EmbedGenesets: Embeds genesets relative to factor coordinates

Description Usage Arguments Value

View source: R/swne_plotting.R

Description

Embeds genesets relative to factor coordinates

Usage

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EmbedGenesets(swne.embedding, feature.assoc, genesets.embed,
  alpha.exp = 1, n_pull = NULL, scale.cols = T, overwrite = F)

Arguments

swne.embedding

Existing swne embedding from EmbedSWNE

feature.assoc

Feature loadings or correlations (features x factors)

genesets.embed

Genesets to embed (in the form of a named list of genes)

alpha.exp

Increasing alpha.exp increases how much the factors "pull" the features

n_pull

Number of factors pulling on each feature. Must be >= 3

scale.cols

Whether or not to scale the input columns to 0 - 1

overwrite

Whether or not to overwrite any existing feature embedding

Value

swne.embedding with updated feature coordinates (feature.coords)


yanwu2014/swne documentation built on Dec. 14, 2018, 3:07 p.m.