EmbedSWNE: Embeds NMF factors and samples in 2 dimensions

In yanwu2014/swne: Similarity Weighted Nonnegative Embedding: A method for visualizing high dimensional datasets

Embeds NMF factors and samples in 2 dimensions

Description

Embeds NMF factors and samples in 2 dimensions

Usage

EmbedSWNE(
  H,
  SNN = NULL,
  alpha.exp = 1,
  snn.exp = 1,
  n_pull = NULL,
  proj.method = "sammon",
  dist.use = "cosine",
  snn.factor.proj = T
)

Arguments

H	NMF factors (factors x samples)
SNN	Shared nearest neighbors matrix (or other similarity matrix)
alpha.exp	Increasing alpha.exp increases how much the NMF factors "pull" the samples
snn.exp	Decreasing snn.exp increases the effect of the similarity matrix on the embedding
n_pull	Number of factors pulling on each sample. Must be >= 3
proj.method	Method to use for projecting factors. Currently only supports "sammon"
dist.use	Similarity function to use for calculating factor positions. Options include pearson (correlation), IC (mutual information), cosine, euclidean.

Value

A list of factor (H.coords) and sample coordinates (sample.coords) in 2D

yanwu2014/swne documentation built on Aug. 5, 2023, 4:42 a.m.