tree-plots

emmanuelle · emmanuelle · commit 7d0bd9fb12bc · 2019-06-12T14:32:23.000+02:00
diff --git a/notebooks/tree-plots.md b/notebooks/tree-plots.md
@@ -1,15 +1,26 @@
 ---
 jupyter:
   jupytext:
+    notebook_metadata_filter: all
     text_representation:
       extension: .md
       format_name: markdown
       format_version: '1.1'
       jupytext_version: 1.1.1
   kernelspec:
-    display_name: Python 2
+    display_name: Python 3
     language: python
-    name: python2
+    name: python3
+  language_info:
+    codemirror_mode:
+      name: ipython
+      version: 3
+    file_extension: .py
+    mimetype: text/x-python
+    name: python
+    nbconvert_exporter: python
+    pygments_lexer: ipython3
+    version: 3.6.7
   plotly:
     description: How to make interactive tree-plot in Python with Plotly. An examples
       of a tree-plot in Plotly.
@@ -25,28 +36,15 @@ jupyter:
     title: Python Tree-plots | plotly
 ---
 
-#### New to Plotly?
-Plotly's Python library is free and open source! [Get started](https://plot.ly/python/getting-started/) by downloading the client and [reading the primer](https://plot.ly/python/getting-started/).
-<br>You can set up Plotly to work in [online](https://plot.ly/python/getting-started/#initialization-for-online-plotting) or [offline](https://plot.ly/python/getting-started/#initialization-for-offline-plotting) mode, or in [jupyter notebooks](https://plot.ly/python/getting-started/#start-plotting-online).
-<br>We also have a quick-reference [cheatsheet](https://images.plot.ly/plotly-documentation/images/python_cheat_sheet.pdf) (new!) to help you get started!
-
+#### Set Up Tree with [igraph](http://igraph.org/python/)
 
-#### Basic Tree-Plot in Plotly with [igraph](http://igraph.org/python/)
+Install igraph with `pip install python-igraph`.
 
 ```python
-import plotly.plotly as py
-import plotly.graph_objs as go
-
 import igraph
-from igraph import *
-igraph.__version__
-```
-
-#### Set Up Tree with [igraph](http://igraph.org/python/)
-
-```python
+from igraph import Graph, EdgeSeq
 nr_vertices = 25
-v_label = map(str, range(nr_vertices))
+v_label = list(map(str, range(nr_vertices)))
 G = Graph.Tree(nr_vertices, 2) # 2 stands for children number
 lay = G.layout('rt')
 
@@ -72,6 +70,7 @@ labels = v_label
 #### Create Plotly Traces
 
 ```python
+import plotly.graph_objs as go
 lines = go.Scatter(x=Xe,
                    y=Ye,
                    mode='lines',
@@ -81,8 +80,8 @@ lines = go.Scatter(x=Xe,
 dots = go.Scatter(x=Xn,
                   y=Yn,
                   mode='markers',
-                  name='',
-                  marker=dict(symbol='dot',
+                  name='bla',
+                  marker=dict(symbol='circle-dot',
                                 size=18, 
                                 color='#6175c1',    #'#DB4551', 
                                 line=dict(color='rgb(50,50,50)', width=1)
@@ -100,10 +99,10 @@ 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()
+    annotations = []
     for k in range(L):
         annotations.append(
-            go.Annotation(
+            dict(
                 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',
@@ -124,10 +123,10 @@ axis = dict(showline=False, # hide axis line, grid, ticklabels and  title
 
 layout = dict(title= 'Tree with Reingold-Tilford Layout',  
               annotations=make_annotations(position, v_label),
-              font=dict(size=12),
+              font_size=12,
               showlegend=False,
-              xaxis=go.XAxis(axis),
-              yaxis=go.YAxis(axis),          
+              xaxis=axis,
+              yaxis=axis,          
               margin=dict(l=40, r=40, b=85, t=100),
               hovermode='closest',
               plot_bgcolor='rgb(248,248,248)'          
@@ -137,34 +136,10 @@ layout = dict(title= 'Tree with Reingold-Tilford Layout',
 #### Plot!
 
 ```python
-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')
+fig=go.Figure(data=[lines, dots], layout=layout)
+fig.show()
 ```
 
 #### Reference
 See https://plot.ly/python/reference/ for more information and chart attribute options and http://igraph.org/python/ for more information about the igraph package!
 
-```python
-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')
-```
-
-```python
-
-```
