How to extract patristic distances from dendropy phylogenetic_distance_matrix












0















I have created a cophenetic distance matrix in dendropy using:



from dendropy.simulate import treesim
tree = treesim.birth_death_tree(birth_rate=1.0, death_rate=0.5, ntax=10)
pdm = tree.phylogenetic_distance_matrix()


However, having read the documentation and trying many things I cannot extract the actual matrix in a usable manner from the object "pdm"



NB there is a method as_data_table with this class that I am also unable to fathom










share|improve this question



























    0















    I have created a cophenetic distance matrix in dendropy using:



    from dendropy.simulate import treesim
    tree = treesim.birth_death_tree(birth_rate=1.0, death_rate=0.5, ntax=10)
    pdm = tree.phylogenetic_distance_matrix()


    However, having read the documentation and trying many things I cannot extract the actual matrix in a usable manner from the object "pdm"



    NB there is a method as_data_table with this class that I am also unable to fathom










    share|improve this question

























      0












      0








      0








      I have created a cophenetic distance matrix in dendropy using:



      from dendropy.simulate import treesim
      tree = treesim.birth_death_tree(birth_rate=1.0, death_rate=0.5, ntax=10)
      pdm = tree.phylogenetic_distance_matrix()


      However, having read the documentation and trying many things I cannot extract the actual matrix in a usable manner from the object "pdm"



      NB there is a method as_data_table with this class that I am also unable to fathom










      share|improve this question














      I have created a cophenetic distance matrix in dendropy using:



      from dendropy.simulate import treesim
      tree = treesim.birth_death_tree(birth_rate=1.0, death_rate=0.5, ntax=10)
      pdm = tree.phylogenetic_distance_matrix()


      However, having read the documentation and trying many things I cannot extract the actual matrix in a usable manner from the object "pdm"



      NB there is a method as_data_table with this class that I am also unable to fathom







      python dendropy






      share|improve this question













      share|improve this question











      share|improve this question




      share|improve this question










      asked Nov 28 '18 at 15:25









      user3329732user3329732

      405




      405
























          1 Answer
          1






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          1














          as_data_table() returns an object of type dendropy.utility.container.DataTable. This DataTable is a custom container class, which implements lots of useful methods you can use to get at your data. You can read the source here to understand it:



          https://dendropy.org/_modules/dendropy/utility/container.html



          You can very quickly see the data in a format you can understand by looking at its _data variable:



          from dendropy.simulate import treesim
          import pprint


          tree = treesim.birth_death_tree(birth_rate=1.0, death_rate=0.5, ntax=10)
          pdm = tree.phylogenetic_distance_matrix()

          pp = pprint.PrettyPrinter(depth=2)
          pp.pprint(pdm.as_data_table()._data)


          Outputs:



          {'T1': {'T1': 0.0,
          'T10': 1.832709865628535,
          'T2': 2.2418431376329204,
          'T3': 1.8146189808922477,
          'T4': 1.832709865628535,
          'T5': 1.832709865628535,
          'T6': 0.5848837844916799,
          'T7': 0,
          'T8': 1.6307174196094565,
          'T9': 1.8146189808922477},
          'T10': {'T1': 1.832709865628535,
          'T10': 0.0,
          'T2': 2.2418431376329204,
          'T3': 1.832709865628535,
          'T4': 0.8434862029618123,
          'T5': 1.215095937098336,
          'T6': 1.832709865628535,
          'T7': 1.832709865628535,
          'T8': 1.832709865628535,
          'T9': 1.832709865628535},
          'T2': {'T1': 2.2418431376329204,
          'T10': 2.2418431376329204,
          'T2': 0.0,
          'T3': 2.2418431376329204,
          'T4': 2.2418431376329204,
          'T5': 2.2418431376329204,
          'T6': 2.2418431376329204,
          'T7': 2.2418431376329204,
          'T8': 2.2418431376329204,
          'T9': 2.2418431376329204},
          'T3': {'T1': 1.8146189808922477,
          'T10': 1.832709865628535,
          'T2': 2.2418431376329204,
          'T3': 0.0,
          'T4': 1.832709865628535,
          'T5': 1.832709865628535,
          'T6': 1.8146189808922477,
          'T7': 1.8146189808922477,
          'T8': 1.8146189808922477,
          'T9': 1.4811625503429378},
          'T4': {'T1': 1.832709865628535,
          'T10': 0.8434862029618123,
          'T2': 2.2418431376329204,
          'T3': 1.832709865628535,
          'T4': 0.0,
          'T5': 1.215095937098336,
          'T6': 1.832709865628535,
          'T7': 1.832709865628535,
          'T8': 1.832709865628535,
          'T9': 1.832709865628535},
          'T5': {'T1': 1.832709865628535,
          'T10': 1.215095937098336,
          'T2': 2.2418431376329204,
          'T3': 1.832709865628535,
          'T4': 1.215095937098336,
          'T5': 0.0,
          'T6': 1.832709865628535,
          'T7': 1.832709865628535,
          'T8': 1.832709865628535,
          'T9': 1.832709865628535},
          'T6': {'T1': 0.5848837844916799,
          'T10': 1.832709865628535,
          'T2': 2.2418431376329204,
          'T3': 1.8146189808922477,
          'T4': 1.832709865628535,
          'T5': 1.832709865628535,
          'T6': 0.0,
          'T7': 0.5848837844916799,
          'T8': 1.6307174196094565,
          'T9': 1.8146189808922477},
          'T7': {'T1': 0,
          'T10': 1.832709865628535,
          'T2': 2.2418431376329204,
          'T3': 1.8146189808922477,
          'T4': 1.832709865628535,
          'T5': 1.832709865628535,
          'T6': 0.5848837844916799,
          'T7': 0.0,
          'T8': 1.6307174196094565,
          'T9': 1.8146189808922477},
          'T8': {'T1': 1.6307174196094565,
          'T10': 1.832709865628535,
          'T2': 2.2418431376329204,
          'T3': 1.8146189808922477,
          'T4': 1.832709865628535,
          'T5': 1.832709865628535,
          'T6': 1.6307174196094565,
          'T7': 1.6307174196094565,
          'T8': 0.0,
          'T9': 1.8146189808922477},
          'T9': {'T1': 1.8146189808922477,
          'T10': 1.832709865628535,
          'T2': 2.2418431376329204,
          'T3': 1.4811625503429378,
          'T4': 1.832709865628535,
          'T5': 1.832709865628535,
          'T6': 1.8146189808922477,
          'T7': 1.8146189808922477,
          'T8': 1.8146189808922477,
          'T9': 0.0}}





          share|improve this answer























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            as_data_table() returns an object of type dendropy.utility.container.DataTable. This DataTable is a custom container class, which implements lots of useful methods you can use to get at your data. You can read the source here to understand it:



            https://dendropy.org/_modules/dendropy/utility/container.html



            You can very quickly see the data in a format you can understand by looking at its _data variable:



            from dendropy.simulate import treesim
            import pprint


            tree = treesim.birth_death_tree(birth_rate=1.0, death_rate=0.5, ntax=10)
            pdm = tree.phylogenetic_distance_matrix()

            pp = pprint.PrettyPrinter(depth=2)
            pp.pprint(pdm.as_data_table()._data)


            Outputs:



            {'T1': {'T1': 0.0,
            'T10': 1.832709865628535,
            'T2': 2.2418431376329204,
            'T3': 1.8146189808922477,
            'T4': 1.832709865628535,
            'T5': 1.832709865628535,
            'T6': 0.5848837844916799,
            'T7': 0,
            'T8': 1.6307174196094565,
            'T9': 1.8146189808922477},
            'T10': {'T1': 1.832709865628535,
            'T10': 0.0,
            'T2': 2.2418431376329204,
            'T3': 1.832709865628535,
            'T4': 0.8434862029618123,
            'T5': 1.215095937098336,
            'T6': 1.832709865628535,
            'T7': 1.832709865628535,
            'T8': 1.832709865628535,
            'T9': 1.832709865628535},
            'T2': {'T1': 2.2418431376329204,
            'T10': 2.2418431376329204,
            'T2': 0.0,
            'T3': 2.2418431376329204,
            'T4': 2.2418431376329204,
            'T5': 2.2418431376329204,
            'T6': 2.2418431376329204,
            'T7': 2.2418431376329204,
            'T8': 2.2418431376329204,
            'T9': 2.2418431376329204},
            'T3': {'T1': 1.8146189808922477,
            'T10': 1.832709865628535,
            'T2': 2.2418431376329204,
            'T3': 0.0,
            'T4': 1.832709865628535,
            'T5': 1.832709865628535,
            'T6': 1.8146189808922477,
            'T7': 1.8146189808922477,
            'T8': 1.8146189808922477,
            'T9': 1.4811625503429378},
            'T4': {'T1': 1.832709865628535,
            'T10': 0.8434862029618123,
            'T2': 2.2418431376329204,
            'T3': 1.832709865628535,
            'T4': 0.0,
            'T5': 1.215095937098336,
            'T6': 1.832709865628535,
            'T7': 1.832709865628535,
            'T8': 1.832709865628535,
            'T9': 1.832709865628535},
            'T5': {'T1': 1.832709865628535,
            'T10': 1.215095937098336,
            'T2': 2.2418431376329204,
            'T3': 1.832709865628535,
            'T4': 1.215095937098336,
            'T5': 0.0,
            'T6': 1.832709865628535,
            'T7': 1.832709865628535,
            'T8': 1.832709865628535,
            'T9': 1.832709865628535},
            'T6': {'T1': 0.5848837844916799,
            'T10': 1.832709865628535,
            'T2': 2.2418431376329204,
            'T3': 1.8146189808922477,
            'T4': 1.832709865628535,
            'T5': 1.832709865628535,
            'T6': 0.0,
            'T7': 0.5848837844916799,
            'T8': 1.6307174196094565,
            'T9': 1.8146189808922477},
            'T7': {'T1': 0,
            'T10': 1.832709865628535,
            'T2': 2.2418431376329204,
            'T3': 1.8146189808922477,
            'T4': 1.832709865628535,
            'T5': 1.832709865628535,
            'T6': 0.5848837844916799,
            'T7': 0.0,
            'T8': 1.6307174196094565,
            'T9': 1.8146189808922477},
            'T8': {'T1': 1.6307174196094565,
            'T10': 1.832709865628535,
            'T2': 2.2418431376329204,
            'T3': 1.8146189808922477,
            'T4': 1.832709865628535,
            'T5': 1.832709865628535,
            'T6': 1.6307174196094565,
            'T7': 1.6307174196094565,
            'T8': 0.0,
            'T9': 1.8146189808922477},
            'T9': {'T1': 1.8146189808922477,
            'T10': 1.832709865628535,
            'T2': 2.2418431376329204,
            'T3': 1.4811625503429378,
            'T4': 1.832709865628535,
            'T5': 1.832709865628535,
            'T6': 1.8146189808922477,
            'T7': 1.8146189808922477,
            'T8': 1.8146189808922477,
            'T9': 0.0}}





            share|improve this answer




























              1














              as_data_table() returns an object of type dendropy.utility.container.DataTable. This DataTable is a custom container class, which implements lots of useful methods you can use to get at your data. You can read the source here to understand it:



              https://dendropy.org/_modules/dendropy/utility/container.html



              You can very quickly see the data in a format you can understand by looking at its _data variable:



              from dendropy.simulate import treesim
              import pprint


              tree = treesim.birth_death_tree(birth_rate=1.0, death_rate=0.5, ntax=10)
              pdm = tree.phylogenetic_distance_matrix()

              pp = pprint.PrettyPrinter(depth=2)
              pp.pprint(pdm.as_data_table()._data)


              Outputs:



              {'T1': {'T1': 0.0,
              'T10': 1.832709865628535,
              'T2': 2.2418431376329204,
              'T3': 1.8146189808922477,
              'T4': 1.832709865628535,
              'T5': 1.832709865628535,
              'T6': 0.5848837844916799,
              'T7': 0,
              'T8': 1.6307174196094565,
              'T9': 1.8146189808922477},
              'T10': {'T1': 1.832709865628535,
              'T10': 0.0,
              'T2': 2.2418431376329204,
              'T3': 1.832709865628535,
              'T4': 0.8434862029618123,
              'T5': 1.215095937098336,
              'T6': 1.832709865628535,
              'T7': 1.832709865628535,
              'T8': 1.832709865628535,
              'T9': 1.832709865628535},
              'T2': {'T1': 2.2418431376329204,
              'T10': 2.2418431376329204,
              'T2': 0.0,
              'T3': 2.2418431376329204,
              'T4': 2.2418431376329204,
              'T5': 2.2418431376329204,
              'T6': 2.2418431376329204,
              'T7': 2.2418431376329204,
              'T8': 2.2418431376329204,
              'T9': 2.2418431376329204},
              'T3': {'T1': 1.8146189808922477,
              'T10': 1.832709865628535,
              'T2': 2.2418431376329204,
              'T3': 0.0,
              'T4': 1.832709865628535,
              'T5': 1.832709865628535,
              'T6': 1.8146189808922477,
              'T7': 1.8146189808922477,
              'T8': 1.8146189808922477,
              'T9': 1.4811625503429378},
              'T4': {'T1': 1.832709865628535,
              'T10': 0.8434862029618123,
              'T2': 2.2418431376329204,
              'T3': 1.832709865628535,
              'T4': 0.0,
              'T5': 1.215095937098336,
              'T6': 1.832709865628535,
              'T7': 1.832709865628535,
              'T8': 1.832709865628535,
              'T9': 1.832709865628535},
              'T5': {'T1': 1.832709865628535,
              'T10': 1.215095937098336,
              'T2': 2.2418431376329204,
              'T3': 1.832709865628535,
              'T4': 1.215095937098336,
              'T5': 0.0,
              'T6': 1.832709865628535,
              'T7': 1.832709865628535,
              'T8': 1.832709865628535,
              'T9': 1.832709865628535},
              'T6': {'T1': 0.5848837844916799,
              'T10': 1.832709865628535,
              'T2': 2.2418431376329204,
              'T3': 1.8146189808922477,
              'T4': 1.832709865628535,
              'T5': 1.832709865628535,
              'T6': 0.0,
              'T7': 0.5848837844916799,
              'T8': 1.6307174196094565,
              'T9': 1.8146189808922477},
              'T7': {'T1': 0,
              'T10': 1.832709865628535,
              'T2': 2.2418431376329204,
              'T3': 1.8146189808922477,
              'T4': 1.832709865628535,
              'T5': 1.832709865628535,
              'T6': 0.5848837844916799,
              'T7': 0.0,
              'T8': 1.6307174196094565,
              'T9': 1.8146189808922477},
              'T8': {'T1': 1.6307174196094565,
              'T10': 1.832709865628535,
              'T2': 2.2418431376329204,
              'T3': 1.8146189808922477,
              'T4': 1.832709865628535,
              'T5': 1.832709865628535,
              'T6': 1.6307174196094565,
              'T7': 1.6307174196094565,
              'T8': 0.0,
              'T9': 1.8146189808922477},
              'T9': {'T1': 1.8146189808922477,
              'T10': 1.832709865628535,
              'T2': 2.2418431376329204,
              'T3': 1.4811625503429378,
              'T4': 1.832709865628535,
              'T5': 1.832709865628535,
              'T6': 1.8146189808922477,
              'T7': 1.8146189808922477,
              'T8': 1.8146189808922477,
              'T9': 0.0}}





              share|improve this answer


























                1












                1








                1







                as_data_table() returns an object of type dendropy.utility.container.DataTable. This DataTable is a custom container class, which implements lots of useful methods you can use to get at your data. You can read the source here to understand it:



                https://dendropy.org/_modules/dendropy/utility/container.html



                You can very quickly see the data in a format you can understand by looking at its _data variable:



                from dendropy.simulate import treesim
                import pprint


                tree = treesim.birth_death_tree(birth_rate=1.0, death_rate=0.5, ntax=10)
                pdm = tree.phylogenetic_distance_matrix()

                pp = pprint.PrettyPrinter(depth=2)
                pp.pprint(pdm.as_data_table()._data)


                Outputs:



                {'T1': {'T1': 0.0,
                'T10': 1.832709865628535,
                'T2': 2.2418431376329204,
                'T3': 1.8146189808922477,
                'T4': 1.832709865628535,
                'T5': 1.832709865628535,
                'T6': 0.5848837844916799,
                'T7': 0,
                'T8': 1.6307174196094565,
                'T9': 1.8146189808922477},
                'T10': {'T1': 1.832709865628535,
                'T10': 0.0,
                'T2': 2.2418431376329204,
                'T3': 1.832709865628535,
                'T4': 0.8434862029618123,
                'T5': 1.215095937098336,
                'T6': 1.832709865628535,
                'T7': 1.832709865628535,
                'T8': 1.832709865628535,
                'T9': 1.832709865628535},
                'T2': {'T1': 2.2418431376329204,
                'T10': 2.2418431376329204,
                'T2': 0.0,
                'T3': 2.2418431376329204,
                'T4': 2.2418431376329204,
                'T5': 2.2418431376329204,
                'T6': 2.2418431376329204,
                'T7': 2.2418431376329204,
                'T8': 2.2418431376329204,
                'T9': 2.2418431376329204},
                'T3': {'T1': 1.8146189808922477,
                'T10': 1.832709865628535,
                'T2': 2.2418431376329204,
                'T3': 0.0,
                'T4': 1.832709865628535,
                'T5': 1.832709865628535,
                'T6': 1.8146189808922477,
                'T7': 1.8146189808922477,
                'T8': 1.8146189808922477,
                'T9': 1.4811625503429378},
                'T4': {'T1': 1.832709865628535,
                'T10': 0.8434862029618123,
                'T2': 2.2418431376329204,
                'T3': 1.832709865628535,
                'T4': 0.0,
                'T5': 1.215095937098336,
                'T6': 1.832709865628535,
                'T7': 1.832709865628535,
                'T8': 1.832709865628535,
                'T9': 1.832709865628535},
                'T5': {'T1': 1.832709865628535,
                'T10': 1.215095937098336,
                'T2': 2.2418431376329204,
                'T3': 1.832709865628535,
                'T4': 1.215095937098336,
                'T5': 0.0,
                'T6': 1.832709865628535,
                'T7': 1.832709865628535,
                'T8': 1.832709865628535,
                'T9': 1.832709865628535},
                'T6': {'T1': 0.5848837844916799,
                'T10': 1.832709865628535,
                'T2': 2.2418431376329204,
                'T3': 1.8146189808922477,
                'T4': 1.832709865628535,
                'T5': 1.832709865628535,
                'T6': 0.0,
                'T7': 0.5848837844916799,
                'T8': 1.6307174196094565,
                'T9': 1.8146189808922477},
                'T7': {'T1': 0,
                'T10': 1.832709865628535,
                'T2': 2.2418431376329204,
                'T3': 1.8146189808922477,
                'T4': 1.832709865628535,
                'T5': 1.832709865628535,
                'T6': 0.5848837844916799,
                'T7': 0.0,
                'T8': 1.6307174196094565,
                'T9': 1.8146189808922477},
                'T8': {'T1': 1.6307174196094565,
                'T10': 1.832709865628535,
                'T2': 2.2418431376329204,
                'T3': 1.8146189808922477,
                'T4': 1.832709865628535,
                'T5': 1.832709865628535,
                'T6': 1.6307174196094565,
                'T7': 1.6307174196094565,
                'T8': 0.0,
                'T9': 1.8146189808922477},
                'T9': {'T1': 1.8146189808922477,
                'T10': 1.832709865628535,
                'T2': 2.2418431376329204,
                'T3': 1.4811625503429378,
                'T4': 1.832709865628535,
                'T5': 1.832709865628535,
                'T6': 1.8146189808922477,
                'T7': 1.8146189808922477,
                'T8': 1.8146189808922477,
                'T9': 0.0}}





                share|improve this answer













                as_data_table() returns an object of type dendropy.utility.container.DataTable. This DataTable is a custom container class, which implements lots of useful methods you can use to get at your data. You can read the source here to understand it:



                https://dendropy.org/_modules/dendropy/utility/container.html



                You can very quickly see the data in a format you can understand by looking at its _data variable:



                from dendropy.simulate import treesim
                import pprint


                tree = treesim.birth_death_tree(birth_rate=1.0, death_rate=0.5, ntax=10)
                pdm = tree.phylogenetic_distance_matrix()

                pp = pprint.PrettyPrinter(depth=2)
                pp.pprint(pdm.as_data_table()._data)


                Outputs:



                {'T1': {'T1': 0.0,
                'T10': 1.832709865628535,
                'T2': 2.2418431376329204,
                'T3': 1.8146189808922477,
                'T4': 1.832709865628535,
                'T5': 1.832709865628535,
                'T6': 0.5848837844916799,
                'T7': 0,
                'T8': 1.6307174196094565,
                'T9': 1.8146189808922477},
                'T10': {'T1': 1.832709865628535,
                'T10': 0.0,
                'T2': 2.2418431376329204,
                'T3': 1.832709865628535,
                'T4': 0.8434862029618123,
                'T5': 1.215095937098336,
                'T6': 1.832709865628535,
                'T7': 1.832709865628535,
                'T8': 1.832709865628535,
                'T9': 1.832709865628535},
                'T2': {'T1': 2.2418431376329204,
                'T10': 2.2418431376329204,
                'T2': 0.0,
                'T3': 2.2418431376329204,
                'T4': 2.2418431376329204,
                'T5': 2.2418431376329204,
                'T6': 2.2418431376329204,
                'T7': 2.2418431376329204,
                'T8': 2.2418431376329204,
                'T9': 2.2418431376329204},
                'T3': {'T1': 1.8146189808922477,
                'T10': 1.832709865628535,
                'T2': 2.2418431376329204,
                'T3': 0.0,
                'T4': 1.832709865628535,
                'T5': 1.832709865628535,
                'T6': 1.8146189808922477,
                'T7': 1.8146189808922477,
                'T8': 1.8146189808922477,
                'T9': 1.4811625503429378},
                'T4': {'T1': 1.832709865628535,
                'T10': 0.8434862029618123,
                'T2': 2.2418431376329204,
                'T3': 1.832709865628535,
                'T4': 0.0,
                'T5': 1.215095937098336,
                'T6': 1.832709865628535,
                'T7': 1.832709865628535,
                'T8': 1.832709865628535,
                'T9': 1.832709865628535},
                'T5': {'T1': 1.832709865628535,
                'T10': 1.215095937098336,
                'T2': 2.2418431376329204,
                'T3': 1.832709865628535,
                'T4': 1.215095937098336,
                'T5': 0.0,
                'T6': 1.832709865628535,
                'T7': 1.832709865628535,
                'T8': 1.832709865628535,
                'T9': 1.832709865628535},
                'T6': {'T1': 0.5848837844916799,
                'T10': 1.832709865628535,
                'T2': 2.2418431376329204,
                'T3': 1.8146189808922477,
                'T4': 1.832709865628535,
                'T5': 1.832709865628535,
                'T6': 0.0,
                'T7': 0.5848837844916799,
                'T8': 1.6307174196094565,
                'T9': 1.8146189808922477},
                'T7': {'T1': 0,
                'T10': 1.832709865628535,
                'T2': 2.2418431376329204,
                'T3': 1.8146189808922477,
                'T4': 1.832709865628535,
                'T5': 1.832709865628535,
                'T6': 0.5848837844916799,
                'T7': 0.0,
                'T8': 1.6307174196094565,
                'T9': 1.8146189808922477},
                'T8': {'T1': 1.6307174196094565,
                'T10': 1.832709865628535,
                'T2': 2.2418431376329204,
                'T3': 1.8146189808922477,
                'T4': 1.832709865628535,
                'T5': 1.832709865628535,
                'T6': 1.6307174196094565,
                'T7': 1.6307174196094565,
                'T8': 0.0,
                'T9': 1.8146189808922477},
                'T9': {'T1': 1.8146189808922477,
                'T10': 1.832709865628535,
                'T2': 2.2418431376329204,
                'T3': 1.4811625503429378,
                'T4': 1.832709865628535,
                'T5': 1.832709865628535,
                'T6': 1.8146189808922477,
                'T7': 1.8146189808922477,
                'T8': 1.8146189808922477,
                'T9': 0.0}}






                share|improve this answer












                share|improve this answer



                share|improve this answer










                answered Nov 28 '18 at 15:42









                Rob BrichenoRob Bricheno

                2,450420




                2,450420
































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