how to visulaize WGCNA network file in cytoscape

Question

[Azhar]

I was using 62103 matrix for network construction onWGCNA after all i got the file so i choose one module to visualize. I have a node and edge file node file is not so big but edge file is 1.4 GB so cytoscape stop working when i upload that file any suggestions what should i do also how can i add node and respective edge file to get network.

[Jake Warner]

Have you tried filtering by only the strongest connections to reduce the number of edges?

[Azhar]

no how can filter ...just simple from excel file interaction which is maximum 4.5 or something for that module...since my adjacency matrix is 24.6GB so should i choose some other module

[Ram]

Stop using Excel for data intensive tasks. With a file that is gigabytes in size, Excel shouldn't even remotely be considered.

[Jake Warner]

I'm not sure how to filter in excel but in R there are a few options from Jeremy Miller. Specifically the get.ranks() function to get the top connected genes in your adjacency or visantPrepOverall() to output the top connections:

https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/collapseRows/Jeremy_Functions_All.R

[Azhar]

Hi thanks for your support I highly appreciate I want to know which function should i use form these functions because there is no get.ranks() and have TOM file of 24.7 GB so can i get top connected or highly correlated connections.

[Ram]

The get.ranks is in the R script Jacob has linked to.

[Azhar]

Thanks for reply but I did not find the function and it and if you kindly can guide me this page has number of functions and how to use it second as far i understand TOM contains the information of overlap modules but when o see the WGCNA tutioal it still try to export a colour module why ?

[Jake Warner]

get.ranks() is in there. Try ctrl F "get.ranks"

[Ram]

Here are a few general tips:

1. Address the problem you mentioned in the original post. Follow up questions can be addressed once the top level problem is solved
2. Please phrase your questions a little better. Run-on sentences make your questions difficult to understand.
3. Explain your situation (the "server" part you mention in the comment below) a little better.

[Azhar]

Another thing I am working on large data set 63k so iuse server for analysis but i do not get visualization pdf files generated to see the results is there any problem