Created
August 3, 2017 10:58
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import scipy | |
import matplotlib.pyplot as plt | |
import scipy.cluster.hierarchy as sch | |
# %matplotlib inline | |
# uncomment the above line if using Jupyter notebook | |
# creating dummy variable for plotting | |
# 'D' is a 2-d array that has our data | |
# for demonstartion purpose we are creating random variables | |
x = scipy.rand(40) | |
D = scipy.zeros([40,40]) | |
for i in range(40): | |
for j in range(40): | |
D[i, j] = abs(x[i] - x[j]) | |
# Dendrogram that comes to the left | |
fig = plt.figure(figsize=(8,8)) | |
# Add an axes at position rect [left, bottom, width, height] | |
ax1 = fig.add_axes([0.09, 0.1, 0.2, 0.6]) | |
Y = sch.linkage(D, method='centroid') | |
# orientation='left' is reponsible for making the | |
# dendrogram appear to the left | |
Z1 = sch.dendrogram(Y, orientation='left') | |
ax1.set_xticks([]) | |
ax1.set_yticks([]) | |
# top side dendogram | |
ax2 = fig.add_axes([0.3, 0.71, 0.6, 0.2]) | |
Y = sch.linkage(D, method='single') | |
Z2 = sch.dendrogram(Y) | |
ax2.set_xticks([]) | |
ax2.set_yticks([]) | |
# main heat-map | |
axmatrix = fig.add_axes([0.3, 0.1, 0.6, 0.6]) | |
idx1 = Z1['leaves'] | |
idx2 = Z2['leaves'] | |
D = D[idx1, :] | |
D = D[:, idx2] | |
# the actual heat-map | |
im = axmatrix.matshow(D, aspect='auto', origin='lower', cmap="YlGnBu") | |
axmatrix.set_xticks([]) | |
axmatrix.set_yticks([]) | |
# xticks to the right (x-axis) | |
axmatrix.set_xticks(range(40)) | |
axmatrix.set_xticklabels(idx1, minor=False) | |
axmatrix.xaxis.set_label_position('bottom') | |
axmatrix.xaxis.tick_bottom() | |
plt.xticks(rotation=-90, fontsize=8) | |
# xticks to the right (y-axis) | |
axmatrix.set_yticks(range(40)) | |
axmatrix.set_yticklabels(idx2, minor=False) | |
axmatrix.yaxis.set_label_position('right') | |
axmatrix.yaxis.tick_right() | |
# to add the color bar | |
# axcolor = fig.add_axes([0.94, 0.1, 0.02, 0.6]) | |
plt.show() |
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