Make a VolcanoPlot from EZbakR comparison

Usage

EZVolcanoPlot(
  obj,
  parameter = "log_kdeg",
  design_factor = NULL,
  reference = NULL,
  experimental = NULL,
  param_name = NULL,
  param_function = NULL,
  features = NULL,
  condition = NULL,
  exactMatch = TRUE,
  plotlog2 = TRUE,
  FDR_cutoff = 0.05,
  difference_cutoff = 0,
  size = NULL
)

Arguments

obj: An object of class EZbakRCompare, which is an EZbakRData object on which you have run CompareParameters
parameter: Name of parameter whose comparison you want to plot.
design_factor: Name of factor from metadf whose parameter estimates at different factor values you would like to compare.
reference: Name of reference condition factor level value.
experimental: Name of condition factor level value to compare to reference.
param_name: If you want to assess the significance of a single parameter, rather than the comparison of two parameters, specify that one parameter's name here.
param_function: NOT YET IMPLEMENTED. Will allow you to specify more complicated functions of parameters when hypotheses you need to test are combinations of parameters rather than individual parameters or simple differences in two parameters.
features: Character vector of feature names for which comparisons were made.
condition: Defunct parameter that has been replaced with design_factor. If provided gets passed to design_factor if design_factor is not already specified.
exactMatch: If TRUE, then features has to exactly match those for a given comparisons table for that table to be used. Means that you can't specify a subset of features by default, since this is TRUE by default.
plotlog2: If TRUE, assume that log(parameter) difference is passed in and that you want to plot log2(parameter) difference. TO-DO: probably best to change this to a more general scale parameter by which the parameter is multiplied. Default would be log2(exp(1)) to convert log() to log2().
FDR_cutoff: False discovery cutoff by which to color points.
difference_cutoff: Minimum absolute difference cutoff by which to color points.
size: Size of points, passed to geom_point() size parameter. If not specified, a point size is automatically chosen.