Notebook

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Version Check¶

Note: Dendrograms are available in version 1.8.7+. Run pip install plotly --upgrade to update your Plotly version.

In [1]:

import plotly
plotly.__version__

Out[1]:

'3.4.2'

Basic Dendrogram¶

In [7]:

import plotly.plotly as py
import plotly.figure_factory as ff

import numpy as np

X = np.random.rand(15, 15)
dendro = ff.create_dendrogram(X)
dendro['layout'].update({'width':800, 'height':500})
py.iplot(dendro, filename='simple_dendrogram')

Out[7]:

Set Color Threshold¶

In [3]:

import plotly.plotly as py
import plotly.figure_factory as ff

import numpy as np

X = np.random.rand(15, 15)
dendro = ff.create_dendrogram(X, color_threshold=1.5)
dendro['layout'].update({'width':800, 'height':500})
py.iplot(dendro, filename='simple_dendrogram_with_color_threshold')

Out[3]:

Set Orientation and Add Labels¶

In [4]:

import plotly.plotly as py
import plotly.figure_factory as ff

import numpy as np

X = np.random.rand(10, 10)
names = ['Jack', 'Oxana', 'John', 'Chelsea', 'Mark', 'Alice', 'Charlie', 'Rob', 'Lisa', 'Lily']
fig = ff.create_dendrogram(X, orientation='left', labels=names)
fig['layout'].update({'width':800, 'height':800})
py.iplot(fig, filename='dendrogram_with_labels')

Out[4]:

Plot a Dendrogram with a Heatmap¶

In [5]:

import plotly.plotly as py
import plotly.graph_objs as go
import plotly.figure_factory as ff

import numpy as np
from scipy.spatial.distance import pdist, squareform


# get data
data = np.genfromtxt("http://files.figshare.com/2133304/ExpRawData_E_TABM_84_A_AFFY_44.tab",
                     names=True,usecols=tuple(range(1,30)),dtype=float, delimiter="\t")
data_array = data.view((np.float, len(data.dtype.names)))
data_array = data_array.transpose()
labels = data.dtype.names

# Initialize figure by creating upper dendrogram
figure = ff.create_dendrogram(data_array, orientation='bottom', labels=labels)
for i in range(len(figure['data'])):
    figure['data'][i]['yaxis'] = 'y2'

# Create Side Dendrogram
dendro_side = ff.create_dendrogram(data_array, orientation='right')
for i in range(len(dendro_side['data'])):
    dendro_side['data'][i]['xaxis'] = 'x2'

# Add Side Dendrogram Data to Figure
for data in dendro_side['data']:
    figure.add_trace(data)

# Create Heatmap
dendro_leaves = dendro_side['layout']['yaxis']['ticktext']
dendro_leaves = list(map(int, dendro_leaves))
data_dist = pdist(data_array)
heat_data = squareform(data_dist)
heat_data = heat_data[dendro_leaves,:]
heat_data = heat_data[:,dendro_leaves]

heatmap = [
    go.Heatmap(
        x = dendro_leaves, 
        y = dendro_leaves,
        z = heat_data,    
        colorscale = 'Blues'
    )
]

heatmap[0]['x'] = figure['layout']['xaxis']['tickvals']
heatmap[0]['y'] = dendro_side['layout']['yaxis']['tickvals']

# Add Heatmap Data to Figure
for data in heatmap:
    figure.add_trace(data)

# Edit Layout
figure['layout'].update({'width':800, 'height':800,
                         'showlegend':False, 'hovermode': 'closest',
                         })
# Edit xaxis
figure['layout']['xaxis'].update({'domain': [.15, 1],
                                  'mirror': False,
                                  'showgrid': False,
                                  'showline': False,
                                  'zeroline': False,
                                  'ticks':""})
# Edit xaxis2
figure['layout'].update({'xaxis2': {'domain': [0, .15],
                                   'mirror': False,
                                   'showgrid': False,
                                   'showline': False,
                                   'zeroline': False,
                                   'showticklabels': False,
                                   'ticks':""}})

# Edit yaxis
figure['layout']['yaxis'].update({'domain': [0, .85],
                                  'mirror': False,
                                  'showgrid': False,
                                  'showline': False,
                                  'zeroline': False,
                                  'showticklabels': False,
                                  'ticks': ""})
# Edit yaxis2
figure['layout'].update({'yaxis2':{'domain':[.825, .975],
                                   'mirror': False,
                                   'showgrid': False,
                                   'showline': False,
                                   'zeroline': False,
                                   'showticklabels': False,
                                   'ticks':""}})

# Plot!
py.iplot(figure, filename='dendrogram_with_heatmap')

Out[5]:

In [6]:

dendro_side['layout']['xaxis']

Out[6]:

layout.XAxis({
    'mirror': 'allticks',
    'rangemode': 'tozero',
    'showgrid': False,
    'showline': True,
    'showticklabels': True,
    'ticks': 'outside',
    'type': 'linear',
    'zeroline': False
})

Reference¶

In [8]:

help(ff.create_dendrogram)

Help on function create_dendrogram in module plotly.figure_factory._dendrogram:

create_dendrogram(X, orientation='bottom', labels=None, colorscale=None, distfun=None, linkagefun=<function <lambda> at 0x000001C336B28048>, hovertext=None, color_threshold=None)
    BETA function that returns a dendrogram Plotly figure object.
    
    :param (ndarray) X: Matrix of observations as array of arrays
    :param (str) orientation: 'top', 'right', 'bottom', or 'left'
    :param (list) labels: List of axis category labels(observation labels)
    :param (list) colorscale: Optional colorscale for dendrogram tree
    :param (function) distfun: Function to compute the pairwise distance from
                               the observations
    :param (function) linkagefun: Function to compute the linkage matrix from
                               the pairwise distances
    :param (list[list]) hovertext: List of hovertext for constituent traces of dendrogram
                               clusters
    :param (double) color_threshold: Value at which the separation of clusters will be made
    
    Example 1: Simple bottom oriented dendrogram
    ```
    import plotly.plotly as py
    from plotly.figure_factory import create_dendrogram
    
    import numpy as np
    
    X = np.random.rand(10,10)
    dendro = create_dendrogram(X)
    plot_url = py.plot(dendro, filename='simple-dendrogram')
    
    ```
    
    Example 2: Dendrogram to put on the left of the heatmap
    ```
    import plotly.plotly as py
    from plotly.figure_factory import create_dendrogram
    
    import numpy as np
    
    X = np.random.rand(5,5)
    names = ['Jack', 'Oxana', 'John', 'Chelsea', 'Mark']
    dendro = create_dendrogram(X, orientation='right', labels=names)
    dendro['layout'].update({'width':700, 'height':500})
    
    py.iplot(dendro, filename='vertical-dendrogram')
    ```
    
    Example 3: Dendrogram with Pandas
    ```
    import plotly.plotly as py
    from plotly.figure_factory import create_dendrogram
    
    import numpy as np
    import pandas as pd
    
    Index= ['A','B','C','D','E','F','G','H','I','J']
    df = pd.DataFrame(abs(np.random.randn(10, 10)), index=Index)
    fig = create_dendrogram(df, labels=Index)
    url = py.plot(fig, filename='pandas-dendrogram')
    ```

In [10]:

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(
    'dendrograms.ipynb', 'python/dendrogram/', 'Python Dendrograms',
    'How to make a dendrogram in Python with Plotly. ',
    name = 'Dendrograms',
    title = "Dendrograms | Plotly",
    thumbnail='thumbnail/dendrogram.jpg', language='python',
    has_thumbnail='true', display_as='scientific', order=6,
    ipynb= '~notebook_demo/262')

Collecting git+https://github.com/plotly/publisher.git
  Cloning https://github.com/plotly/publisher.git to c:\users\thars\appdata\local\temp\pip-req-build-p1ivo3bg
Building wheels for collected packages: publisher
  Running setup.py bdist_wheel for publisher: started
  Running setup.py bdist_wheel for publisher: finished with status 'done'
  Stored in directory: C:\Users\thars\AppData\Local\Temp\pip-ephem-wheel-cache-jom4cebv\wheels\99\3e\a0\fbd22ba24cca72bdbaba53dbc23c1768755fb17b3af0f33966
Successfully built publisher
Installing collected packages: publisher
  Found existing installation: publisher 0.13
    Uninstalling publisher-0.13:
      Successfully uninstalled publisher-0.13
Successfully installed publisher-0.13

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