Run TSNE — run_tsne • scooter

The default method runs Rtsne::Rtsne() on a matrix; the Seurat method runs Seurat::RunTSNE() on the object and stores a "tsne<suffix>" reduction.

Usage

run_tsne(x, ...)

# Default S3 method
run_tsne(x, seed.use = 1, dim.embed = 2, suffix = "", ...)

# S3 method for class 'Seurat'
run_tsne(
  x,
  seed.use = 1,
  dim.embed = 2,
  suffix = "",
  assay = "RNA",
  reduction = NULL,
  num_dim = NULL,
  features = NULL,
  var_features = FALSE,
  file_format = c("png", "pdf"),
  ...
)

Arguments

x: A matrix (default) or a Seurat object.
...: Passed to the underlying function.
seed.use: Seed to use.
dim.embed: Number of tSNE embeddings to return.
suffix: Tag inserted into the reduction/column names.
assay: Assay to use (Seurat method). Always set explicitly.
reduction: Existing reduction to take dimensions from (Seurat method).
num_dim: Number of dimensions to take from reduction (Seurat method).
features: Explicit features to use (Seurat method).
var_features: Use the assay's variable features (Seurat method).
file_format: File formats to write the scatter plot in (Seurat method).

Value

A tSNE embedding matrix (default) or a Seurat object with the reduction added. The Seurat method also writes a sample-colored scatter of the result to the working directory, as dr.<reduction>.png/.pdf (or just .png if file_format = "png").