{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# JointView\n",
"JointView can be used to visualize trans or cis-remote region by composing frames around a hicmat."
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"execution": {
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},
"pycharm": {
"name": "#%%\n"
}
},
"outputs": [],
"source": [
"import coolbox\n",
"from coolbox.api import *"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"execution": {
"iopub.execute_input": "2025-11-10T03:54:16.495008Z",
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"shell.execute_reply": "2025-11-10T03:54:16.507726Z"
},
"pycharm": {
"name": "#%%\n"
}
},
"outputs": [
{
"data": {
"text/plain": [
"'0.4.0'"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"coolbox.__version__"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Visualize the cis-remote region:"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"execution": {
"iopub.execute_input": "2025-11-10T03:54:16.540796Z",
"iopub.status.busy": "2025-11-10T03:54:16.540192Z",
"iopub.status.idle": "2025-11-10T03:54:19.650381Z",
"shell.execute_reply": "2025-11-10T03:54:19.648773Z"
},
"tags": [
"nbsphinx-thumbnail"
]
},
"outputs": [
{
"data": {
"image/svg+xml": [
"\n",
"\n"
],
"text/plain": [
""
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"DATA_DIR = f\"../../../tests/test_data\"\n",
"test_interval = \"chr9:4000000-6000000\"\n",
"empty_interval = \"chr10:4000000-6000000\"\n",
"test_itv = test_interval.replace(':', '_').replace('-', '_')\n",
"\n",
"\n",
"frame1 = XAxis() + GTF(f\"{DATA_DIR}/gtf_{test_itv}.gtf\") + Title(\"GTF\")\n",
"frame1 += BigWig(f\"{DATA_DIR}/bigwig_{test_itv}.bw\") + TrackHeight(2) + MinValue(0)\n",
"frame2 = XAxis()\n",
"frame2 += GTF(f\"{DATA_DIR}/gtf_{test_itv}.gtf\") + TrackHeight(5)\n",
"\n",
"cool1 = Cool(f\"{DATA_DIR}/cool_{test_itv}.mcool\", color_bar=False, style='matrix')\n",
"\n",
"sub_frames = {\n",
" \"top\": frame1,\n",
" \"right\": frame1,\n",
" \"bottom\": frame2,\n",
" \"left\": frame2\n",
"}\n",
"\n",
"jv = JointView(cool1, **sub_frames, space=0, padding_left=0)\n",
"fig = jv.plot(\"chr9:4500000-5000000\", \"chr9:5200000-5850000\")\n",
"fig"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Or you can just use it to compose track in joint style,\n",
"pass one genome region to the `plot` method:"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"execution": {
"iopub.execute_input": "2025-11-10T03:54:19.653501Z",
"iopub.status.busy": "2025-11-10T03:54:19.653009Z",
"iopub.status.idle": "2025-11-10T03:54:23.034975Z",
"shell.execute_reply": "2025-11-10T03:54:23.028292Z"
},
"scrolled": false
},
"outputs": [
{
"data": {
"image/svg+xml": [
"\n",
"\n"
],
"text/plain": [
""
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"cool1 = Cool(f\"{DATA_DIR}/cool_{test_itv}.mcool\", color_bar=False) + \\\n",
" HiCPeaksCoverage(f\"{DATA_DIR}/peak_{test_itv}.bedpe\")\n",
"\n",
"sub_frames = {\n",
" \"top\": frame1,\n",
" \"right\": frame1,\n",
" \"bottom\": frame2,\n",
" \"left\": frame2\n",
"}\n",
"\n",
"jv = JointView(cool1, **sub_frames, space=0, padding_left=0)\n",
"fig = jv.plot(\"chr9:4000000-6000000\")\n",
"fig"
]
},
{
"cell_type": "markdown",
"metadata": {
"pycharm": {
"name": "#%% md\n"
}
},
"source": [
"### CLI code"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"execution": {
"iopub.execute_input": "2025-11-10T03:54:23.041813Z",
"iopub.status.busy": "2025-11-10T03:54:23.041587Z",
"iopub.status.idle": "2025-11-10T03:54:31.560482Z",
"shell.execute_reply": "2025-11-10T03:54:31.560025Z"
},
"pycharm": {
"name": "#%%\n"
}
},
"outputs": [],
"source": [
"%%bash\n",
"\n",
"DATA_DIR=\"../../../tests/test_data\"\n",
"test_itv=\"chr9_4000000_6000000\"\n",
"coolbox \\\n",
" joint_view top - \\\n",
" add XAxis - \\\n",
" add GTF ${DATA_DIR}/gtf_${test_itv}.gtf - \\\n",
" add Title GTF - \\\n",
" joint_view right - \\\n",
" add XAxis - \\\n",
" add BigWig ${DATA_DIR}/bigwig_${test_itv}.bw - \\\n",
" add TrackHeight 2 - \\\n",
" add MinValue 0 - \\\n",
" joint_view center - \\\n",
" add Cool ${DATA_DIR}/cool_${test_itv}.mcool - \\\n",
" goto 'chr9:4500000-5000000' 'chr9:5200000-5850000' - \\\n",
" plot /tmp/test_coolbox_joint_view.svg"
]
}
],
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"celltoolbar": "编辑元数据",
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"name": "python3"
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"file_extension": ".py",
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"name": "python",
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