plot.fdr_cube {SWATH2stats} | R Documentation

## 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)
     }

[Package SWATH2stats version 1.20.1 Index]