Visualize feature activity/expression gradient overlaid on UMAP

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
)

Arguments

object

Seurat object.

feature

scaling constant used to determine optimal point size.

umap.key

name of UMAP reduction. Default is "umap". Requires that UMAP embedding was calculated using Seurat::RunUMAP() prior to running scMiko::featureGradient().

min.quantile.cutoff

upper quantile threshold at which values are winsorized. Default is 0.975

max.quantile.cutoff

lower quantile threshold at which values are winsorized. Default is 0.025

arrow.color

gradient arrow color. Default is "black".

arrow.size

gradient arrow size Default is 1.

Value

ggplot handle

Examples

 gg.plot <-  featureGradient(object = so, feature = "S.Score")
#> Error in data.frame(object@reductions[[umap.key]]@cell.embeddings): object 'so' not found