Re: [Bioc-devel] Classes to be supported by ggraph
hi, i use the part of the functionality of the graph package within my packages qpgraph and VariantFiltering. I mostly use the 'graphBAM' class that provides a memory-efficient representation of the graph and the possiblity to store data associated with nodes and edges via the 'nodeData()' and 'edgeData()' setters and getters. while the graph package is not among the most actively developed one, it may have about 80 other packages that depend or import its functionality. i guess there are ways to explore automatically what functionality is used or just what is more popular, which can give you a hint about what to implement in 'ggraph'. cheers, robert. On 2/6/16 12:20 PM, Thomas Lin Pedersen wrote: I’m in the process of developing ggraph (https://github.com/thomasp85/ggraph) - An extensive plotting framework for graph/tree/network data based on ggplot2. Currently the class support is focused on igraph and dendrogram, but the idea is to extend it with support for additional graph representations in R. The easy way to do this is through conversion to one of the two currently supported classes, but I would like to hear from the developers and users of especially the graph package, whether there are any downsides to this approach, i.e. are there features/information captured by the graphNEL class that would disappear with conversion to an igraph object. Also if someone is working with, or developing other graph representations and would like to see support in ggraph, please let me know… best Thomas [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Classes to be supported by ggraph
Possibly of interest on this topic, though it implements a different sort of (interactive) solution, are two Bioc packages: RCyjs and RCy3. RCyjs renders to the browser, using the cytoscape.js javascript library and websockets: http://js.cytoscape.org/ RCy3 renders to Cytoscape, the mature and popular network visualization desktop app: http://cytoscape.org/ Both bioc packages forgo the relatively non-interactive tradition of plotting in R, for a fully interactive approach. Both R and the rendering platforms are simultaneously and reciprocally fully interactive. The devel versions of each of these packages would be the ones to look at if you are interested. RCyjs http://bioconductor.org/packages/3.3/bioc/html/RCyjs.html RCy3 http://bioconductor.org/packages/3.3/bioc/html/RCy3.html RCyjs is currently a little bit more mature, but RCy3 is rapidly catching up. RCyjs is based upon the Bioc class “BrowserViz” and uses he httpuv package maintained by the Shiny project and nicely extended by Hector Corrado Bravo for http and web socket. The goal of both of these packages is 1) use community standard network visualization tools (Cytoscape for the desktop, cytoscape.js in the browser) 2) preserve and extend the fully interactive nature of both R, and the Cytoscape* rendering and analysis platforms. The unit tests for each package are extensive. They, along with the package vignettes, are a good introduction to the capabilities and programming idioms of the packages. They may be of interest to some. Questions, bug reports, requests for new features are always welcome. Regards, - Paul ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
