected_neighbors object detailing composite distance values and components, default = FALSE
plot	if TRUE, plots graph and force-directed layout
cell.colors	cell.colors to use for plotting
title	title to use for plot

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

m <- log10(curr+1)
pca <- RSpectra::svds(A = Matrix::t(m), k=3,
opts = list(center = FALSE, scale = FALSE, maxitr = 2000, tol = 1e-10))
pca.curr <- Matrix::t(m) %*% pca$v[,1:3]

m <- log10(proj+1)
pca.proj <- Matrix::t(m) %*% pca$v[,1:3]

graphViz(t(pca.curr), t(pca.proj), k=10,
cell.colors=NA, similarity_threshold=-1, distance_weight = 1,
distance_threshold = 1, weighted = TRUE, remove_unconnected = TRUE,
plot = FALSE, return_graph = TRUE)

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