How To Convert Ccytoscape Network Format Table Data To Json/Xgmml Format Without Using Cytoscape?
1
1
Entering edit mode
7.3 years ago
sayonidas03 ▴ 100

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.

cytoscape • 3.8k views
ADD COMMENT
1
Entering edit mode
6.7 years ago
Kizuna ▴ 830

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 !

 

ADD COMMENT

Login before adding your answer.

Traffic: 1246 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6