docs/functions/plot.feature.expression.md

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

plot.feature.expression

Plot feature expression from a SPEARobject.

Description

Plot feature expression from a SPEARobject.

Usage

list(list("plot"), list("feature.expression"))(
  factor = 1,
  datasets = NULL,
  order.by.factor.score = TRUE,
  order.by.sign = TRUE,
  show.factor.scores = TRUE,
  data = "train",
  cv = FALSE,
  rank = "probability",
  coefficient.cutoff = 0,
  probability.cutoff = 0.95,
  upper.cap = NULL,
  show.top.n = 50,
  show.all.names = FALSE,
  abbrev.names = TRUE,
  dark = 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) order.by.factor.score | Order the samples by factor score? Defaults to TRUE order.by.sign | Order the samples by projection.coefficient sign? Defaults to TRUE show.factor.scores | Should the factor scores be plotted on top of the heatmap? Defaults to TRUE data | Which data? Defaults to "train". cv | Use CV factor scores 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 upper.cap | Cap the expression at a particular magnitude? Set as an integer. Useful if there are any large outliers. Defaults to NULL 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. dark | Use dark theme? Defaults to TRUE plot.by.dataset | Should the features be separated by dataset? Defaults to TRUE

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