This repo tracks the work of integrating networks (pathway models) with ptm data. This includes data-driven visualization of phosphorylation sites on proteins in networks, visualization of phosphoproteomics data on manually curated phosphorylation sites, and utility scripts for related tasks.
The RShiny tool is designed as an interactive tool where users can visualize data on relevant phospho sites on pathways. Phospho sites can be visualized in multiple ways: an oval PTM node offset from the parent node for each phospho site, or as a pie chart offset from the node visualizing all phospho sites. The user can choose to visualize all sites in the data, or restrict the sites added based on various methods/data (relevant kinases/phosphatase on the pathway, pan-cancer PROGENy data, inhibitor data).
This app is designed to:
- Import and preprocess data: Load phosphoproteomics, proteomics, PROGENy, kinase–substrate, and BioMart mapping files.
- Connect to Cytoscape: Ensure Cytoscape is running, and use RCy3 to import pathways and update network layouts.
- Visualize PTM data, two visualization modes:
- Traditional PTM: Places up to four PTM nodes around each parent protein node.
- Pie Chart: Creates one pie chart visualization of multiple phospho sites per parent protein node.
Install Cytoscape. (See https://cytoscape.org/download.html) Install R Studio. (See https://posit.co/download/rstudio-desktop/)
- Launch Cytoscape on your local machine.
- Then launch the Shiny App:
- Run the R script containing the app code in R or RStudio.
- The app will open in your default web browser.
Example script showing how to do data visualization of proteomics and phosphoproteomics on WikiPathways with manually annotated PTM sites.
Extract all manually annotated PTMs in WikiPathways.