{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "0",
   "metadata": {},
   "source": [
    "# Basic plotting tools\n",
    "\n",
    "hv resources\n",
    "- Gallery: https://holoviews.org/reference/\n",
    "- https://holoviews.org/user_guide/Customizing_Plots.html\n",
    "- https://holoviews.org/user_guide/Style_Mapping.html\n",
    "- https://holoviews.org/user_guide/Colormaps.html\n",
    "- https://holoviews.org/user_guide/Plotting_with_Bokeh.html"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "1",
   "metadata": {},
   "outputs": [],
   "source": [
    "%load_ext autoreload\n",
    "%autoreload 2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "2",
   "metadata": {},
   "outputs": [],
   "source": [
    "import holoviews as hv\n",
    "\n",
    "import hv_anndata\n",
    "from hv_anndata import A, register\n",
    "from hv_anndata import scanpy as hv_sc\n",
    "\n",
    "register()\n",
    "\n",
    "hv.extension(\"bokeh\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "3",
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import scanpy as sc\n",
    "\n",
    "rng = np.random.default_rng()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "4",
   "metadata": {},
   "outputs": [],
   "source": [
    "adata = sc.datasets.pbmc68k_reduced()\n",
    "adata.layers[\"counts\"] = adata.raw.X\n",
    "del adata.raw\n",
    "sc.tl.umap(adata)\n",
    "adata"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "5",
   "metadata": {},
   "source": [
    "{func}`scanpy.pl.scatter`\n",
    "\n",
    "missing features:\n",
    "- `use_raw` (deprecated!)\n",
    "- `na_color` (not super important)\n",
    "- `color=dimension` in plotly backend: {issue}`holoviz/holoviews#5222`\n",
    "\n",
    "missing convenience:\n",
    "- `basis` for easy X&Y"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "6",
   "metadata": {},
   "outputs": [],
   "source": [
    "(\n",
    "    hv_sc.scatter(adata, A.X[:, [\"PSAP\", \"C1QA\"]], color=A.obs[\"bulk_labels\"]).opts(\n",
    "        cmap=\"tab10\", show_legend=False\n",
    "    )\n",
    "    + hv_sc.scatter(\n",
    "        adata, A.layers[\"counts\"][:, [\"PSAP\", \"C1QA\"]], color=A.obs[\"bulk_labels\"]\n",
    "    ).opts(cmap=\"tab10\")\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "7",
   "metadata": {},
   "outputs": [],
   "source": [
    "# add NAs to check how missing values look\n",
    "adata_scatter = adata.copy()\n",
    "adata_scatter.obs.loc[\n",
    "    (\n",
    "        (adata_scatter.obs[\"bulk_labels\"] == \"Dendritic\")\n",
    "        & rng.choice([True, False], size=len(adata_scatter))\n",
    "    ),\n",
    "    \"bulk_labels\",\n",
    "] = np.nan\n",
    "\n",
    "hv_sc.umap(adata_scatter) + hv_sc.umap(adata_scatter, color=A.obs[\"bulk_labels\"]).opts(\n",
    "    cmap=\"tab10\"\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "8",
   "metadata": {},
   "source": [
    "{func}`scanpy.pl.heatmap`\n",
    "\n",
    "missing:\n",
    "- `groupby` / [TickBar](https://github.com/holoviz/holoviews/issues/6658)\n",
    "- `standard_scale` (see implemantation in {class}`hv_anndata.Dotmap`)\n",
    "  - maybe done using [`dim` expressions](https://holoviews.org/user_guide/Transforming_Elements.html)?\n",
    "- dendrogram doesn’t work on heatmap (again ndim problem: dendrogram should tread `(n, 1)` as 1D)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "9",
   "metadata": {},
   "outputs": [],
   "source": [
    "markers = [\"C1QA\", \"PSAP\", \"CD79A\", \"CD79B\", \"CST3\", \"LYZ\"]\n",
    "(\n",
    "    hv_sc.heatmap(adata[:, markers], A.X, [A.obs[\"n_counts\"]], add_dendrogram=\"obs\")\n",
    "    + hv_sc.heatmap(adata[:, markers], A.layers[\"counts\"], [A.obs[\"n_counts\"]])\n",
    ").cols(1).opts(hv.opts.HeatMap(xticks=0, width=800, height=300)).opts(shared_axes=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "10",
   "metadata": {},
   "source": [
    "TODO: support sparse data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "11",
   "metadata": {},
   "outputs": [],
   "source": [
    "hv_sc.heatmap(adata[:40], A.obsp[\"distances\"]).opts(tools=[\"hover\"])"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "12",
   "metadata": {},
   "source": [
    "{func}`scanpy.pl.dotplot`\n",
    "\n",
    "missing:\n",
    "- `var_group_*` (highlight groups of `var_names` by drawing brackets)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "13",
   "metadata": {},
   "outputs": [],
   "source": [
    "markers = [\"C1QA\", \"PSAP\", \"CD79A\", \"CD79B\", \"CST3\", \"LYZ\"]\n",
    "dm = hv_anndata.Dotmap(adata=adata, marker_genes=markers, groupby=\"bulk_labels\")\n",
    "dm"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "14",
   "metadata": {},
   "outputs": [],
   "source": [
    "hv.operation.dendrogram(\n",
    "    dm.plot(), adjoint_dims=[\"cluster\"], main_dim=\"mean_expression\", invert=True\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "15",
   "metadata": {},
   "source": [
    "{func}`scanpy.pl.tracksplot`\n",
    "\n",
    "missing:\n",
    "- `shared_xaxis=False` doesn’t seem to work on GridSpace\n",
    "- GridSpace can only be 2D or row-only, not col-only\n",
    "- [GridSpace `show_legend` broken](https://github.com/holoviz/holoviews/issues/5438)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "16",
   "metadata": {},
   "outputs": [],
   "source": [
    "hv_sc.tracksplot(\n",
    "    adata,\n",
    "    A.X[:, [\"C1QA\", \"PSAP\", \"CD79A\", \"CD79B\", \"CST3\", \"LYZ\"]],\n",
    "    color=A.obs[\"bulk_labels\"],\n",
    ").opts(hv.opts.Curve(aspect=20))"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "17",
   "metadata": {},
   "source": [
    "{func}`scanpy.pl.violin`\n",
    "\n",
    "missing:\n",
    "- `density_norm`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "18",
   "metadata": {},
   "outputs": [],
   "source": [
    "hv_sc.violin(adata, A.obs[[\"percent_mito\", \"n_counts\", \"n_genes\"]]).opts(\n",
    "    hv.opts.Violin(ylim=(0, None))\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "19",
   "metadata": {},
   "outputs": [],
   "source": [
    "hv_sc.violin(adata, A.obs[\"S_score\"], color=A.obs[\"bulk_labels\"]).opts(\n",
    "    width=500, xrotation=30\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "20",
   "metadata": {},
   "source": [
    "{func}`scanpy.pl.stacked_violin`\n",
    "\n",
    "missing:\n",
    "- see tracksplot above\n",
    "- can’t do `.hist()` or `.operations.dendrogram` on GridSpace\n",
    "- slow!"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "21",
   "metadata": {},
   "outputs": [],
   "source": [
    "markers = [\"C1QA\", \"PSAP\", \"CD79A\", \"CD79B\", \"CST3\", \"LYZ\"]\n",
    "hv_sc.stacked_violin(adata[:, markers], A.var.index, A.obs[\"bulk_labels\"]).opts(\n",
    "    hv.opts.Violin(frame_height=50, frame_width=50)\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "22",
   "metadata": {},
   "source": [
    "{func}`scanpy.pl.matrixplot`\n",
    "\n",
    "missing:\n",
    "- `aspect=\"equal\"` breaks (bokeh tries to divide `None/None`)\n",
    "- hist doesn’t align properly"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "23",
   "metadata": {},
   "outputs": [],
   "source": [
    "markers = [\"C1QA\", \"PSAP\", \"CD79A\", \"CD79B\", \"CST3\", \"LYZ\"]\n",
    "hv_sc.matrixplot(\n",
    "    adata[:, markers], A.obs[\"bulk_labels\"], data=A.layers[\"counts\"], add_totals=True\n",
    ").opts(hv.opts.Bars(width=150))"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "24",
   "metadata": {},
   "source": [
    "{func}`scanpy.pl.clustermap`\n",
    "\n",
    "missing:\n",
    "- TickBar (see above)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "25",
   "metadata": {},
   "outputs": [],
   "source": [
    "hv_anndata.ClusterMap(adata=adata)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "26",
   "metadata": {},
   "source": [
    "{func}`scanpy.pl.dendrogram`: {class}`holoviews.operation.dendrogram`"
   ]
  }
 ],
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