plot.projection: Show UMAP projection of query on reference map

In carmonalab/ProjecTILs: Reference-based analysis of scRNA-seq data

Show UMAP projection of query on reference map

Description

Plots the UMAP representation of the reference map, together with the projected coordinates of a query dataset.

Usage

## S3 method for class 'projection'
plot(
  ref,
  query = NULL,
  labels.col = "functional.cluster",
  cols = NULL,
  linesize = 1,
  pointsize = 1,
  ref.alpha = 0.3,
  ref.size = NULL,
  ...
)

Arguments

ref	Reference object
query	Seurat object with query data
labels.col	The metadata field to annotate the clusters (default: functional.cluster)
cols	Custom color palette for clusters
linesize	Contour line thickness for projected query
pointsize	Point size for cells in projected query
ref.alpha	Transparency parameter for reference cells
ref.size	Adjust point size for reference cells
...	Additional parameters for DimPlot, e.g. raster=T to limit image size

Value

UMAP plot of reference map with projected query set in the same space

Examples

data(query_example_seurat)
ref <- load.reference.map()
q <- Run.ProjecTILs(query_example_seurat, ref=ref, fast.umap.predict=TRUE)
plot.projection(ref=ref, query=q)

carmonalab/ProjecTILs documentation built on April 13, 2025, 10:04 p.m.