dendrogram.md

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jupytext kernelspec language_info plotly notebook_metadata_filter text_representation all extension format_name format_version jupytext_version .md markdown 1.1 1.1.1 display_name language name Python 3 python python3 codemirror_mode file_extension mimetype name nbconvert_exporter pygments_lexer version name version ipython 3 .py text/x-python python python ipython3 3.6.7 description display_as language layout name order page_type permalink thumbnail How to make a dendrogram in Python with Plotly. scientific python base Dendrograms 6 u-guide python/dendrogram/ thumbnail/dendrogram.jpg

Basic Dendrogram

A dendrogram is a diagram representing a tree. The figure factory called create_dendrogram performs hierarchical clustering on data and represents the resulting tree. Values on the tree depth axis correspond to distances between clusters.

Dendrogram plots are commonly used in computational biology to show the clustering of genes or samples, sometimes in the margin of heatmaps.

import plotly.figure_factory as ff
import numpy as np
np.random.seed(1)

X = np.random.rand(15, 12) # 15 samples, with 12 dimensions each
fig = ff.create_dendrogram(X)
fig.update_layout(width=800, height=500)
fig.show()

Set Color Threshold

import plotly.figure_factory as ff

import numpy as np

X = np.random.rand(15, 10) # 15 samples, with 10 dimensions each
fig = ff.create_dendrogram(X, color_threshold=1.5)
fig.update_layout(width=800, height=500)
fig.show()

Set Orientation and Add Labels

import plotly.figure_factory as ff

import numpy as np

X = np.random.rand(10, 12)
names = ['Jack', 'Oxana', 'John', 'Chelsea', 'Mark', 'Alice', 'Charlie', 'Rob', 'Lisa', 'Lily']
fig = ff.create_dendrogram(X, orientation='left', labels=names)
fig.update_layout(width=800, height=800)
fig.show()

Plot a Dendrogram with a Heatmap

See also the Dash Bio demo.

import plotly.graph_objects 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((float, len(data.dtype.names)))
data_array = data_array.transpose()
labels = data.dtype.names

# Initialize figure by creating upper dendrogram
fig = ff.create_dendrogram(data_array, orientation='bottom', labels=labels)
for i in range(len(fig['data'])):
    fig['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']:
    fig.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'] = fig['layout']['xaxis']['tickvals']
heatmap[0]['y'] = dendro_side['layout']['yaxis']['tickvals']

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

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

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

# Plot!
fig.show()

Reference

For more info on ff.create_dendrogram(), see the full function reference