

In [2]:

    
import dendropy
import pandas as pd

Import tree with node labels. Because we'll use a pandas dataframe to associate the tip data with the tree, we want to preserve the underscores, assuming they exist in your data file of tip states. If not, set to false.



In [1]:

    
taxa = dendropy.TaxonSet()
mle = dendropy.Tree.get_from_path('vec_tree', 'newick', taxon_set=taxa, preserve_underscores=True)









    



---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-1-4fbee3a8739d> in <module>()
----> 1 taxa = dendropy.TaxonSet()
      2 mle = dendropy.Tree.get_from_path('vec_tree', 'newick', taxon_set=taxa, preserve_underscores=True)

NameError: name 'dendropy' is not defined

Import data. CSV with one column of taxon labels, one of tip states.



In [4]:

    
data = pd.read_csv('PyronParityData.csv', index_col=0)

Iterate over nodes, associating them with the tip states in the pandas dataframe.



In [5]:

    
for idx, nd in enumerate(mle.postorder_node_iter()):
    if nd.label is None:
        lookup = '{}'.format(nd.taxon)
        nd.label = int(data.ix[lookup])
    else: 
        pass

Associate value ranges with colors.



In [6]:

    
for nd in mle.postorder_node_iter():    
    if float(nd.label) == 0:
       nd.annotations.add_new(name = '!color', value = '#0000FF') #Dark blue, zeroes
    elif float(nd.label) > 0.00000000000001 and float(nd.label) < 0.16:
        nd.annotations.add_new(name = '!color', value = 'E50000') #Red, strongly viviparous        
    elif float(nd.label) > 0.17 and float(nd.label) < 0.41:
        nd.annotations.add_new(name = '!color', value = '##ffa500')#orangey-red, ambiguous viviparous     
    elif float(nd.label) > 0.42 and float(nd.label) < 0.67:
        nd.annotations.add_new(name = '!color', value = '#00ff00') #green, equivocal
    elif float(nd.label) > 0.66 and float(nd.label) < 0.85:
        nd.annotations.add_new(name = '!color', value = '#4DBD33') #darker green, ambiguous oviparous        
    elif float(nd.label) > .85 and float(nd.label) < 0.99999999999999:
        nd.annotations.add_new(name = '!color', value = '#0000FF') #Blue, strongly oviparous 
    elif float(nd.label) == 1.0:
         nd.annotations.add_new(name = '!color', value = '#ff0000') #Red, viviparous



In [367]:

    
#for index, node in enumerate(mle.postorder_node_iter()):
#   print node.label
#Change this to a print if you want to see a really long vector of node.labels. I just had this in as a check.



In [7]:

    
mle.write_to_path('attempt_1', 'nexus', suppress_annotations = False, annotations_as_nhx=False,
                  suppress_taxa_block=True,suppress_internal_taxon_labels=True)

You now have a FigTree-readable nexus with node and tip annotations.

Copyright (c) <2014> <April Wright, wright.aprilm@gmail.com>


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