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jameshadfield avatar jameshadfield commented on July 19, 2024

@trvrb I've implemented this as a post-augur export step. (In augur v6, augur export will be able to do this, but I think we want SFS to run on augur v5.)

Steps needed for the snakefile:
(1) rule export_aggregated should save the tree JSON into "./results", (the meta JSON should be saved in "./auspice" as it is currently.
(2):

python scripts/annotate_hidden_nodes.py \
    --input results/seattle_flu_seasonal_h3n2_genome_2y_tree.json \
    --output auspice/seattle_flu_seasonal_h3n2_genome_2y_tree.json 

This script has the side effect of labeling internal nodes with the cluster (previously only terminal nodes).

image

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jameshadfield avatar jameshadfield commented on July 19, 2024

Branch exploded Now modified to remove the trailing branch & maximize what's shown in auspice -- see cef2d75 for more info.

temporal view:
image

divergence:
image

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jameshadfield avatar jameshadfield commented on July 19, 2024

@trvrb if you modify https://github.com/seattleflu/augur-build/blob/exploded/scripts/annotate_hidden_nodes.py#L53 to be, e.g.

        "attr": {
            "num_date": node["attr"]["num_date"] - 1/12,
            "div": node["attr"]["div"] - 0.0002
        },

Then you'll have little stubs which you can click on to zoom into each cluster, like so:

image

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trvrb avatar trvrb commented on July 19, 2024

Thanks @jameshadfield! This is great.

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