Node degree exponent for co-expression network
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2.2 years ago
imaparna27 ▴ 20

Hi,

I am trying to calculate the node degree exponent for a co-expression network.

I understand, in order to do that degree should be plotted against the number of nodes having that degree.

Following are the columns in my data

AverageShortestPathLength BetweennessCentrality ClosenessCentrality ClusteringCoefficient Degree Eccentricity IsSingleNode NeighborhoodConnectivity NumberOfDirectedEdges NumberOfUnDirectedEdges PartnerOfMultiEdgedNodePairs Radiality Selfloops Stress TopologicalCoefficient Matching.Attribute

Which of the abovementioned columns should be plotted against each other in cyChart to work out degree exponent? Also, is there any alternative to work out the node-degree exponent?

Thanks.

co-expression cytoscape • 956 views
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There is a Degree column in your list. I am guessing you want to make a plot to set the exponent for the network to achieve scale-free topology? A plot like we use here in Fig. 3 where you plot scale-free fit over exponent and connectivity over exponent is commonly used. scaleFreePlot functions are implemented in the WGCNA package, there is a tutorial here.

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That's right. I want to plot scale-free fit over degree exponent. I am basically trying to know the value of node degree exponent, γ. I see degree can be plotted on x-axis, what should be the y-axis?

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The power parameter is plotted on the x-axis (e.g. using integers from 1-20) and the connectivity or scale-free fit are plotted on the y-axis.

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You want to plot a Degree histogram and then do a regression plot of that histogram. This should give you y.

-- scooter

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Thanks a lot. Although I was able to resolve this issue using older version of Cytoscape - (v3.7.0).

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