Python Networkx graph draw - labels/values inside tuple

Question

I want to draw a single networkX graph with items inside the tuple 'new'. My graph nodes will have labels such as "AXIN", and color will be green or yellow.

I want the node to be green color, if 'UNREPORTED'. If item[2] within tuple 'reported', I want this node to be yellow color.

> new = (('AXIN', 37, 'reported'),  ('LGR', 30, 'reported'),  ('NKD',
> 24, 'reported'),  ('TNFRSF', 23, 'UNREPORTED'),  ('CCND', 19,
> 'reported'),  ('APCDD', 18, 'reported'),  ('TR', 16, 'UNREPORTED'), 
> ('TOX', 15, 'UNREPORTED'),   ('LEF', 15, 'reported'),  ('MME', 13,
> 'reported'))
> 
> X, Y, _ = zip(*new) import seaborn as sns sns.set() import
> matplotlib.pyplot as plt  %matplotlib inline plt.figure(figsize = (20,
> 10)) mytitle = "Most common genes coexpressed with {gene1}, {gene2},
> {gene3}, {gene4}".format(gene1="axin2", gene2="lef", gene3="nkd1",
> gene4="lgr5") plt.title(mytitle, fontsize=40) plt.ylabel('Number of
> same gene encounters across studies', fontsize=20) ax =
> plt.bar(range(len(X)), Y, 0.6, align='center', tick_label = X,
> color="red")  ax = plt.xticks(rotation=90) new = tuple(new)
> 
> import networkx as nx children = sorted(new, key=lambda x: x[1])
> parent = children.pop()[0]
> 
> G = nx.Graph() for child, weight, _ in children: G.add_edge(parent,
> child, weight=weight) width = list(nx.get_edge_attributes(G,
> 'weight').values()) colors = [] for i in new:
>         if i[2] == 'UNREPORTED':
>                 colors.append('green')
>         elif i[2] == 'reported':
>                 colors.append('yellow') print(colors) plt.savefig("plt.gene-expression.pdf") plt.figure(figsize = (20, 10))
> mytitle = "Most common genes coexpressed with {gene1}, {gene2},
> {gene3}, {gene4}".format(gene1="axin2", gene2="lef", gene3="nkd1",
> gene4="lgr5") plt.title(mytitle, fontsize=40)
> 
> nx.draw_networkx(G, font_size=10, node_size=2000, alpha=0.6,
> node_color=colors) plt.savefig("gene-expression-graph.pdf")

With this code, I get two different graphs, with yellow nodes, other with green nodes.

harryscholes · Accepted Answer · 2017-03-12 12:47:32Z

0

You could use a dictionary comprehension with the ternary operator to build a mapping of the nodes to colors. This can be used to color the nodes when drawing the graph.

import networkx as nx

new = (('AXIN', 37, 'reported'),  ('LGR', 30, 'reported'),  ('NKD', 24, 'reported'),  ('TNFRSF', 23, 'UNREPORTED'),  ('CCND', 19, 'reported'),  ('APCDD', 18, 'reported'),  ('TR', 16, 'UNREPORTED'), ('TOX', 15, 'UNREPORTED'),   ('LEF', 15, 'reported'),  ('MME', 13, 'reported'))
children = sorted(new, key=lambda x: x[1])
node_color = {node[0]: 'y' if node[2] == 'reported' else 'g' for node in children}
parent = children.pop()[0]
G = nx.Graph()
for child in children: G.add_edge(parent, child[0])
nx.draw_networkx(G, node_color=[node_color[i] for i in G.nodes()])

edited Mar 12, 2017 at 12:47

answered Mar 11, 2017 at 18:21

harryscholes

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2 Comments

J.A Over a year ago

Thanks @h_s. unfortunately, it assigns the green color to any of the nodes. Not specifically to the "UNREPORTED" nodes only. I expected TNFRSF, TOX & TR to be green nodes. But I got APCDD as a green node, which is wrong because APCDD is reported.

harryscholes Over a year ago

@J.A I've now provided a fuller answer with a minimal working example. Hope this helps!

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