Plotly clustered heatmap (with dendrogram)/Python

Question

I am trying to create a clustered heatmap (with a dendrogram) using plotly in Python. The one they have made in their website does not scale well, I have come to various solutions, but most of them are in R or JavaScript. I am trying to create a heatmap with a dendrogram from the left side of the heatmap only, showing clusters across the y axis (from the hierarchical clustering). A really good looking example is this one: https://chart-studio.plotly.com/~jackp/6748. My purpose is to create something like this, but only with the left-side dendrogram. If someone can implement something like this in Python, I will be really grateful!

Let the data be X = np.random.randint(0, 10, size=(120, 10))

It may seem like it sometimes, but StackOverflow is not a code-ordering service. Rather, you present what you've tried and the rest of us help out with whatever challenges you experience. Though since you're fairly new in the game and we're all very nice in here I'll see if I can work something together to at least get you started. — vestland

vestland vestland · Accepted Answer · 2021-03-09T22:29:04

The following suggestion draws on elements from both Dendrograms in Python and chart-studio.plotly.com/~jackp. This particular plot uses your data X = np.random.randint(0, 10, size=(120, 10)). One thing that the linked approaches had in common, was, in my opinion, that the datasets and data munging procedures were a bit messy. So I decided to build the following figure on a pandas dataframe with df = pd.DataFrame(X) to hopefully make everything a bit clearer

Plot

Complete code

import plotly.graph_objects as go
import plotly.figure_factory as ff

import numpy as np
import pandas as pd
from scipy.spatial.distance import pdist, squareform
import random
import string

X = np.random.randint(0, 10, size=(120, 10))
df = pd.DataFrame(X)

# Initialize figure by creating upper dendrogram
fig = ff.create_dendrogram(df.values, orientation='bottom')
fig.for_each_trace(lambda trace: trace.update(visible=False))

for i in range(len(fig['data'])):
    fig['data'][i]['yaxis'] = 'y2'

# Create Side Dendrogram
# dendro_side = ff.create_dendrogram(X, orientation='right', labels = labels)
dendro_side = ff.create_dendrogram(X, 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(df.values)
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, 1],
                                  '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':""})

fig.update_layout(paper_bgcolor="rgba(0,0,0,0)",
                  plot_bgcolor="rgba(0,0,0,0)",
                  xaxis_tickfont = dict(color = 'rgba(0,0,0,0)'))

fig.show()

Plotly clustered heatmap (with dendrogram)/Python

1 Answers

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Complete code