{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# hv-anndata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import holoviews as hv\n",
    "import panel as pn\n",
    "import scanpy as sc\n",
    "\n",
    "import hv_anndata\n",
    "from hv_anndata import A"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "hv_anndata.register()\n",
    "hv.extension(\"bokeh\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Example workflow 1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "adata = sc.datasets.paul15()\n",
    "sc.pp.pca(adata)\n",
    "sc.pp.neighbors(adata)\n",
    "sc.tl.umap(adata)\n",
    "adata"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Simple HoloViews/Bokeh scatter of UMAP results"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "(\n",
    "    hv\n",
    "    .Scatter(\n",
    "        adata, A.obsm[\"X_umap\"][0], [A.obsm[\"X_umap\"][1], A.obs[\"paul15_clusters\"]]\n",
    "    )\n",
    "    .opts(\n",
    "        color=A.obs[\"paul15_clusters\"],\n",
    "        cmap=\"Category20\",\n",
    "        legend_position=\"left\",\n",
    "        frame_width=500,\n",
    "        height=500,\n",
    "        alpha=0.5,\n",
    "        tools=[\"hover\"],\n",
    "    )\n",
    "    .hist()\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### `ManifoldMap` App to explore all dimensionality reduction results"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "hv_anndata.ManifoldMap(\n",
    "    adata=adata, datashade=False, reduction=\"X_umap\", show_labels=True\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Holoviews/Bokeh Dotmap plot "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### `ManifoldMap` App to explore all dimensionality reduction results"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "hv_anndata.ManifoldMap(\n",
    "    adata=adata, datashade=False, reduction=\"X_umap\", show_labels=True\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Holoviews/Bokeh Dotmap widget"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Required for the GeneSelector to render properly\n",
    "pn.extension(\"jsoneditor\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "marker_genes = {\n",
    "    \"Erythroids\": [\"Gata1\", \"Klf1\", \"Epor\", \"Gypa\", \"Hba-a2\"],\n",
    "    # \"Neutrophils\": [\"Elane\", \"Cebpe\", \"Ctsg\", \"Mpo\", \"Gfi1\"],\n",
    "    \"Monocytes\": [\"Irf8\", \"Csf1r\", \"Ctsg\", \"Mpo\"],\n",
    "    \"Megakaryocytes\": [\"Itga2b\", \"Pbx1\", \"Sdpr\", \"Vwf\"],\n",
    "    \"Basophils\": [\"Mcpt8\", \"Prss34\"],\n",
    "    \"Mast cells\": [\"Cma1\", \"Gzmb\"],\n",
    "}\n",
    "hv_anndata.Dotmap(adata=adata, marker_genes=marker_genes, groupby=\"paul15_clusters\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Example workflow 2"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Dotmap plot with dendrogram"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "adata2 = sc.datasets.pbmc68k_reduced()\n",
    "sel_marker_genes = {\n",
    "    \"CD14+ Mono\": [\"FCN1\"],\n",
    "    \"CD16+ Mono\": [\"FCGR3A\"],\n",
    "    \"ID2-hi myeloid prog\": [\"ID2\", \"S100A9\"],\n",
    "    \"cDC2\": [\"CST3\", \"LYZ\", \"CLEC10A\", \"FCER1A\"],\n",
    "    \"Lymph prog\": [\"CD79B\", \"IGLL1\"],\n",
    "    \"B1 B\": [\"MS4A1\", \"BLK\"],\n",
    "    \"Plasma cells\": [\"MZB1\"],\n",
    "    \"CD4+ T activated\": [\"CD4\", \"IL7R\"],\n",
    "    \"pDC\": [\"GZMB\"],\n",
    "}\n",
    "\n",
    "hv_anndata.Dotmap(\n",
    "    adata=adata2,\n",
    "    marker_genes=sel_marker_genes,\n",
    "    groupby=\"bulk_labels\",\n",
    "    dendrogram=True,\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Example workflow 3\n",
    "\n",
    "### Linked brushing enabled between the Manifoldmap and the Dotmap plots"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "ls = hv.link_selections.instance()\n",
    "\n",
    "mm = hv_anndata.ManifoldMap(\n",
    "    adata=adata, reduction=\"X_umap\", show_labels=True, responsive=True, ls=ls\n",
    ")\n",
    "\n",
    "marker_genes = {\n",
    "    \"Erythroids\": [\"Gata1\", \"Klf1\", \"Epor\", \"Gypa\", \"Hba-a2\"],\n",
    "    \"Neutrophils\": [\"Elane\", \"Cebpe\", \"Ctsg\", \"Mpo\", \"Gfi1\"],\n",
    "    \"Monocytes\": [\"Irf8\", \"Csf1r\", \"Ctsg\", \"Mpo\"],\n",
    "    \"Megakaryocytes\": [\"Itga2b\", \"Pbx1\", \"Sdpr\", \"Vwf\"],\n",
    "    \"Basophils\": [\"Mcpt8\", \"Prss34\"],\n",
    "    \"Mast cells\": [\"Cma1\", \"Gzmb\"],\n",
    "}\n",
    "\n",
    "dmop = hv_anndata.dotmap_from_manifoldmap(\n",
    "    mm,\n",
    "    marker_genes=marker_genes,\n",
    "    groupby=\"paul15_clusters\",\n",
    "    plot_opts=dict(height=500),\n",
    ")\n",
    "\n",
    "pn.Column(mm, dmop)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "```{toctree}\n",
    ":hidden:\n",
    ":maxdepth: 2\n",
    "\n",
    "api/index\n",
    "examples/AnnData\n",
    "examples/Violin\n",
    "examples/scanpy/index\n",
    "```"
   ]
  }
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