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Bioconductor build status: - Devel: [![Bioconductor devel build Status](]( - Release: [![Bioconductor release build Status](]( Exploring and visualising spatial proteomics data ================================================= <img align = "right" src="" height="200"> ## Introduction The [`pRolocGUI`]( package is an interactive interface to explore and visualise experimental mass spectrometry-based spatial proteomics data. It relies on the [`shiny`]( framework for interactive visualisation, the [`MSnbase`]( package to handle data and metadata and the [`pRoloc`]( software for spatial proteomics specific data matters. Example spatial data is available in the [`pRolocdata`]( experiment package. The `pRoloc` suite set of software are distributed as part of the `R`/[Bioconductor]( project and are developed by Lisa Breckels at the [Cambridge Centre for Proteomics]( at the University of Cambridge and by [Laurent Gatto](, director of the Computational Biology and Bioinformatics (CBIO) group at UCLouvain, in Belgium. This document describes the installation of the software, followed by a basic quick start guide for using `pRolocGUI` to search and visualise spatial proteomics data. Please refer to the respective documentation and vignettes for full details about the software. If you use these open-source software for your research, please cite: > Gatto L, Breckels LM, Wieczorek S, Burger T, Lilley KS. > Mass-spectrometry-based spatial proteomics data analysis using > pRoloc and pRolocdata. Bioinformatics. 2014 May 1;30(9):1322-4. > doi:10.1093/bioinformatics/btu013. Epub 2014 Jan 11. PMID:24413670; > PMCID:PMC3998135. > Breckels LM, Gatto L, Christoforou A, Groen AJ, Lilley KS, Trotter > MW. The effect of organelle discovery upon sub-cellular protein > localisation. J Proteomics. 2013 Mar 21. doi:pii: > S1874-3919(13)00094-8. 10.1016/j.jprot.2013.02.019. PMID:23523639. > Gatto L., Breckels L.M., Burger T, Nightingale D.J.H., Groen A.J., > Campbell C., Mulvey C.M., Christoforou A., Ferro M., Lilley K.S. 'A > foundation for reliable spatial proteomics data analysis' Mol Cell > Proteomics. 2014 May 20. ## Installation `pRolocGUI` is written in the [`R`]( programming language. Before installing the software you need to download `R` and (optionally) `RStudio`. 1) Download the latest `R` release for your operating system from the [R website]( and install it. 2) Optional, but recommended. [Download]( and install the RStudio IDE. `RStudio` provides a good code editor and excellent integration with the `R` terminal. 3) Start `R` or `RStudio`. 4) Install the Bioconductor packages `pRoloc`, `pRolocdata` and `pRolocGUI`: `pRolocGUI` requires `R >= 3.1.1` and Bioconductor version `>= 3.0`. In an `R` console, type ``` if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install(c("pRoloc", "pRolocdata", "pRolocGUI")) ``` #### Development version The development code on github can also be installed using `BiocManager::install` (or `install_github`). New pre-release features might not be documented or thoroughly tested and could substantially change prior to release. Use at your own risks. ``` BiocManager::install("ComputationalProteomicsUnit/pRolocGUI") ``` ## Getting started Before using a package's functionality, it needs to be loaded: ``` library("pRolocGUI") ``` We first load data from [Christoforou et al 2016]( distributed in the `pRolocdata` package: ``` library("pRolocdata") data(hyperLOPIT2015) ``` There are 3 different visualisation applications currently available: `explore`, `compare` and `aggregate`. These apps are launched using the `pRolocVis` function and passing `object`, which is an `MSnSet` containing the data one wishes to interrogate. One may also specify which app they wish to use by using the `app` argument, see `?pRolocVis` for more details. The default app that is loaded if `app` is not specified is the `explore` application: ``` pRolocVis(hyperLOPIT2015) ``` ![Screenshot - PCA]( The graphical interface is described in details in the package vignette that is included in the package itself (get it by typing `vignette("pRolocGUI")` in `R`), available by clicking the `?` once the interface is loaded or can be [consulted online]( ## More resources ### Support * The Bioconductor [support forum]( * Open a `pRolocGUI` GitHub [issue]( (requires a free GitHub account). ### Videos (new videos will appear shortly for the new apps) 0. [An introduction to Bioconductor]( 1. [A brief introduction to `pRolocGUI`]( 2. [Downloading and install `R`]( 3. [Using RStudio]( 4. [Installing the `pRolocGUI` interface]( 5. [Starting `pRolocGUI`]( - This tutorial is for the older legacy applications. New videos will appear shortly for the new applications. 6. [Using `pRolocGUI` to explore and visualise experimental spatial proteomics data]( - This tutorial is for the older legacy applications. New videos will appear shortly for the new applications. Tutorial [playlist]( ### General resources - [Teaching material]( - R and Bioconductor for proteomics [web page]( and [package](