Digits dataset



In [1]:

    
%load_ext autoreload
%autoreload 2



In [2]:

    
import numpy as np
import sklearn
from sklearn import datasets
try:
    import umap
except ImportError:
    print("This example requires the UMAP library. You can install it with the command `!pip install umap-learn`")
import warnings
warnings.filterwarnings("ignore")



In [3]:

    
import kmapper as km
from kmapper.plotlyviz import plotlyviz
from kmapper.plotlyviz import *
import plotly.graph_objs as go
import ipywidgets as ipw



In [4]:

    
data, labels = datasets.load_digits().data, datasets.load_digits().target



In [ ]:

    
mapper = km.KeplerMapper(verbose=0)

projected_data = mapper.fit_transform(data, projection=umap.UMAP(n_neighbors=8,
                                                                 min_dist=0.65,
                                                                 n_components=2,
                                                                 metric='euclidean',
                                                                 random_state=3571))

# Get the simplicial complex  
scomplex = mapper.map(projected_data,
                      clusterer=sklearn.cluster.DBSCAN(eps=0.3, min_samples=15),
                      coverer=km.Cover(35, 0.9))

The mapper graph nodes associated to this data set are colored according to the color_function values with Viridis colorscale, which is the default color scale, defined in plotlyviz.



In [ ]:

    
color_function = projected_data[:, 1]-projected_data[:, 1].min()
plotlyviz(scomplex, 
          title='Mapper graph of digits dataset',
          color_function=color_function, 
          color_function_name='Distance to y-min', 
          node_linecolor='rgb(100,100,100)',
          bgcolor='rgb(240,240,240)',
          width=620, height=620,
          summary_height=350,
          summary_left=10,
          hist_left=25,
          hist_right=10,
          graph_data=True)



In [ ]:

    
color_function = projected_data[:, 1]-projected_data[:, 1].min()
plotlyviz(scomplex, 
          title='Mapper graph of digits dataset',
          color_function=color_function, 
          color_function_name='Distance to y-min', 
          node_linecolor='rgb(100,100,100)',
          bgcolor='rgb(240,240,240)',
          width=620, height=620,
          summary_height=350,
          summary_left=10,
          hist_left=25,
          hist_right=10,
          member_textbox_width=500,
          dashboard=True)



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