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songw01 / MEGENA

Multiscale embedded gene co-expression network analysis
GNU General Public License v3.0
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About the global BRCA PFN #10

Open millersan opened 3 years ago

millersan commented 3 years ago

Hi, I am using MEGENA for co-expression analysis. This package is useful for me! I have read the paper, but I don`t know how to draw the global BRCA PFN. Is it the plot_module function, or I have to export it to Cytoscape? pcbi 1004574 g004

yimwy commented 3 years ago

Hi, same problem, the plot_module function doesn't seems to have a global plot option to me...

songw01 commented 3 years ago

Hi there, The network is generated using Cytoscape. Perhaps you want to check out RCy3 package that lets you to interact between R and Cytoscape with igraph objects. MEGENA stores the network in igraph object, and should work accordingly. For the network partitioning, you can use "get.union.cut(module.output,alpha.cut = 1,output.plot = F, plotfname = "validModules_alpha",module.pval = 0.05,remove.unsig = T)" to get the default partition at alpha = 1. Note that this is for visualization purpose, and the output from get.union.cut does not represent the entirety of MEGENA modules.

Regards,

millersan commented 3 years ago

Thank you very much!!

millersan commented 3 years ago

Hi, I tried this method, but I found that some genes were not classified to any of the clusters compared to the PFN objects. After I delete all the nodes that are not in the cluster, the tree diagram will be broken like the second figure. Could you help me to solve this problem? Thank you very much for your help! figure1 33333 figure2 myIgraph

sunynping commented 1 year ago

Hi, I tried this method, but I found that some genes were not classified to any of the clusters compared to the PFN objects. After I delete all the nodes that are not in the cluster, the tree diagram will be broken like the second figure. Could you help me to solve this problem? Thank you very much for your help! figure1 33333 figure2 myIgraph

Hi, same problem. Can you provide some ideas