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msarc (version 1.3.2)

msarc-package: msarc: Mass Spectrometry Experiment Plots

Description

Plots the results of mass spectrometry experiments in a circular format. Lines represent identified proteins, with the length of the line indicating the relevant score, typically the likelihood that the ID is correct, or change relative to some reference. Proteins are clustered by GO categories.

Arguments

Details

There are several steps to generating mass spec plots:
  1. Load the mass spec result file into R;
  2. Subtract the proteins that also occur in the control sample;
  3. Cluster the proteins into GO categories;
  4. Filter the list of categories to be shown;
  5. Plot the results.
These steps are largely independent; any one may be replaced with a different function, with some work. For example, the default clustering is according to Gene Ontology terms, but another clustering is also fine. Similarly, although the package is designed for mass spec experiments, it could in principle be used with other sorts of data, provided that it is based on Uniprot IDs, corresponding protein symbols (e.g. CTCF), and some sort of score.

The output format is svg (scalable vector graphics), suitable for editing with Adobe Illustrator or similar.

Please be aware that this program does not produce finished, polished figures. They usually need some editing to look right. Also, a few iterations are usually needed to decide exactly which GO terms are most meaningful (at the step where you manually select the set of interest).

Caveat: These plots mis-represent the clustering into GO categories. Most proteins are in more than one category; most GO categories have more than one parent. These plots do not reflect this, but instead show any given protein in only one category (the one with fewest members in this plot), and any given GO category under only one parent (the one with fewest...).

References

This package was inspired in part by the Circos package http://circos.ca/, by Martin Krzywinski (Martin I Krzywinski, Jacqueline E Schein, Inanc Birol, Joseph Connors, Randy Gascoyne, Doug Horsman, Steven J Jones, and Marco A Marra, "Circos: An information aesthetic for comparative genomics". Genome Research 19 (2000), pages 1639--1645).