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Dendrograms in Python

How to make a dendrogram in Python with Plotly.

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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]:
'2.0.2'
Basic Dendrogram
In [2]:
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[2]:
Set Orientation and Add Labels
In [3]:
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[3]:
Plot a Dendrogram with a Heatmap
In [3]:
import plotly.plotly as py
from plotly.graph_objs import *
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
figure['data'].extend(dendro_side['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 = Data([
    Heatmap(
        x = dendro_leaves,
        y = dendro_leaves,
        z = heat_data,
        colorscale = 'YIGnBu'
    )
])

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

# Add Heatmap Data to Figure
figure['data'].extend(Data(heatmap))

# 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[3]:
In [4]:
dendro_side['layout']['xaxis']
Out[4]:
{'mirror': 'allticks',
 'rangemode': 'tozero',
 'showgrid': False,
 'showline': True,
 'showticklabels': True,
 'ticks': 'outside',
 'type': 'linear',
 'zeroline': False}

Reference

In [5]:
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>>)
    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

        clusters

    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')
    ```

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