PrIntMap-R

A shiny app for viewing protein coverage in a quantitative manner

Champion Lab
University of Notre Dame
By Simon D. Weaver and Christine M. DeRosa

Protein Intensity Mapper

Online version can be found hosted on shiny apps:

https://championlab.shinyapps.io/printmap-r/

Latest Release can be found at Zenodo:

To run locally in R:

• Download and install R and optionally (but encouraged), RStudio.
• Either clone this directory, use the latest release from Zenodo (above), or download a zip file containing the contents of this repository by navigating to https://github.com/Champion-Lab/PrIntMap-R/zipball/master. If necessary, unzip this file. The location of this on your local computer is the 'App directory'.
• Open R (or RStudio if installed).
• Ensure that the shiny package is loaded by running install.packages("shiny") and active library(shiny) in the R console.
• Ensure that all of the packages you need are installed on your computer. The required packages can be found in 'global.R'. You can either install them manually, or run this code in the R console:

  install.packages(c("stringr", "ggplot2", "seqinr", "plotly", "scales", "dplyr", "tidyr", "shinycssloaders", "markdown", "data.table", "readr", "purrr", "shinyBS", "shinyWidgets", "shinyjs"))

• Change your working directory to the path of the cloned or downloaded app directory setwd('path/to/directory')
• In Rstudio, open either 'ui.R' or 'Server.R'.
• A 'Run App' button should appear in the top right of the '.R' file that you just opened. Click this to start a local version of the app.
• Alternatively, you can launch the app directly from the R console: runApp("path/to/appDirectory"). If you already set the working directory to this path, you can simply run: runApp().
• If there are errors, you may not have all the correct packages installed. Open the 'global.R' file and ensure that all the packages used are in your 'packages' tab.

Alternative Method to run locally:

• After following the instructions above to install R and all required packages (including shiny), simply execute this line: runGitHub("Champion-Lab/PrIntMap-R") in the R console.
• This will re-download the github version of the app each time it is run, so is not an efficient way to use the app repeatedly, but will work for easy testing and quick use.

Errors that occur when trying to run the app locally are almost always due to old versons of R, or the installed packages. To troubleshoot, install the most recent version of R, as well as the most recent version of all the packages referenced above.

PrIntMap-R has been tested and optimized on Windows and MacOS. The app also runs on linux, although it has not been optimized. Some versions of linux may open a new tab every time a plot is updated, making use impractical. If you experience this, try one of the following solutions:

• Run PrIntMap-R on the online version
• Run PrIntMap-R on Windows or MacOS
• Run PrIntMap-R using Ubuntu locally on a virtual machine

If you use PrIntMap-R, please cite:
Weaver, SD., DeRosa, CM., Schultz, SR., Champion, MM. (2023). “PrIntMap-R: an online application for intra-protein intensity and peptide visualization in bottom-up proteomics” Journal of Proteome Research. DOI: 10.1021/acs.jproteome.2c00606