plotIdFDRspace: Plot FDR gridsearch

In CCprofiler/CCprofiler: Complex feature detection using SEC protein chromatograms.

Description

Plot the result of a grid search depending on a specified parameter.

Usage

plotIdFDRspace(grid_search_stats, best_parameters, level = "complex",
  id_level = "TP", FDR_cutoff = 0.1,
  colour_parameter = "min_feature_completeness", PDF = TRUE,
  name = "ID_FDR_plot.pdf")

Arguments

grid_search_stats	Table of grid search statistics (obtained from estimateGridSearchDecoyFDR).
best_parameters	data.table with one row containing the selected parameter set.
level	Character string, either 'complex' or 'protein'. Specifies which feature finding was performed. Defaults to 'complex'.
id_level	Character string, either 'TP' or 'P'. Plot with true-positive numbers or all positives as y axis. Defaults to 'TP'
FDR_cutoff	Numeric, the cutoff for the FDR (indicated by a vertical line in the plot). Defaults to 0.1.
colour_parameter	Character string, Which parameter to color. Defaults to 'completeness_cutoff'
PDF	Logical, wether to save the plot as a PDF file in working directory. Defaults to TRUE.
name	Character string, filename of the PDF output.

Value

Either a plot to the R console or a PDF file in the working directory.

Examples

## NOT RUN
gridStats # see function \code{\link{estimateGridSearchDecoyFDR}} to see how to generate this object.

## Plot the result of the grid search depending on the within feature correlation
plotIdFDRspace(gridStats, PDF = F, colour_parameter = "min_peak_corr")

CCprofiler/CCprofiler documentation built on May 19, 2021, 7:40 p.m.