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[igraph] igraph : Each Node showing double connections : How to change

From: Sandipan Samaddar
Subject: [igraph] igraph : Each Node showing double connections : How to change
Date: Fri, 12 May 2017 08:06:44 +0000 (UTC)

Dear R Community,
I’m relatively new user of R and igraph, so please excuse me if my question is naive. I found igraph very useful in my work however I experienced a problem with plotting the graph, which I cannot overcome.

I have an OTU Table (attached) which I used in Sparcc http://psbweb05.psb.ugent.be/conet/microbialnetworks/sparcc.php to compute P-values from bootstrapped correlations as instructed in Sparcc Tutorial.

Nextly, the computed p-values (pvals_two_sided.txt ,attached herewith this email) were used in igraph to convert it into matrix of significance and graph was plotted.The code I used :

# set p-values of 0 to a non-zero, small p-value so we can take the logarithm
# convert into significance
# remove all edges with significance below 1
# convert adjacency matrix into a graph
# display the graph
plot(sparcc.graph, layout=layout)

The graph generated is Network_igraph.jpeg.
Inline image
The graph generated was converted to visualize in Cytoscape .graphml format using write.graph command but dual connections were observed between two nodes which are unwanted.The cytoscape version is shown below.
Inline image

How can I remove the dual connectivity and generate a proper network for visualization.It would be highly appreciated if I am kindly instructed how should I deal with this problem.

Looking forward to hear from the community.

Thanks and Regards,


Attachment: OTU_Table.txt
Description: Text document

Attachment: pvals_two_sided.txt
Description: Text document

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