Question: how to visulaize WGCNA network file in cytoscape
0
gravatar for Azhar
2.1 years ago by
Azhar40
China
Azhar40 wrote:

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.

rna-seq • 1.9k views
ADD COMMENTlink written 2.1 years ago by Azhar40
1

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

ADD REPLYlink written 2.1 years ago by Jake Warner690

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

ADD REPLYlink written 2.1 years ago by Azhar40
1

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

ADD REPLYlink written 2.1 years ago by RamRS21k

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

ADD REPLYlink written 2.1 years ago by Jake Warner690

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.

ADD REPLYlink written 2.0 years ago by Azhar40

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

ADD REPLYlink written 2.0 years ago by RamRS21k

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 ?

ADD REPLYlink written 2.0 years ago by Azhar40
1

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

ADD REPLYlink written 2.0 years ago by Jake Warner690
1

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.
ADD REPLYlink written 2.0 years ago by RamRS21k

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

ADD REPLYlink written 2.0 years ago by Azhar40
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