featureGradient: Visualize feature activity/expression gradient overlaid on...

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

Visualize feature activity/expression gradient overlaid on UMAP

Description

Visualize feature activity/expression gradient overlaid on UMAP

Usage

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")

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.