In Command Line:

  • Launch the PathVisioRPC server
java -jar PathVisioRPC-standalone.jar 1234

In R :

  • Load XMLRPC library
 library("XMLRPC")
  • Set server address
 server = "http://localhost:1234"
  • Import Data
 xml.rpc(server,"PathVisio.importData", "/home/anwesha/combidata.txt","/home/anwesha/PathVisio-Data/gene-databases","/home/anwesha/")
  • Create Visualization
 xml.rpc(server, "PathVisio.createVisualization","/home/anwesha/combidata.txt.pgex","log2FC","blue,white,red","-2,0,2","pvalue","green","[pvalue]<0.05")
  • Visualize Data on Wikipathways pathways directly and export as HTML
xml.rpc(server,"PathVisio.visualizeDataByURI", "WP1","/home/anwesha/combidata.txt.pgex","/home/anwesha/PathVisio-Data/gene-databases","/home/bohler/PathVisio-Data/results")

Result:
Statin Pathway