How To Convert Ccytoscape Network Format Table Data To Json/Xgmml Format Without Using Cytoscape?

Question

[sayonidas03]

Hi,

I have tabular data for many biological networks in cytoscape format. However, in order to display them in webpages using gcytoscapeweb, I would need to convert them to json or xgmml webpages. Since there are hundred of different networks, it would not be feasible to import the network tabular data into Cytoscape and then exporting the network to json or gxmml formats. It would be very helpful if anyone can suggest a way around this. Are there cytoscape network file format converters ? Or any scripts available which do this? What other ways can I tackle this.. I saw some csv to xml converters but I am not sure whether they can do the same thing or not.

I am working with networks where the edge lengths between nodes reflect their similarity values.

Thanks in advance.

Answer 1

[Kizuna]

I think you can use R to go from tabulated .txt file in .JSON:

install.packages("jsonlite")
install.packages("plyr")`

library(jsonlite); library(plyr)

file1=read.delim(file="\\...\.txt",header=,sep="")
file1.JSON=toJSON(file1,pretty=T)

Hope this helps!