plotVeloviz: Plot function

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

Plot function

Description

Plot function

Usage

plotVeloviz(
  vig,
  layout.method = igraph::layout_with_fr,
  clusters = NA,
  cluster.method = igraph::cluster_louvain,
  col = NA,
  alpha = 0.05,
  verbose = TRUE
)

Arguments

vig	output of buildVeloviz
layout.method	igraph method to use for generating 2D graph representation, default = igraph::layout_with_fr
clusters	cluster annotations for cells in data
cluster.method	igraph method to use for clustering if clusters are not provided, default = igraph::cluster_louvain
col	colors to use for plotting
alpha	transparency for plotting graph nodes
verbose	logical for verbosity setting, default = FALSE

Value

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

Examples

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

vv <- 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)

plotVeloviz(vv)

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