Example : Data Visualization & Pathway statistics with PathVisioRPC

PathVisioRPC Anwesha Dutta 1,2, Martijn P van Iersel 3, Martina Kutmon Egon L Willighagen 1, Chris T Evelo 1,2

1,2

, Lars Eijssen 1, Magali Jaillard 1,

1. Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, The Netherlands 2. Netherlands Consortium for Systems Biology (NCSB), The Netherlands 3. General Bioinformatics, Reading, UK

Use PathVisioRPC in your chosen language to :

Connecting PathVisio to the World

Create pathways with a set of significant genes, proteins, metabolites, interactions, …

PathVisioRPC1 is an

Get a list of participating genes from a pathway

XMLRPC2 interface of

Visualize gene, protein, metabolite, flux, … data on pathways

PathVisio3 allowing access to PathVisio

Perform pathway statistics

functions from within different programming

Export analysis results in pdf, png, svg, html formats

languages.

Easily incorporate PathVisio into workflows

PathVisioRPC

INPUT

CODE

Example : Data Visualization & Pathway statistics with PathVisioRPC ## Set Variables PATHWAY.DIR = "home/anwesha/Pathways" WORK.DIR = "/home/anwesha/Work" port = 8080 inputFile = "/home/anwesha/Work/ncsb.txt“ dbFile = "/home/anwesha/Work/Hs_Derby_20110601.bridge" Species = "HomoSapiens" Gradient = "logFC;Fold Change" Gcolors = "blue,white,red;green,red” Gvalues = "-1,0,1;-2,2" Rule = "P.Value“ Rcolors = "yellow” Rexpression = "[P.Value] < 0.5" Zexpression = "[P.Value]< 0.5" ## Load library library(XMLRPC) ## Set working directory setwd (WORK.DIR) ## Set server address host