I try to add colored rectangle to dendrogram results like as follow:
this is my dendrogram codes:
from scipy.cluster.hierarchy import dendrogram ... plt.figure(figsize=(250, 100)) labelsize=20 ticksize=15 plt.title(file_name.split(".")[0], fontsize=labelsize) plt.xlabel('stock', fontsize=labelsize) plt.ylabel('distance', fontsize=labelsize) dendrogram( Z, leaf_rotation=90., # rotates the x axis labels leaf_font_size=8., # font size for the x axis labels labels = corr.columns ) pylab.yticks(fontsize=ticksize) pylab.xticks(rotation=-90, fontsize=ticksize)
However, this is only add colorful line not a rectangle like in the above image. How can I create image like this?
Thanks
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Answer
You can loop through the generated path collections and draw a bounding box.
Optionally, you could set the height to the color_threshold=
parameter, which defaults to Z[:, 2].max() * 0.7
.
The last collection is are the unclassified lines, so the example code below loops through all earlier collections.
import matplotlib.pyplot as plt from scipy.cluster import hierarchy import numpy as np N = 15 ytdist = np.random.randint(10, 1000, N * (N + 1) // 2) Z = hierarchy.linkage(ytdist) fig, ax = plt.subplots(1, 1, figsize=(8, 3)) dn1 = hierarchy.dendrogram(Z, ax=ax) for coll in ax.collections[:-1]: # the last collection is the ungrouped level xmin, xmax = np.inf, -np.inf ymax = -np.inf for p in coll.get_paths(): box = p.get_extents() (x0, _), (x1, y1) = p.get_extents().get_points() xmin = min(xmin, x0) xmax = max(xmax, x1) ymax = max(ymax, y1) rec = plt.Rectangle((xmin - 4, 0), xmax - xmin + 8, ymax*1.05, facecolor=coll.get_color()[0], alpha=0.2, edgecolor="none") ax.add_patch(rec) plt.show()