buildVeloviz {veloviz} | R Documentation

## 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)

[Package veloviz version 1.0.0 Index]