plot.discriminant.3d: 3D plot of reference map with extra discriminant dimension

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

3D plot of reference map with extra discriminant dimension

Description

Add an extra dimension to the reference map (it can be suggested by 'find.discriminant.dimensions'), to explore additional axes of variability in a query dataset compared to the reference map.

Usage

## S3 method for class 'discriminant.3d'
plot(
  ref,
  query,
  query.control = NULL,
  query.assay = "RNA",
  labels.col = "functional.cluster",
  extra.dim = "ICA_1",
  query.state = NULL
)

Arguments

ref	Seurat object with reference object
query	Seurat object with query data
query.control	Optionally, you can compare your query with a control sample, instead of the reference
query.assay	The data slot to be used for enrichment analysis
labels.col	The metadata field used to annotate the clusters
extra.dim	The additional dimension to be added on the z-axis of the plot. Can be either: An ICA or PCA dimension (e.g. ICA_10). See 'find.discriminant.dimensions' Any numeric metadata field associated to the cells (e.g. 'cycling.score')
query.state	Only plot the query cells from this specific state

Value

A three dimensional plot with UMAP_1 and UMAP_2 on the x and y axis respectively, and the specified 'extra.dim' on the z-axis.

Examples

plot.discriminant.3d(ref, query=query, extra.dim="ICA_19")
plot.discriminant.3d(ref, query=treated.set, query.control=control.set, extra.dim="ICA_2")

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