Visualize gene expression on UMAP — exprUMAP • scMiko

Visualize gene expression on UMAP. Wrapper for Nebulosa::plot_density() and scMiko::scExpression.UMAP() functions.

exprUMAP(
  object,
  feature,
  plot.subtitle = NULL,
  do.neb = F,
  title.size = 10,
  slot = "data",
  assay = DefaultAssay(object),
  reduction = "umap",
  size = autoPointSize(ncol(object)),
  scale.color = "tomato",
  ...
)

Arguments

object: Seurat object.
feature: feature name.
plot.subtitle: Plot title.
do.neb: Logical to use Nebulosa::plot_density instead of scMiko::scExpression.UMAP. Default is F.
title.size: Size of plot title. Default is 10.
slot: which slot to pull from? Default is "data".
assay: assay to retrieve data from.
reduction: reduction name. Default is "umap".
size: point size for plots.
scale.color: color of scale. Default is "tomato".
...: additional parameters passed to scExpression.UMAP (do.neb = F) or plot_density (do.neb = T)

Value

ggplot handle

Examples


 gg.plot <-  exprUMAP(object = so, feature = "Prrx1")
#> Error in DefaultAssay(object): object 'so' not found