make.reference: Make a ProjecTILs reference

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

Make a ProjecTILs reference

Description

Converts a Seurat object to a ProjecTILs reference atlas. You can preserve your low-dimensionality embeddings (e.g. UMAP) in the reference atlas by setting 'recalculate.umap=FALSE', or recalculate the UMAP using one of the two methods (umap::umap or uwot::umap). Recalculation allows exploting the 'predict' functionalities of these methods for embedding of new points; skipping recalculation will make the projection use an approximation for UMAP embedding of the query.

Usage

make.reference(
  ref,
  assay = NULL,
  assay.raw = "RNA",
  atlas.name = "custom_reference",
  annotation.column = "functional.cluster",
  recalculate.umap = FALSE,
  umap.method = c("umap", "uwot"),
  metric = "cosine",
  min_dist = 0.3,
  n_neighbors = 30,
  ndim = 20,
  dimred = "umap",
  nfeatures = 1000,
  color.palette = NULL,
  scGate.model.human = NULL,
  scGate.model.mouse = NULL,
  store.markers = FALSE,
  n.markers = 10,
  seed = 123,
  layer1_link = NULL
)

Arguments

ref	Seurat object with reference atlas
assay	The assay storing the reference expression data (e.g. "integrated")
assay.raw	The assay storing raw expression data (e.g. "RNA")
atlas.name	An optional name for your reference
annotation.column	The metadata column with the cluster annotations for this atlas
recalculate.umap	If TRUE, run the 'umap' or 'uwot' algorithm to generate embeddings. Otherwise use the embeddings stored in the 'dimred' slot.
umap.method	Which method to use for calculating the umap reduction
metric	Distance metric to use to find nearest neighbors for UMAP
min_dist	Effective minimum distance between UMAP embedded points
n_neighbors	Size of local neighborhood for UMAP
ndim	Number of PCA dimensions
dimred	Use the pre-calculated embeddings stored at 'Embeddings(ref, dimred)'
nfeatures	Number of variable features (only calculated if not already present)
color.palette	A (named) vector of colors for the reference plotting functions. One color for each cell type in 'functional.cluster'
scGate.model.human	A mouse scGate model to purify the cell types represented in the map.
store.markers	Whether to store the top differentially expressed genes in 'ref@misc$gene.panel'
n.markers	Store the top 'n.markers' for each subtype given by differential expression analysis
seed	Random seed
layer1_link	Broad cell type contained in this reference atlas (i.e. CD4T, CL:0000624...) to link with broad cell type annotation (layer1).

Value

A reference atlas compatible with ProjecTILs

Examples

custom_reference <- ProjecTILs::make.reference(myref, recalculate.umap=T)

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