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xavierdidelot / TransPhylo

Reconstruction of transmission trees using genomic data
http://xavierdidelot.github.io/TransPhylo/
GNU General Public License v2.0
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Printing Edges of the Transmission Tree #36

Closed MarriaK closed 2 months ago

MarriaK commented 2 months ago

Hi,

I am currently working with the TransPhylo model and I have successfully followed the instructions provided for inferring a transmission tree (https://xavierdidelot.github.io/TransPhylo/articles/infer.html). I was able to generate a transmission tree using the sample data provided.

However, I am now interested in accessing and printing the edges of the inferred transmission tree. Could you please guide me on how to achieve this? Any help or examples would be greatly appreciated.

xavierdidelot commented 2 months ago

As indicated towards the end of the tutorial, you can compute the medoid transmission tree using:

t=extractTTree(medTTree(res))

You can then plot this transmission tree in detailed format using plotTTree(t,w.shape,w.scale) or in economic format using plotTTree2(t), cf help on these functions for some options of how to plot.

Or if you want the list of who infected whom in this transmission tree then you take a look at t$ttree[,3] which is a vector of infectors, with indexes corresponding to t$nam.