Notebook

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Basic Tree-Plot in Plotly with igraph ¶

In [3]:

import plotly.plotly as py
import plotly.graph_objs as go

import igraph
from igraph import *
igraph.__version__

Out[3]:

'0.7.1'

Set Up Tree with igraph ¶

In [4]:

nr_vertices = 25
v_label = map(str, range(nr_vertices))
G = Graph.Tree(nr_vertices, 2) # 2 stands for children number
lay = G.layout('rt')

position = {k: lay[k] for k in range(nr_vertices)}
Y = [lay[k][1] for k in range(nr_vertices)]
M = max(Y)

es = EdgeSeq(G) # sequence of edges
E = [e.tuple for e in G.es] # list of edges

L = len(position)
Xn = [position[k][0] for k in range(L)]
Yn = [2*M-position[k][1] for k in range(L)]
Xe = []
Ye = []
for edge in E:
    Xe+=[position[edge[0]][0],position[edge[1]][0], None]
    Ye+=[2*M-position[edge[0]][1],2*M-position[edge[1]][1], None] 

labels = v_label

Create Plotly Traces¶

In [5]:

lines = go.Scatter(x=Xe,
                   y=Ye,
                   mode='lines',
                   line=dict(color='rgb(210,210,210)', width=1),
                   hoverinfo='none'
                   )
dots = go.Scatter(x=Xn,
                  y=Yn,
                  mode='markers',
                  name='',
                  marker=dict(symbol='dot',
                                size=18, 
                                color='#6175c1',    #'#DB4551', 
                                line=dict(color='rgb(50,50,50)', width=1)
                                ),
                  text=labels,
                  hoverinfo='text',
                  opacity=0.8
                  )

Create Text Inside the Circle via Annotations¶

In [6]:

def make_annotations(pos, text, font_size=10, font_color='rgb(250,250,250)'):
    L=len(pos)
    if len(text)!=L:
        raise ValueError('The lists pos and text must have the same len')
    annotations = go.Annotations()
    for k in range(L):
        annotations.append(
            go.Annotation(
                text=labels[k], # or replace labels with a different list for the text within the circle  
                x=pos[k][0], y=2*M-position[k][1],
                xref='x1', yref='y1',
                font=dict(color=font_color, size=font_size),
                showarrow=False)
        )
    return annotations  

Add Axis Specifications and Create the Layout¶

In [7]:

axis = dict(showline=False, # hide axis line, grid, ticklabels and  title
            zeroline=False,
            showgrid=False,
            showticklabels=False,
            )

layout = dict(title= 'Tree with Reingold-Tilford Layout',  
              annotations=make_annotations(position, v_label),
              font=dict(size=12),
              showlegend=False,
              xaxis=go.XAxis(axis),
              yaxis=go.YAxis(axis),          
              margin=dict(l=40, r=40, b=85, t=100),
              hovermode='closest',
              plot_bgcolor='rgb(248,248,248)'          
              )

Plot!¶

In [8]:

data=go.Data([lines, dots])
fig=dict(data=data, layout=layout)
fig['layout'].update(annotations=make_annotations(position, v_label))
py.iplot(fig, filename='Tree-Reingold-Tilf')

Out[8]:

Reference¶

See https://plotly.com/python/reference/ for more information and chart attribute options and http://igraph.org/python/ for more information about the igraph package!

In [1]:

from IPython.display import display, HTML

display(HTML('<link href="//fonts.googleapis.com/css?family=Open+Sans:600,400,300,200|Inconsolata|Ubuntu+Mono:400,700" rel="stylesheet" type="text/css" />'))
display(HTML('<link rel="stylesheet" type="text/css" href="http://help.plot.ly/documentation/all_static/css/ipython-notebook-custom.css">'))

! pip install git+https://github.com/plotly/publisher.git --upgrade
import publisher
publisher.publish(
    'tree-plot.ipynb', 'python/tree-plots/', 'Python Tree-plots | plotly',
    'How to make interactive tree-plot in Python with Plotly. '
    'An examples of a tree-plot in Plotly.',
    title = 'Python Tree-plots | plotly',
    name = 'Tree-plots',
    thumbnail='thumbnail/treeplot.jpg', language='python',
    page_type='example_index', has_thumbnail='true', display_as='statistical', order=10.5,
    ipynb= '~notebook_demo/28')

Collecting git+https://github.com/plotly/publisher.git
  Cloning https://github.com/plotly/publisher.git to /var/folders/ld/6cl3s_l50wd40tdjq2b03jxh0000gp/T/pip-aq6dfc11-build
Installing collected packages: publisher
  Found existing installation: publisher 0.10
    Uninstalling publisher-0.10:
      Successfully uninstalled publisher-0.10
  Running setup.py install for publisher ... - \ done
Successfully installed publisher-0.10

/Users/brandendunbar/Desktop/test/venv/lib/python2.7/site-packages/IPython/nbconvert.py:13: ShimWarning: The `IPython.nbconvert` package has been deprecated. You should import from nbconvert instead.
  "You should import from nbconvert instead.", ShimWarning)
/Users/brandendunbar/Desktop/test/venv/lib/python2.7/site-packages/publisher/publisher.py:53: UserWarning: Did you "Save" this notebook before running this command? Remember to save, always save.
  warnings.warn('Did you "Save" this notebook before running this command? '

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