plot scvelo

run scvelo on a gene or transcript level object

plot_scvelo(
  object,
  mode = c("steady_state", "deterministic", "stochastic", "dynamical"),
  embedding = c("UMAP", "PCA", "TSNE"),
  ...
)

Arguments

object

a object

mode

deterministic, stochastic, or dynamical

embedding

UMAP, PCA or TSNE

...

extra args passed to run_scvelo

Value

a SingleCellExperiment object with velocity calculated

Examples

chevreul_sce <- chevreuldata::human_gene_transcript_sce()
#> see ?chevreuldata and browseVignettes('chevreuldata') for documentation
#> loading from cache
plot_scvelo(chevreul_sce, embedding = "UMAP", color_by = "velocity_pseudotime")
#> Error in value[[3L]](cond): invalid subscript 'e' in 'altExp(<SingleCellExperiment>, type="character", ...)':
#>   'velocity' not in 'altExpNames(<SingleCellExperiment>)'