featureGradient.Rd
Visualize feature activity/expression gradient overlaid on UMAP
featureGradient(
object,
feature,
umap.key = "umap",
min.quantile.cutoff = 0.025,
max.quantile.cutoff = 0.975,
arrow.color = "black",
arrow.size = 1
)
Seurat object.
scaling constant used to determine optimal point size.
name of UMAP reduction. Default is "umap". Requires that UMAP embedding was calculated using Seurat::RunUMAP() prior to running scMiko::featureGradient().
upper quantile threshold at which values are winsorized. Default is 0.975
lower quantile threshold at which values are winsorized. Default is 0.025
gradient arrow color. Default is "black".
gradient arrow size Default is 1.
ggplot handle
gg.plot <- featureGradient(object = so, feature = "S.Score")
#> Error in data.frame(object@reductions[[umap.key]]@cell.embeddings): object 'so' not found