plot.fdr_cube {SWATH2stats} | R Documentation |
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.
## S3 method for class 'fdr_cube' plot( x, output = "Rconsole", filename = "FDR_report_byrun", plot_mscore_levels = c(0.01, 0.001), ... )
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. |
Plots in Rconsole or report files.
Moritz Heusel
{ 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) }