{
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    {
      "cell_type": "code",
      "execution_count": null,
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      "source": [
        "%matplotlib inline"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "\n# Extracting parts of a contact map\n\n\nThis example shows how to extract contact counts associated to some chromosomes\nof the contact maps. Here, we extract chromosomes 1, 4 and 5 of the budding\nyeasts contact map\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "import matplotlib.pyplot as plt\nfrom matplotlib import colors\n\nfrom iced import datasets\nfrom iced.utils import extract_sub_contact_map\n\n\n# Loading a sample dataset\ncounts, lengths = datasets.load_sample_yeast()\nsub_counts, sub_lengths = extract_sub_contact_map(counts, lengths, [0, 3, 4])\n\nfig, ax = plt.subplots()\nm = ax.matshow(sub_counts, cmap=\"Blues\", norm=colors.SymLogNorm(1),\n               origin=\"bottom\",\n               extent=(0, len(sub_counts), 0, len(sub_counts)))\n[ax.axhline(i, linewidth=1, color=\"#000000\") for i in sub_lengths.cumsum()]\n[ax.axvline(i, linewidth=1, color=\"#000000\") for i in sub_lengths.cumsum()]\ncb = fig.colorbar(m)\nax.set_title(\"Chromosomes I, IV and V of yeast\")"
      ]
    }
  ],
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      "display_name": "Python 3",
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