plot.fdr_cube: S3 plot function for FDR assessment result arrays

In peterblattmann/SWATH2stats: Transform and Filter SWATH Data for Statistical Packages

S3 plot function for FDR assessment result arrays

Description

This function creates standard plots from result arrays as produced by e.g. the function assess_fdr_byrun(), visualizig assay, peptide and protein level FDR for each run at m-score cutoffs 1e-2 and 1e-3. Furthermore, Target and Decoy ID numbers are visualized.

Usage

## S3 method for class 'fdr_cube'
plot(
  x,
  output = "Rconsole",
  filename = "FDR_report_byrun",
  plot_mscore_levels = c(0.01, 0.001),
  ...
)

Arguments

x	Array of by-run FDR assessment results as produced e.g. by the function assess_fdr_byrun() from this package.
output	Choose output type. "pdf_csv" creates the output as files in the working directory, "Rconsole" triggers delivery of the output to the console enabling further computation and/or custom plotting / output.
filename	Basename for output files to be created (if output = "pdf_csv" has been selected).
plot_mscore_levels	Define m-score levels to plot the estimated FDR results.
...	Extra arguments passed on to functions inside this.

Value

Plots in Rconsole or report files.

Author(s)

Moritz Heusel

Examples

{
 data("OpenSWATH_data", package="SWATH2stats")
 data("Study_design", package="SWATH2stats")
 data <- sample_annotation(OpenSWATH_data, Study_design)
 x <- assess_fdr_byrun(data, FFT=0.7, output="Rconsole", plot=FALSE)
 retlist <- plot(x, output="Rconsole", filename="Assess_fdr_byrun_testplot",
                          plot_mscore_levels=0.01)
 }

peterblattmann/SWATH2stats documentation built on July 2, 2023, 9:42 p.m.