plot.fdr_table: S3 plot function for results of class "fdr_table" as produced...

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

S3 plot function for results of class "fdr_table" as produced by e.g. the function assess_fdr_overall()

Description

This function created standard plots from results of class "fdr_table" as produced by e.g. the function assess_fdr_overall() visualizig ID numbers in dependence of estimated FDR and also estimated FDR in dependence of m_score cutoff.

Usage

## S3 method for class 'fdr_table'
plot(x, output = "Rconsole", filename = "FDR_report_overall", ...)

Arguments

x	List of class "fdr_table" as produced e.g. by the function assess_fdr_overall() 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 or custom plotting / output.
filename	Basename for output files to be created (if output = "pdf_csv" has been selected).
...	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_overall(data, FFT=0.7, output="Rconsole", plot=FALSE)
 plot(x, output="Rconsole", filename="Assess_fdr_overall_testplot")
 }

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