Run dimensionality reduction: pca, tsne, or umap

Run dimensionality reduction: pca, tsne, or umap

Usage

run_dr(x, dr_method, suffix = "", assay = "RNA", ...)

Arguments

x

A matrix or a Seurat object.

dr_method

Dimensionality reduction method ("pca", "tsne", or "umap").

suffix

Tag inserted into the reduction name and key.

assay

Assay to use (Seurat methods). Always passed explicitly here rather than left NULL, which would otherwise fall back on whatever DefaultAssay(x) happens to be.

...

Passed to the chosen reduction function.

Value

The reduced data (matrix input) or a Seurat object with the reduction added. For a Seurat object, also writes the diagnostic plot(s) for the chosen method to the working directory: PCA gets a sample-colored scatter and an elbow plot (plus a heatmap past 15 components); tSNE/UMAP get a sample-colored scatter.

Details

run_dr() is a thin dispatcher: it routes to run_pca(), run_tsne(), or run_umap() based on dr_method, forwarding suffix and anything in .... It only carries the parameters common to every method; method-specific ones (num_pcs, num_neighbors, reduction, ...) are passed through ... to the chosen function. Each of those functions is itself generic: a plain matrix takes the .default method (irlba/Rtsne/uwot), a Seurat object takes the .Seurat method (native RunPCA()/RunTSNE()/RunUMAP(), storing a "<method><suffix>" reduction).

See also

run_pca(), run_tsne(), run_umap()