plot.fdr_cube {SWATH2stats} | R Documentation

## Plot functionality for FDR assessment result arrays as produced by e.g. the function assess_fdr_byrun()

### 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.
`...` | further arguments passed to method.

### 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)
    plot.fdr_cube(x, output = "pdf_csv", filename = "Assess_fdr_byrun_testplot",
    plot_mscore_levels=0.01)

[Package SWATH2stats version 1.17.5 Index]