Hi,

I Use WGCNA for network analysis. So, one of the WGCNA steps is designing plot of Module-Trait Relationship. In this plot, we can see the relationship between different extracted modules and different Trait variables. Also, in this plot we can see P-Value for each Module-Trait Relationship.So, via these P-Values we can find significant relationships between modules and Traits. In my study, the number of modules is high and in the plot, the number of P-values for each relationship is mixed and not readable. I need help for extracting these p-value as a .csv file out of this plot. I appreciate if any body help me for my problem.

Best Regards,

Mohammad

What have you tried? - please edit the post to show code, and describe your problem in detail.

Hi,

Thanks for your comment. I need to attached my module-trait relationship plot for showing problem. could you please guide me how can I upload my .pdf file via this post?

Description My Problem: I have to work on 53 cancer samples from one of the TCGA Cancer dataset. I used WGCNA for constructing network and finding significant modules. my data dimension is 53 samples and 56000 gene type. after running WGCNA, I see 99 modules. Now, I don't know 99 module is ok or my analysis has problem? secondly, I plot Modules-Trait relationship. in tutorial of WGCNA, you can see p-value for each relationship but in my plot because of lots of modules, numbers of p-value mix together and I cant see it(I can zoom on it). so, I am looking for function for getting P-value based on each module-trait relationship.

I appericiate if you share your comment with me

Best Regards,

Mohammad

Please paste the code that you have used to generate the module-trait relationships.

Dear Dr. Blighe

Hi,

Thanks for your comments.my code is in below:

So, as I the number of modules is 99, in this heatmap I can't see p-values for each relationship.