Phylo BioPython building trees
I trying to build a tree with BioPython, Phylo module.
What I've done so far is this image:each name has a four digit number followed by - and a number: this number refer to the number of times that sequence is represented. That means 1578 - 22, that node should represent 22sequences.
the file with the sequences aligned: file
the file with the distance to build a tree: fileSo now I known how to change each size of the node. Each node has a different size, this is easy doing an array of the different values:
fh = open(MEDIA_ROOT + "groupsnp.txt")
list_size = {}
for line in fh:
if '>' in line:
labels = line.split('>')
label = labels[-1]
label = label.split()
num = line.split('-')
size = num[-1]
size = size.split()
for lab in label:
for number in size:
list_size[lab] = int(number)
a = array(list_size.values())
But the array is arbitrary, I would like to put the correct node size into the right node, I tried this:
for elem in list_si开发者_C百科ze.keys():
if labels == elem:
Phylo.draw_graphviz(tree_xml, prog="neato", node_size=a)
but nothing appears when I use the if statement.
Anyway of doing this?
I would really appreciate!
Thanks everybody
I finally got this working. The basic premise is that you're going to use the labels/nodelist
to build your node_sizes
. This way they correlate properly. I'm sure I'm missing some important options to make the tree look 100% but it appears the node sizes are showing up properly.
#basically a stripped down rewrite of Phylo.draw_graphviz
import networkx, pylab
from Bio import Phylo
#taken from draw_graphviz
def get_label_mapping(G, selection):
for node in G.nodes():
if (selection is None) or (node in selection):
try:
label = str(node)
if label not in (None, node.__class__.__name__):
yield (node, label)
except (LookupError, AttributeError, ValueError):
pass
kwargs={}
tree = Phylo.read('tree.dnd', 'newick')
G = Phylo.to_networkx(tree)
Gi = networkx.convert_node_labels_to_integers(G, discard_old_labels=False)
node_sizes = []
labels = dict(get_label_mapping(G, None))
kwargs['nodelist'] = labels.keys()
#create our node sizes based on our labels because the labels are used for the node_list
#this way they should be correct
for label in labels.keys():
if str(label) != "Clade":
num = label.name.split('-')
#the times 50 is just a guess on what would look best
size = int(num[-1]) * 50
node_sizes.append(size)
kwargs['node_size'] = node_sizes
posi = networkx.pygraphviz_layout(Gi, 'neato', args='')
posn = dict((n, posi[Gi.node_labels[n]]) for n in G)
networkx.draw(G, posn, labels=labels, node_color='#c0deff', **kwargs)
pylab.show()
Resulting Tree
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