SWATH2stats (version 1.2.3)

plot.fdr_cube: 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

"plot"(x, output = "Rconsole", filename = "FDR_report_byrun", ...)

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).

...

further arguments passed to method.

Value

Plots in Rconsole or report files.

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")