docs/functions/plot.probabilities.md

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

plot.probabilities

Plot the probabilities of a SPEAR model.

Description

Plot the probabilities of a SPEAR model.

Usage

list(list("plot"), list("probabilities"))(
  prob.type = "joint",
  plot.type = "heatmap",
  factors = NULL,
  datasets = NULL,
  cluster = FALSE,
  dendrogram.scale = 1,
  force.dendrogram = FALSE,
  show.all.names = FALSE,
  abbrev.names = TRUE,
  log.probabilities = TRUE,
  dark = FALSE
)

Arguments

Argument |Description ------------- |---------------- prob.type | Which probabilities to plot? Can be "joint" (default), "nonzero", "marginal", or "projection" plot.type | Which type of plot? Defaults to "heatmap". (currently working on other plot.types) factors | Which factors to return features for? Accepts integers (i.e. factors = c(1,2,4) or factors = 1) Defaults to NULL (all). datasets | Which datasets? Check names via names(SPEARobject$data$train$Xlist). Defaults to NULL (all) cluster | Should features be clustered? Defaults to FALSE dendrogram.scale | How large should the dendrogram from cluster be compared to each factor? Defaults to 1 (make > 1 for larger dendrogram). force.dendrogram | Should the dendrogram be plotted even if there are over 2000 features? Defaults to FALSE show.all.names | Should all feature names be shown? Defaults to FALSE (if num.features > 100, can be very crowded). abbrev.names | Should feature names be abbreviated to 20 characters? Defaults to TRUE log.probabilities | Should the probabilites return the -log10(probabilities)? Defaults to TRUE dark | Use dark theme? Defaults to FALSE

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