From 309238d0e476e2dd44636914a94eb183c2d472e5 Mon Sep 17 00:00:00 2001
From: Sergei Rybakov <koncopd@gmail.com>
Date: Mon, 5 Aug 2024 15:34:22 +0200
Subject: [PATCH] =?UTF-8?q?=F0=9F=93=9D=20Mutate=20tiledbsoma=20store=20(#?=
 =?UTF-8?q?137)?=
MIME-Version: 1.0
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---
 docs/scrna6.ipynb | 87 ++++++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 83 insertions(+), 4 deletions(-)

diff --git a/docs/scrna6.ipynb b/docs/scrna6.ipynb
index 4d3ac11..641b720 100644
--- a/docs/scrna6.ipynb
+++ b/docs/scrna6.ipynb
@@ -37,6 +37,7 @@
    "source": [
     "import lamindb as ln\n",
     "import pandas as pd\n",
+    "import scanpy as sc\n",
     "import tiledbsoma\n",
     "import tiledbsoma.io\n",
     "from functools import reduce"
@@ -288,14 +289,14 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Query the array"
+    "## Query the array store"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Open and query the experiment. We can use the registered `Artifact`."
+    "Open and query the experiment. We can use the registered `Artifact`. We query `X` and `obs` from the array store."
    ]
   },
   {
@@ -308,8 +309,86 @@
    },
    "outputs": [],
    "source": [
-    "with soma_artifact.open() as soma_array:\n",
-    "    print(soma_array[\"obs\"].read().concat().to_pandas())"
+    "with soma_artifact.open() as soma_store:\n",
+    "    obs = soma_store[\"obs\"]\n",
+    "    ms_rna = soma_store[\"ms\"][\"RNA\"]\n",
+    "    \n",
+    "    n_obs = len(obs)\n",
+    "    n_var = len(ms_rna[\"var\"])\n",
+    "    X = ms_rna[\"X\"][\"data\"].read().coos((n_obs, n_var)).concat().to_scipy()\n",
+    "    \n",
+    "    print(obs.read().concat().to_pandas())"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Update the array store"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Calculate PCA from the queried `X`."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "pca_array = sc.pp.pca(X, n_comps=2)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "soma_artifact"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Open the array store in write mode and add PCA. When the store is updated, the corresponding artifact also gets updated with a new version. "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "with soma_artifact.open(mode=\"w\") as soma_store:\n",
+    "    tiledbsoma.io.add_matrix_to_collection(\n",
+    "        exp=soma_store,\n",
+    "        measurement_name=\"RNA\",\n",
+    "        collection_name=\"obsm\",\n",
+    "        matrix_name=\"pca\",\n",
+    "        matrix_data=pca_array\n",
+    "    )"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Note that the artifact has been changed."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "soma_artifact"
    ]
   }
  ],