Entering edit mode

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.

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.

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?

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.

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

-- scooter

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