NonLinearEmbeddingMatrix: NonLinearEmbeddingMatrix class

In sa-lee/sneezy: Interactively explore non-linear projections like t-SNE

Description

The NonLinearEmbeddingMatrix class is used for storing low-dimensional embeddings from non-linear dimensionality reduction techniques.

Usage

NonLinearEmbeddingMatrix(sampleFactors = matrix(nrow = 0, ncol = 0),
  featureLoadings = matrix(nrow = 0, ncol = 0), factorData = NULL,
  metadata = list(), param)

Arguments

sampleFactors	A matrix-like object of sample embeddings, where rows are samples and columns are factors.
featureLoadings	A matrix-like object of feature loadings, where rows are features and columns are factors.
factorData	A DataFrame containing factor-level information, with one row per factor.
metadata	An optional list of arbitrary content describing the overall experiment.
param	An NonLinearEmbeddingParam object

Details

The NonLinearEmbeddingMatrix class inherits from SingleCellExperiment::LinearEmbeddingMatrix() and is designed to be stored inside a TourExperiment() object. It gains an additional slot, storing NonLinearEmbeddingParam-class object, allowing us to maintain the arguments used to generate the embedding matrix. This is useful for running diagnostics over the same parameter set.

See Also

SingleCellExperiment::LinearEmbeddingMatrix()

sa-lee/sneezy documentation built on Nov. 25, 2019, 12:38 p.m.