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run-plot-recal.md

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Plotting recalibration results

This describes how to install the software needed to create plots using the R script plot-recal.R script, and how to run this script. This script can only be used with search results of Comet.

Note: plot-recal.R is purely used for visualisation and thus not an "official" part of mzRecal. We can offer no support in using this script. The procedure described here was tested with R version 4.1.0 and BioConductor version 3.14.

Installation

Note: installation must be executed with root (Linux)/ Administrator (Windows) privileges.

  • Install R from https://cran.r-project.org/
  • Start R: 
    cd "\Program Files\R\R-4.1.0"
R
  • Install standard R packages, install BioConductor and install MSnbase. From the R command prompt: 
    install.packages(c("stringr", "futile.logger", "optparse", "ggplot2", "gridExtra"))
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.14")
BiocManager::install("MSnbase")

Execution

After the above software is installed, plots can be generated by running from the command prompt:

Rscript plot-recal.R -e 0.01 -m 10 --outfile=recalplot --name="Plot of mRecal results" orig.mzid recalibrated.mzid

Where option -e is the cutoff value for the Comet expect score and option -m is the maximum ppm error included in the plot, and the final arguments are the mzID file of the original and recalibrated data.