heatmap and dendrogram (clustermap) error using Plotly

Question

The last example in Plotly’s documentation for Dendrograms has an error. When executing this code, I get this error in two locations due to ‘extend’:

AttributeError: ‘tuple’ object has no attribute ‘extend’

They are produced by these lines: figure.add_traces(heatmap) and figure['data'].extend(dendro_side['data'])

If anyone has run into this problem, please see my solution below! Happy coding!

Asked By: amc

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Source

Answer 1

I have a quick and accurate solution to run the last example code in Plotly’s documentation for Dendrograms. Note that I am using Plotly offline in a Jupyter Notebook.

Figure has methods to add_traces, and these should replace extend.

The three key lines are :

figure.add_traces(dendro_side[‘data’])
figure.add_traces(heatmap)
plotly.offline.iplot(figure, filename=‘dendrogram_with_heatmap’)

Here is the full example code with my corrections and necessary imports, below:

# Import Useful Things
import plotly
import plotly.plotly as py
import plotly.graph_objs as go
import plotly.figure_factory as ff
from plotly.offline import download_plotlyjs, init_notebook_mode, plot, iplot
init_notebook_mode(connected=True)    
plotly.offline.init_notebook_mode(connected=True)
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
figure.add_traces(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 = [
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']

figure.add_traces(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 using Plotly Offline
plotly.offline.iplot(figure, filename='dendrogram_with_heatmap')

This outputs:

Answered By: amc

heatmap and dendrogram (clustermap) error using Plotly

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