docs/functions/plot.factor.scores.md

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

plot.factor.scores

Plot factor scores from a SPEARobject for a particular dataset data.

Description

Plot factor scores from a SPEARobject for a particular dataset data.

Usage

list(list("plot"), list("factor.scores"))(
  data = "train",
  cv = FALSE,
  group = "response",
  factors = NULL,
  plot.type = "violin",
  show.legend = FALSE
)

Arguments

Argument |Description ------------- |---------------- data | Which dataset to use? Can be any dataset listed under $data$____. Defaults to "train". cv | If data = "train", get factor scores generated from $run.cv.spear? If $run.spear was used or if data != "train" this parameter is ignored. Defaults to FALSE. NOTE: There is an element of randomness if the factor scores are not correlated with the response, so it is recomended to view the factor scores with cv = FALSE group | What to plot on the x.axis? Defaults to "response" (indicated by $options$current.response.idx), but can be any feature name found in colnames(SPEARobj$data$train$X) factors | Which factors to show? Defaults to NULL (all factors). Use a vector of integers (i.e. c(1, 2, 4)) to specify fewer factors. plot.type | Which type of plot (for ordinal, binomial, and multinomial families)? Can be "violin" (default) or "boxplot". Ignored if family == "gaussian". show.legend | Show the legend of the plot (for group)? Defaults to FALSE

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