0efcba3479ba1899c660eaff69afe0c57418adb8,atlas/scripts/utils/tree.py,,root_tree_by_phyla,#,31

Before Change

    


    Freq_pyla= phyla.value_counts()

    for p in reversed(Freq_pyla.index):
        LCA = T.get_common_ancestor(*tuple(phyla.index[phyla==p].values))

        if not T== LCA:
            T.set_outgroup(LCA)
            print(f"set {p} as outgroup for Tree rooting")
            break


    T.unroot()

def layout_black_circles(node):
    // If node is a leaf

After Change

     Root the tree next to the phylum that is as far apart as possible from the other phyla

    
    phylum_LCA={}

    for p in phyla.unique():
        phylum_LCA[p]=T.get_common_ancestor(*tuple(phyla.index[phyla==p].values))

    Dist= pd.DataFrame()
    for p1,lca1 in phylum_LCA.items():
        for p2,lca2 in phylum_LCA.items():
            Dist.loc[p1,p2]=T.get_distance(lca1,lca2)

    furthest_phylum= Dist.mean().idxmax()
    outgroup=phylum_LCA[furthest_phylum]

    if not outgroup== LCA:

Instances