{
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "\n# Showing clusters\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "A cluster is displayed as a subtree in the dendrogram. The :func:`~pdendro.attach_dendrogram`\nfunction can display clusters by specifying their root nodes. Let us assume that we have\nthe following linkage matrix:\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "import scipy\n\nX = [[0.0], [1.0], [3.0], [6.0]]\nZ = scipy.cluster.hierarchy.linkage(X)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "The data points can be assigned to clusters using the :func:`scipy.cluster.hierarchy.fcluster`\nfunction, and their root nodes can be obtained using the :func:`scipy.cluster.hierarchy.leaders`\nfunction:\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "T = scipy.cluster.hierarchy.fcluster(Z, 1.5, criterion=\"distance\")\nL, _ = scipy.cluster.hierarchy.leaders(Z, T)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Then, the clusters can be shown with root node markers and different colors:\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "import plotly.graph_objects as go\nimport plotly.io as pio\n\nfrom pdendro import attach_dendrogram\n\nfig = go.Figure()\nattach_dendrogram(fig, Z, subtrees=L)\npio.show(fig)"
      ]
    }
  ],
  "metadata": {
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      "display_name": "Python 3",
      "language": "python",
      "name": "python3"
    },
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      "codemirror_mode": {
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      },
      "file_extension": ".py",
      "mimetype": "text/x-python",
      "name": "python",
      "nbconvert_exporter": "python",
      "pygments_lexer": "ipython3",
      "version": "3.14.4"
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  "nbformat": 4,
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