runReduction: Dimensionality reduction

In dibbelab/gficf: Gene Frequency - Inverse Cell Frequency

Dimensionality reduction

Description

Run t-SNE or UMAP or t-UMAP dimensionality reduction on selected features from PCA or LSA. See ?umap or ?Rtsne for additional parameter to use.

Usage

runReduction(
  data,
  reduction = "tumap",
  nt = 2,
  seed = 18051982,
  ret_model_pred = T,
  verbose = T,
  ...
)

Arguments

data	list; GFICF object
reduction	characters; Reduction method to use. One of: "tsne" "umap" "tumap" (the default)
nt	integer; Number of thread to use (default 2).
seed	integer; Initial seed to use.
ret_model_pred	boolean; If true, the umap model is retained to be used for prediction.
verbose	boolean; Icrease verbosity.
...	Additional arguments to pass to Rtsne/umap/tumap call.

Value

The updated gficf object.

dibbelab/gficf documentation built on Nov. 2, 2022, 2:28 a.m.