phanstiellab / coralp

Flexible visualization of the human phosphatome

Overview

http://phanstiel-lab.med.unc.edu/coralp/

CoralP is a user-friendly interactive web application for visualizing both quantitative and qualitative data. Qualitative and quantitative features can be represented in branch colors, node colors, and node sizes. Phosphatases can be organized using the published phosphatome tree or as radial or force directed networks. CoralP is simple to use, well documented, and freely available. It is the first and only dedicated tool for phosphatome visualization and is widely applicable to a variety of data types including those generated from proteomic, genomic, epidemiological, and high-throughput screening experiments.

CoralP builds off a Coral, our tool for human kinome visualization which can be found at http://phanstiel-lab.med.unc.edu/CORAL/.

Web App

The CoralP web app can be found at http://phanstiel-lab.med.unc.edu/coralp/.

Running Locally

The easiest way to use CoralP is via the web app linked above. But you can also run it locally if you wish.

Downloading Code

The first step is to download the code. You can do this with Git:

git clone https://github.com/PhanstielLab/coralp.git

or download and extract a compressed .zip file of the latest revision of the repository from https://github.com/PhanstielLab/coralp/archive/master.zip.

Prerequisites

CoralP uses a number of packages. You can use the following code in R to install any you don't already have:

list.of.packages <- c(
  "shiny", 
  "shinydashboard", 
  "shinyBS", 
  "readr", 
  "rsvg", 
  "shinyWidgets", 
  "RColorBrewer", 
  "svgPanZoom", 
  "colourpicker", 
  "DT", 
  "data.tree", 
  "jsonlite")
new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[, "Package"])]
if(length(new.packages)) install.packages(new.packages)

Running the App

From R, run the following command:

shiny::runApp("/path/to/coralp")

and it should launch the app in your default web browser.

Credit

CoralP was adapated from Coral in the Phanstiel Lab at UNC by Amit Min and Erika Deoudes. Coral is written in R and relies on the following packages: shiny, shinydashboard, shinyBS, readr, rsvg, shinyWidgets, RColorBrewer. Circle and Force Layouts are written in javascript using the amazing D3 library.

Citation

We are currently preparing a manuscript describing CoralP. CoralP makes use of phylogenetic information and tree plots derived from Chen et al., Science Signaling, 2017.

Contributions

We welcome user feedback and contributions on this software. If you have a question or a problem, the best approach is to report it is through GitHub's issue tracker. If you want to propose a change to the source code, either to fix a bug or make an improvement, use a pull request.

coralp's Issues

CoralP not identifying phosphatases and kinase isoforms

Hello,
I am a Postdoctoral researcher working in Angus Nairn’s lab, Department of Psychiatry, Yale University. We used a proximity labelling proteomics approach to identify the protein interactome of a brain phosphoprotein in rats. We identified 1945 proximal proteins (organism: rat) to this phosphoprotein. We used CORALP software to identify the phosphatases and kinases in the proximal protein interactome.
Though the software identified and plotted PPIs with hierarchical information, there are lots of isoforms which are missing. For example, the software identified PPP2CB but not PPP2R2A, PPP2R5D, PPP1R9A. Like this many phosphatases were not identified. We believe that the proteins which were not identified are not in the phosphatase database of the software. The same happened with kinases as well.
We would like to know if there is an updated version of the software that could include these missing phosphatases and kinase isoforms? We would appreciate it if you could suggest some solutions.
Thank you for your time.
Boby

Installation instructions

Part of JOSS review (openjournals/joss-reviews#1837):

Could you add installation instructions? There is a list of R packages dependencies but no information about the installation of CoralP itself. Would be good as well to convert it to an R package [1-2].

[1] https://cran.r-project.org/doc/manuals/r-release/R-exts.html
[2] http://r-pkgs.had.co.nz/

Error message when searching in shinyapp.

When I type in a string in the search box I get the following error message window popup. It also shows the same message when I click the sort arrow in the column.

DataTables warning: table id=DataTables_Table_17 - Error in tolower(x): invalid input 'Protein Phosphatase 1 Catalytic Subunit Beta<ca>' in 'utf8towcs'

locally running error

I am trying to run the shiny app from my mac locally.
when I type the command I get the following. Can you tell me why I am getting this error?
Thank you.

> shiny::runApp()
Loading required package: shiny

Attaching package: ‘shinydashboard’

The following object is masked from ‘package:graphics’:

    box

Linking to librsvg 2.48.4

Attaching package: ‘colourpicker’

The following object is masked from ‘package:shiny’:

    runExample

Attaching package: ‘DT’

The following objects are masked from ‘package:shiny’:

    dataTableOutput, renderDataTable

Attaching package: ‘jsonlite’

The following object is masked from ‘package:shiny’:

    validate

Error in dots_list(...) : object 'outputjsonshort' not found    

Typo in paper

Part of JOSS review (openjournals/joss-reviews#1837):

Could you fix the legend of figure 1? i.e.: "Figure 1: Figure1. ....", there is a duplication of "Figure 1".

There is also a problem with the reference Bailey2015-ft which is not considered during the generation of the pdf.