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‎pr-20/_sources/notebooks/examples/colouring_points.ipynb‎

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"\n",
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"We use the real Xenium `cells` dataset from `squidpy` (its `transcripts` element), downloaded and\n",
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"cached on first use. Point colouring uses the **matplotlib backend** (`method=\"matplotlib\"`) so every\n",
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"point keeps its own colour; `render_points` otherwise switches to datashader for very large sets — see\n",
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"the *Point density maps* and *Speeding up rendering* notebooks."
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"point keeps its own colour; `render_points` otherwise switches to datashader above ~10,000 points, which aggregates them and so\n",
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"cannot keep a distinct colour per point — see the *Point density maps* and *Speeding up rendering*\n",
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"notebooks."
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"sdata"
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]
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},
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{
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"cell_type": "markdown",
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"id": "71aaf0d7",
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"metadata": {},
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"source": [
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"The `cells` dataset is a small (~3 MB) crop of a real 10x **Xenium** breast-cancer section,\n",
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"cached locally after the first download. The colouring below draws on the columns of its\n",
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"`transcripts` points element:"
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]
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},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"['x',\n",
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" 'y',\n",
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" 'z',\n",
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" 'feature_name',\n",
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" 'cell_id',\n",
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" 'fov_name',\n",
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" 'codeword_index',\n",
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" 'qv',\n",
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" 'transcript_id',\n",
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" 'is_gene',\n",
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" 'codeword_category',\n",
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" 'nucleus_distance',\n",
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" 'overlaps_nucleus']"
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]
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},
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"execution_count": 2,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"list(sdata[\"transcripts\"].columns)"
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]
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},
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"cell_type": "markdown",
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"id": "997ac2bb",
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"## 4. Subsetting categories — `groups` and `na_color`\n",
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"\n",
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"`groups` restricts colouring to selected categories; everything else is drawn in `na_color`. Here we\n",
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"pick a few marker genes and grey out the rest."
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"pick a few marker genes and grey out the rest. Omit `na_color` and the non-matching points are hidden\n",
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"entirely instead of greyed."
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"- A **categorical** `color=` column draws a legend; set colours with `palette`, subset with `groups`,\n",
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" and style the remainder with `na_color`.\n",
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"- `size` and `alpha` tune the markers.\n",
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"- Per-point colouring uses the matplotlib backend; for millions of points switch to datashader\n",
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" (`method=\"datashader\"`, or `density=True`) — see the *Point density maps* and *Speeding up\n",
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" rendering* notebooks."
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"- Per-point colouring uses the matplotlib backend; `render_points` auto-switches to datashader above\n",
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" 10,000 points (which drops per-point colour), so pass `method=\"matplotlib\"` to force it — or reach\n",
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" for datashader deliberately (`method=\"datashader\"`, or `density=True`) for millions of points. See\n",
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" the *Point density maps* and *Speeding up rendering* notebooks."
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‎pr-20/_static/documentation_options.js‎

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const DOCUMENTATION_OPTIONS = {
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VERSION: '0.1.dev1+g375c17330.d20260818',
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VERSION: '0.1.dev1+g375c17330.d20260819',
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LANGUAGE: 'en',
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BUILDER: 'html',

‎pr-20/api.html‎

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‎pr-20/changelog.html‎

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<link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=90905a2f556bf617f1a9" />
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‎pr-20/contributing.html‎

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‎pr-20/gallery.html‎

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‎pr-20/genindex.html‎

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