Make an MAPlot from EZbakR comparison
EZMAPlot.Rd
Make an MAPlot from EZbakR comparison
Usage
EZMAPlot(
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 anEZbakRData
object on which you have runCompareParameters
- 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 todesign_factor
ifdesign_factor
is not already specified.- exactMatch
If TRUE, then
features
andpopulations
have to exactly match those for a given fractions table for that table to be used. Means that you can't specify a subset of features or populations 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.
- 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.