{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "e133670f",
   "metadata": {},
   "source": [
    "# Quick Start\n",
    "This guide gives you the essential steps to get started with CellDyc.\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4bfba01c",
   "metadata": {},
   "source": [
    "## Import CellDyc"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "c3130531",
   "metadata": {
    "vscode": {
     "languageId": "plaintext"
    }
   },
   "outputs": [],
   "source": [
    "import celldyc as cdc"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "data-loading",
   "metadata": {},
   "source": [
    "## Load the Data\n",
    "Built‑in Dataset:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "2e61ec42",
   "metadata": {
    "vscode": {
     "languageId": "plaintext"
    }
   },
   "outputs": [],
   "source": [
    "adata = cdc.datasets.celegans()  # 3 sampling time points, 333 cells"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "5ae60e04",
   "metadata": {},
   "source": [
    "Your Own Dataset:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "80834ff5",
   "metadata": {
    "vscode": {
     "languageId": "plaintext"
    }
   },
   "outputs": [],
   "source": [
    "import scanpy as sc\n",
    "adata = sc.read_h5ad(\"my_data.h5ad\")  # requires .obs[\"time_point\"] with discrete time labels"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "preprocessing",
   "metadata": {},
   "source": [
    "## Preprocess the Data\n",
    "One-liner to filter, normalize, pick HVGs, run PCA, and build the neighbor graph:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "fec7fcf8",
   "metadata": {
    "vscode": {
     "languageId": "plaintext"
    }
   },
   "outputs": [],
   "source": [
    "adata = cdc.tl.preprocess(adata)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "reconstruction",
   "metadata": {},
   "source": [
    "## Estimation of Time Representation and Transcriptomic Velocity"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "90518002",
   "metadata": {
    "vscode": {
     "languageId": "plaintext"
    }
   },
   "outputs": [],
   "source": [
    "cdc.tl.recover_dyc(adata, time_key=\"time_point\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "29780199",
   "metadata": {},
   "source": [
    "**Outputs**\n",
    "- `adata.obs[\"getime\"]` – Continuous time representation (0‑1)\n",
    "- `adata.layers[\"velocity\"]` – Velocity matrix"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "visualization",
   "metadata": {},
   "source": [
    "**Visualization**\n",
    "- `cdc.pl.plot_velocity_projection(adata)` \n",
    "- `cdc.pl.getime_violin(adata, key_cont=\"getime\", key_cat=\"time_point\")` \n",
    "- ......"
   ]
  }
 ],
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