docs/functions/plot.features.md

In jgygi/SPEAR: SPEAR - Sparse Supervised Bayesian Factor Model for Multi-omic Analyses

plot.features

Plot features from a SPEARobject.

Description

Plot features from a SPEARobject.

Usage

list(list("plot"), list("features"))(
  factor = 1,
  datasets = NULL,
  rank = "probability",
  coefficient.cutoff = 0,
  probability.cutoff = 0.95,
  plot.by.dataset = TRUE,
  show.top.n = 50,
  show.all.names = FALSE,
  abbrev.names = TRUE
)

Arguments

Argument |Description ------------- |---------------- factor | Which factor to return features for? Accepts a single integer or factors = 1) Defaults to 1 (factor 1). datasets | Which datasets? Check names via names(SPEARobject$data$train$Xlist). Defaults to NULL (all) rank | How to rank features? Defaults to "probability" (joint.probability) followed by projection.coefficient. Can also be "coefficient" (only projection.coefficient magnitude). coefficient.cutoff | What projection.coefficient value to use as the cutoff? Defaults to 0 probability.cutoff | What joint.probability value to use as the cutoff? Defaults to .95 plot.by.dataset | Should the features be separated by dataset? Defaults to TRUE show.top.n | Stop showing features after the top stop.by.n features. Defaults to 50. Set to a number higher than the total number of features to plot all of them. show.all.names | Should all feature names be shown? Defaults to FALSE (if num.features > 100, can be very crowded). abbrev.names | Abbreviate long feature names to 20 characters? Defaults to TRUE.

jgygi/SPEAR documentation built on July 5, 2023, 5:35 p.m.