plotTerms: Plot relevance for all terms

Description Usage Arguments Value Examples

View source: R/plotting.R

Description

Plot relevance for all terms

Usage

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plotTerms(object, terms = NULL, order_terms = TRUE, mad_filter = 0.2,
  annotated = TRUE, unannotated_dense = TRUE, unannotated_sparse = FALSE)

Arguments

object

an object of class Rcpp_SlalomModel

terms

integer or character vector, providing either indices for desired terms (if an integer) or the term names (if character); default is NULL, in which case all terms are plotted.

order_terms

logical(1), should factors be ordered by relevance ( TRUE, default), or in the order the come

mad_filter

numeric(1), filter factors by this mean absolute deviation to exclude outliers. For large datasets this can be set close to 0; default is 0.2.

annotated

logical(1), should annotated factors be plotted? Default is TRUE

unannotated_dense

logical(1), should dense unannotated factors be plotted? Default is TRUE

unannotated_sparse

logical(1), should sparse unannotated factors be plotted? Default is TRUE

Value

a ggplot plot object

Examples

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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)
plotTerms(model)

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