Plot functionality 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

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## 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).

...

further arguments passed to method.

Value

Plots in Rconsole or report files.

Author(s)

Moritz Heusel

Examples

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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.fdr_table(x, output = "pdf_csv", filename = "Assess_fdr_overall_testplot")

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