plotVeloviz {veloviz} | R Documentation

## 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)

[Package veloviz version 1.0.0 Index]