plotTerms {slalom} | R Documentation |
Plot relevance for all terms
plotTerms(object, terms = NULL, order_terms = TRUE, mad_filter = 0.2, annotated = TRUE, unannotated_dense = TRUE, unannotated_sparse = FALSE)
object |
an object of class |
terms |
integer or character vector, providing either indices for
desired terms (if an integer) or the term names (if character); default is
|
order_terms |
logical(1), should factors be ordered by relevance (
|
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 |
annotated |
logical(1), should annotated factors be plotted? Default is
|
unannotated_dense |
logical(1), should dense unannotated factors be
plotted? Default is |
unannotated_sparse |
logical(1), should sparse unannotated factors be
plotted? Default is |
a ggplot plot object
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)