Project dimensionally-reduced features onto UMAP

Project dimensionally-reduced features (e.g., PC, IC) onto UMAP

projectReduction(
  object,
  reduction = "pca",
  n.components = NA,
  show.n.features = 50,
  pca.min.var.exp = 0.05,
  pca.cum.pca.thresh = 0.8,
  umap.reduction = "umap",
  rel.width = c(2.5, 1),
  size = autoPointSize(ncol(object)),
  ...
)

Arguments

object

Seurat Object

reduction

Character specifying reduction key. Default: "pca"

n.components

Numeric. Number of top components to project.

show.n.features

Numeric. Show top n features alongside projection. Default is 50.

pca.min.var.exp

Threshold for minimum variance explained by principal component.

pca.cum.pca.thresh

Threshold for maximum cumulative variance explained by principal component.

umap.reduction

Character specifying reduction key for umap coordinates.

rel.width

Relative widths of umap and top feature plots. Default: c(2.5,1)

...

additional parameters passed to geom_point(). Generally used to specify point size.

Value

list of ggplot handles

Author

Nicholas Mikolajewicz