plotLoadings: Plot highest loadings of a factor

In slalom: Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data

Description

Plot highest loadings of a factor

Usage

plotLoadings(object, term, n_genes = 10)

Arguments

object	an object of class Rcpp_SlalomModel
term	integer(1) or character(1), providing either index for desired term (if an integer) or the term name (if character)
n_genes	integer(1), number of loadings (genes) to show

Details

Show the factor loadings for a genes with the highest loadings for a given factor. Absolute weights are shown, with genes ordered by absolute weight. Indications are given on the plot as to whether the gene was originally in the factor geneset or added to it by the slalom model.

Value

a ggplot plot object

Examples

gmtfile <- system.file("extdata", "reactome_subset.gmt", package = "slalom")
genesets <- GSEABase::getGmt(gmtfile)
data("mesc")
model <- newSlalomModel(mesc, genesets, n_hidden = 5, min_genes = 10)
model <- initSlalom(model)
model <- trainSlalom(model, nIterations = 10)
plotLoadings(model, term = 2)

slalom documentation built on Nov. 8, 2020, 5:24 p.m.