From eb8dd9df574f76761164256bf46ad529c68b5811 Mon Sep 17 00:00:00 2001 From: Danila Date: Tue, 2 Jul 2024 20:27:17 -0700 Subject: [PATCH] Update notebooks with the upcoming changes in v0.3 --- .../notebooks/annotations_management.ipynb | 34 +- docs/source/notebooks/axes.ipynb | 16 +- docs/source/notebooks/nuances.ipynb | 291 ++++++++++++++---- docs/source/notebooks/quickstart_mudata.ipynb | 26 +- 4 files changed, 261 insertions(+), 106 deletions(-) diff --git a/docs/source/notebooks/annotations_management.ipynb b/docs/source/notebooks/annotations_management.ipynb index 5252406..3ad518f 100644 --- a/docs/source/notebooks/annotations_management.ipynb +++ b/docs/source/notebooks/annotations_management.ipynb @@ -2059,7 +2059,7 @@ { "data": { "text/html": [ - "
MuData object with n_obs × n_vars = 60 × 100\n",
+       "
MuData object with n_obs × n_vars = 60 × 100 (shared var) \n",
        "  3 modalities\n",
        "    mod1:\t10 x 100\n",
        "      obs:\t'dataset'\n",
@@ -2069,7 +2069,7 @@
        "      obs:\t'dataset', 'species', 'reference'
"
       ],
       "text/plain": [
-       "MuData object with n_obs × n_vars = 60 × 100\n",
+       "MuData object with n_obs × n_vars = 60 × 100 (shared var) \n",
        "  3 modalities\n",
        "    mod1:\t10 x 100\n",
        "      obs:\t'dataset'\n",
@@ -2211,7 +2211,7 @@
     {
      "data": {
       "text/html": [
-       "
MuData object with n_obs × n_vars = 10 × 100\n",
+       "
MuData object with n_obs × n_vars = 10 × 100 (shared obs and var) \n",
        "  2 modalities\n",
        "    raw:\t10 x 100\n",
        "      obs:\t'status'\n",
@@ -2220,7 +2220,7 @@
        "      var:\t'filtered'
"
       ],
       "text/plain": [
-       "MuData object with n_obs × n_vars = 10 × 100\n",
+       "MuData object with n_obs × n_vars = 10 × 100 (shared obs and var) \n",
        "  2 modalities\n",
        "    raw:\t10 x 100\n",
        "      obs:\t'status'\n",
@@ -2337,10 +2337,10 @@
     {
      "data": {
       "text/html": [
-       "
MuData object with n_obs × n_vars = 10 × 300\n",
+       "
MuData object with n_obs × n_vars = 10 × 300 (shared obs and var) \n",
        "  obs:\t'dataset'\n",
        "  2 modalities\n",
-       "    mod1:\tMuData object with n_obs × n_vars = 10 × 300\n",
+       "    mod1:\tMuData object with n_obs × n_vars = 10 × 100 (shared obs and var) \n",
        "      2 modalities\n",
        "        raw:\t10 x 100\n",
        "          obs:\t'status'\n",
@@ -2350,10 +2350,10 @@
        "    mod2:\t10 x 200
"
       ],
       "text/plain": [
-       "MuData object with n_obs × n_vars = 10 × 300\n",
+       "MuData object with n_obs × n_vars = 10 × 300 (shared obs and var) \n",
        "  obs:\t'dataset'\n",
        "  2 modalities\n",
-       "    mod1:\tMuData object with n_obs × n_vars = 10 × 300\n",
+       "    mod1:\tMuData object with n_obs × n_vars = 10 × 100 (shared obs and var) \n",
        "      2 modalities\n",
        "        raw:\t10 x 100\n",
        "          obs:\t'status'\n",
@@ -2383,13 +2383,11 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "{'mod1': MuData object with n_obs × n_vars = 10 × 100\n",
-      "  2 modalities\n",
-      "    raw:\t10 x 100\n",
-      "      obs:\t'status'\n",
-      "    qced:\t8 x 50\n",
-      "      obs:\t'status', 'filtered'\n",
-      "      var:\t'filtered', 'mod2': AnnData object with n_obs × n_vars = 10 × 200}\n"
+      "MuData\n",
+      "├─ mod1 MuData [shared obs and var] (10 × 100)\n",
+      "│  ├─ raw AnnData (10 x 100)\n",
+      "│  └─ qced AnnData (8 x 50)\n",
+      "└─ mod2 AnnData (10 x 200)\n"
      ]
     }
    ],
@@ -2514,9 +2512,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "ad0.9 (issue126)",
+   "display_name": "Python 3.12 (main)",
    "language": "python",
-   "name": "issue126"
+   "name": "main"
   },
   "language_info": {
    "codemirror_mode": {
@@ -2528,7 +2526,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.0"
+   "version": "3.12.3"
   }
  },
  "nbformat": 4,
diff --git a/docs/source/notebooks/axes.ipynb b/docs/source/notebooks/axes.ipynb
index 6999d93..dcf1abe 100644
--- a/docs/source/notebooks/axes.ipynb
+++ b/docs/source/notebooks/axes.ipynb
@@ -59,7 +59,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "! pip install mudata"
+    "%pip install mudata"
    ]
   },
   {
@@ -127,7 +127,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/usr/local/opt/python@3.8/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/mudata/_core/mudata.py:445: UserWarning: Cannot join columns with the same name because var_names are intersecting.\n",
+      "/usr/local/opt/python@3.8/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/mudata/src/mudata/_core/mudata.py:869: UserWarning: Cannot join columns with the same name because var_names are intersecting.\n",
       "  warnings.warn(\n"
      ]
     },
@@ -314,13 +314,13 @@
     {
      "data": {
       "text/html": [
-       "
MuData object with n_obs × n_vars = 600 × 1000\n",
+       "
MuData object with n_obs × n_vars = 600 × 1000 (shared var) \n",
        "  2 modalities\n",
        "    dat1:\t100 x 1000\n",
        "    dat2:\t500 x 1000
"
       ],
       "text/plain": [
-       "MuData object with n_obs × n_vars = 600 × 1000\n",
+       "MuData object with n_obs × n_vars = 600 × 1000 (shared var) \n",
        "  2 modalities\n",
        "    dat1:\t100 x 1000\n",
        "    dat2:\t500 x 1000"
@@ -441,13 +441,13 @@
     {
      "data": {
       "text/html": [
-       "
MuData object with n_obs × n_vars = 100 × 900\n",
+       "
MuData object with n_obs × n_vars = 100 × 900 (shared obs and var) \n",
        "  2 modalities\n",
        "    raw:\t100 x 900\n",
        "    preproc:\t100 x 300
"
       ],
       "text/plain": [
-       "MuData object with n_obs × n_vars = 100 × 900\n",
+       "MuData object with n_obs × n_vars = 100 × 900 (shared obs and var) \n",
        "  2 modalities\n",
        "    raw:\t100 x 900\n",
        "    preproc:\t100 x 300"
@@ -466,7 +466,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -480,7 +480,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.13"
+   "version": "3.12.3"
   },
   "toc": {
    "base_numbering": 1,
diff --git a/docs/source/notebooks/nuances.ipynb b/docs/source/notebooks/nuances.ipynb
index 24404b6..e48daf7 100644
--- a/docs/source/notebooks/nuances.ipynb
+++ b/docs/source/notebooks/nuances.ipynb
@@ -36,7 +36,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "! pip install mudata"
+    "%pip install mudata"
    ]
   },
   {
@@ -45,7 +45,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import mudata as md\n",
+    "import mudata\n",
     "from mudata import MuData, AnnData"
    ]
   },
@@ -83,6 +83,13 @@
     "mod2 = AnnData(X=np.dot(z, w2.T))"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    " "
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -138,9 +145,9 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/usr/local/opt/python@3.8/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/mudata/_core/mudata.py:404: UserWarning: Cannot join columns with the same name because var_names are intersecting.\n",
+      "/usr/local/opt/python@3.8/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/mudata/src/mudata/_core/mudata.py:869: UserWarning: Cannot join columns with the same name because var_names are intersecting.\n",
       "  warnings.warn(\n",
-      "/usr/local/opt/python@3.8/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/mudata/_core/mudata.py:852: UserWarning: Modality names will be prepended to var_names since there are identical var_names in different modalities.\n",
+      "/usr/local/opt/python@3.8/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/mudata/src/mudata/_core/mudata.py:1478: UserWarning: Modality names will be prepended to var_names since there are identical var_names in different modalities.\n",
       "  warnings.warn(\n"
      ]
     }
@@ -156,13 +163,15 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Variable names in AnnData objects"
+    " "
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
+    "### Variable names in AnnData objects\n",
+    "\n",
     "In the example above it is worth pointing out that `.var_names_make_unique()` is an in-place operation, just as [the same method](https://anndata.readthedocs.io/en/stable/anndata.AnnData.var_names_make_unique.html) is in `anndata`.\n",
     "\n",
     "Hence original AnnData objects' `.var_names` have also been modified:"
@@ -194,35 +203,41 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Update"
+    "## Update\n",
+    "\n",
+    "> ***NB:** If individual modalities are changed, updating the MuData object containing it might be required.*\n",
+    "\n",
+    "Modalities in ``MuData`` objects are full-featured ``AnnData`` objects. Hence they can be operated individually, and their ``MuData`` parent will have to be updated to fetch this information."
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "> ***NB:** If individual modalities are changed, updating the MuData object containing it might be required.*"
+    ">**NB:** Starting from `v0.3`, `mudata` will be adopting a more flexible approach to metadata management: updating global index with `.update()` will become independent from managing columns, which can now be done with `.pull_obs()`/`.pull_var()` and `.push_obs()`/`.push_var()`."
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Modalities in ``MuData`` objects are full-featured ``AnnData`` objects. Hence they can be operated individually, and their ``MuData`` parent will have to be updated to fetch this information."
+    "See more about annotations management in [in the respective tutorial](./annotations_management.ipynb)."
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Observations"
+    " "
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Consider the following example: a new column has been added to a modality-specific metadata table:"
+    "### Filtering data\n",
+    "\n",
+    "In rare cases some observations (or variables) can be dropped from all the contained modalities:"
    ]
   },
   {
@@ -231,14 +246,17 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "mod1.obs[\"mod1_profiled\"] = True"
+    "smaller_mdata = MuData({\n",
+    "    \"mod1\": mod1[:900].copy(),\n",
+    "    \"mod2\": mod2[:900].copy(),\n",
+    "})"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "While `mdata` includes `mod1` as its first modality, it currently does not know about this change:"
+    "While `smaller_mdata` includes `mod1` and `mod2` as its modalities, it currently does not know about this change:"
    ]
   },
   {
@@ -248,8 +266,17 @@
    "outputs": [
     {
      "data": {
+      "text/html": [
+       "
MuData object with n_obs × n_vars = 900 × 300\n",
+       "  2 modalities\n",
+       "    mod1:\t900 x 100\n",
+       "    mod2:\t900 x 200
"
+      ],
       "text/plain": [
-       "Index([], dtype='object')"
+       "MuData object with n_obs × n_vars = 900 × 300\n",
+       "  2 modalities\n",
+       "    mod1:\t900 x 100\n",
+       "    mod2:\t900 x 200"
       ]
      },
      "execution_count": 8,
@@ -258,14 +285,14 @@
     }
    ],
    "source": [
-    "mdata.obs.columns"
+    "smaller_mdata"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "`.update()` method will fetch these updates and propagate them to the global `.obs` table."
+    "`.update()` method will fetch these updates:"
    ]
   },
   {
@@ -273,54 +300,19 @@
    "execution_count": 9,
    "metadata": {},
    "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Index(['mod1:mod1_profiled'], dtype='object')\n"
-     ]
-    },
     {
      "data": {
       "text/html": [
-       "
\n",
-       "\n",
-       "\n",
-       "  \n",
-       "    \n",
-       "      \n",
-       "      \n",
-       "    \n",
-       "  \n",
-       "  \n",
-       "    \n",
-       "      \n",
-       "      \n",
-       "    \n",
-       "    \n",
-       "      \n",
-       "      \n",
-       "    \n",
-       "  \n",
-       "
mod1:mod1_profiled
0True
1True
\n",
-       "
"
+       "
MuData object with n_obs × n_vars = 900 × 300\n",
+       "  2 modalities\n",
+       "    mod1:\t900 x 100\n",
+       "    mod2:\t900 x 200
"
       ],
       "text/plain": [
-       "   mod1:mod1_profiled\n",
-       "0                True\n",
-       "1                True"
+       "MuData object with n_obs × n_vars = 900 × 300\n",
+       "  2 modalities\n",
+       "    mod1:\t900 x 100\n",
+       "    mod2:\t900 x 200"
       ]
      },
      "execution_count": 9,
@@ -328,17 +320,182 @@
      "output_type": "execute_result"
     }
    ],
+   "source": [
+    "smaller_mdata.update()\n",
+    "smaller_mdata"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Notice the global dimensions are now correctly reflected in the `MuData` object."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "  "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Observations annotations\n",
+    "\n",
+    "Consider the following example: a new column has been added to a modality-specific metadata table:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "mod1.obs[\"mod1_profiled\"] = True"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "While `mdata` includes `mod1` as its first modality, nothing has changed at the global level of the annotation:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "Index([], dtype='object')"
+      ]
+     },
+     "execution_count": 11,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "mdata.obs.columns"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "`.update()` method will only sync the `obs_names`:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       ""
+      ]
+     },
+     "execution_count": 12,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# default from v0.4\n",
+    "mudata.set_options(pull_on_update=False)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Index([], dtype='object')\n"
+     ]
+    }
+   ],
    "source": [
     "mdata.update()\n",
-    "print(mdata.obs.columns)\n",
-    "mdata.obs.head(2)"
+    "print(mdata.obs.columns)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "If we need the annotation at the global level, we can copy it from the all the underlying modalities:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Index(['mod1:mod1_profiled'], dtype='object')\n"
+     ]
+    }
+   ],
+   "source": [
+    "mdata.pull_obs()\n",
+    "print(mdata.obs.columns)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "del mdata.obs[\"mod1:mod1_profiled\"]"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "As `MuData` objects are designed with shared observations by default, this annotation is automatically prefixed by the modality that originated this annotation."
+    "As `MuData` objects are designed with shared observations by default, this annotation is automatically prefixed by the modality that originated this annotation.\n",
+    "\n",
+    "There is however flexibility when it comes to using prefixes for observations annotations that are specific to individual modalities:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 16,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Index(['mod1_profiled'], dtype='object')\n"
+     ]
+    }
+   ],
+   "source": [
+    "mdata.pull_obs(prefix_unique=False)\n",
+    "print(mdata.obs.columns)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    " "
    ]
   },
   {
@@ -357,7 +514,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 17,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -365,12 +522,12 @@
     "mod2.var[\"assay\"] = \"B\"\n",
     "\n",
     "# Will fetch these values\n",
-    "mdata.update()"
+    "mdata.pull_var()"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 18,
    "metadata": {},
    "outputs": [
     {
@@ -431,7 +588,7 @@
        "mod2:88      B"
       ]
      },
-     "execution_count": 11,
+     "execution_count": 18,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -458,7 +615,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -472,7 +629,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.13"
+   "version": "3.12.3"
   },
   "toc": {
    "base_numbering": 1,
diff --git a/docs/source/notebooks/quickstart_mudata.ipynb b/docs/source/notebooks/quickstart_mudata.ipynb
index 0026ac7..bf6946f 100644
--- a/docs/source/notebooks/quickstart_mudata.ipynb
+++ b/docs/source/notebooks/quickstart_mudata.ipynb
@@ -31,7 +31,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "! pip install mudata"
+    "%pip install mudata"
    ]
   },
   {
@@ -482,11 +482,11 @@
        "\n",
        "                                       B  bool  numpy.ndarray  \n",
        "                                   
Distances
.obsp0 elementsNo distances
A
1000 × 100AnnData object 1000 obs × 100 var
Matrix
.X
\n",
-       "            float32    numpy.ndarray\n",
+       "            float64    numpy.ndarray\n",
        "         
Layers
.layers0 elementsNo layers
Metadata
.obs0 elementsNo metadata
Embeddings
.obsm0 elementsNo embeddings
Distances
.obsp0 elementsNo distances
Miscellaneous
.uns1 elements
\n",
        "                                \n",
        "                            
misc  dict  1 element  adata: True
B
1000 × 50AnnData object 1000 obs × 50 var
Matrix
.X
\n",
-       "            float32    numpy.ndarray\n",
+       "            float64    numpy.ndarray\n",
        "         
Layers
.layers0 elementsNo layers
Metadata
.obs0 elementsNo metadata
Embeddings
.obsm0 elementsNo embeddings
Distances
.obsp0 elementsNo distances
Miscellaneous
.uns0 elementsNo miscellaneous

"
       ],
       "text/plain": [
@@ -543,14 +543,14 @@
     {
      "data": {
       "text/html": [
-       "
MuData object with n_obs × n_vars = 1000 × 150 backed at '/var/folders/xt/tvy3s7w17vn1b700k_351pz00000gp/T/muon_getting_started_m8own7bb.h5mu'\n",
+       "
MuData object with n_obs × n_vars = 1000 × 150 backed at '/var/folders/6f/ht39xtd54tv4n5p35ccnpgf80000gn/T/muon_getting_started_x3o0r9iz.h5mu'\n",
        "  2 modalities\n",
        "    A:\t1000 x 100\n",
        "      uns:\t'misc'\n",
        "    B:\t1000 x 50
"
       ],
       "text/plain": [
-       "MuData object with n_obs × n_vars = 1000 × 150 backed at '/var/folders/xt/tvy3s7w17vn1b700k_351pz00000gp/T/muon_getting_started_m8own7bb.h5mu'\n",
+       "MuData object with n_obs × n_vars = 1000 × 150 backed at '/var/folders/6f/ht39xtd54tv4n5p35ccnpgf80000gn/T/muon_getting_started_x3o0r9iz.h5mu'\n",
        "  2 modalities\n",
        "    A:\t1000 x 100\n",
        "      uns:\t'misc'\n",
@@ -690,21 +690,21 @@
        "details[open] > .summary-mod::before {\n",
        "  content: '○';\n",
        "}\n",
-       "MuData object 1000 obs × 150 var in 2 modalities
↳ backed at /var/folders/xt/tvy3s7w17vn1b700k_351pz00000gp/T/muon_getting_started_m8own7bb.h5mu
Metadata
.obs0 elementsNo metadata
Embeddings & mappings
.obsm2 elements
\n",
+       "MuData object 1000 obs × 150 var in 2 modalities
↳ backed at /var/folders/6f/ht39xtd54tv4n5p35ccnpgf80000gn/T/muon_getting_started_x3o0r9iz.h5mu
Metadata
.obs0 elementsNo metadata
Embeddings & mappings
.obsm2 elements
\n",
        "                                       \n",
        "                                   \n",
        "\n",
        "                                       \n",
-       "                                   
A  bool  numpy.ndarray  
B  bool  numpy.ndarray  
Distances
.obsp0 elementsNo distances
A
1000 × 100AnnData object 1000 obs × 100 var
↳ backed at /var/folders/xt/tvy3s7w17vn1b700k_351pz00000gp/T/muon_getting_started_m8own7bb.h5mu
Matrix
.X
\n",
-       "            float32    h5py._hl.dataset.Dataset\n",
+       "                                   
Distances
.obsp0 elementsNo distances
A
1000 × 100AnnData object 1000 obs × 100 var
↳ backed at /var/folders/6f/ht39xtd54tv4n5p35ccnpgf80000gn/T/muon_getting_started_x3o0r9iz.h5mu
Matrix
.X
\n",
+       "            float64    h5py._hl.dataset.Dataset\n",
        "         
Layers
.layers0 elementsNo layers
Metadata
.obs0 elementsNo metadata
Embeddings
.obsm0 elementsNo embeddings
Distances
.obsp0 elementsNo distances
Miscellaneous
.uns1 elements
\n",
        "                                \n",
-       "                            
misc  dict  1 element  adata: True
B
1000 × 50AnnData object 1000 obs × 50 var
↳ backed at /var/folders/xt/tvy3s7w17vn1b700k_351pz00000gp/T/muon_getting_started_m8own7bb.h5mu
Matrix
.X
\n",
-       "            float32    h5py._hl.dataset.Dataset\n",
+       "                            
B
1000 × 50AnnData object 1000 obs × 50 var
↳ backed at /var/folders/6f/ht39xtd54tv4n5p35ccnpgf80000gn/T/muon_getting_started_x3o0r9iz.h5mu
Matrix
.X
\n",
+       "            float64    h5py._hl.dataset.Dataset\n",
        "         
Layers
.layers0 elementsNo layers
Metadata
.obs0 elementsNo metadata
Embeddings
.obsm0 elementsNo embeddings
Distances
.obsp0 elementsNo distances
Miscellaneous
.uns0 elementsNo miscellaneous

"
       ],
       "text/plain": [
-       "MuData object with n_obs × n_vars = 1000 × 150 backed at '/var/folders/xt/tvy3s7w17vn1b700k_351pz00000gp/T/muon_getting_started_m8own7bb.h5mu'\n",
+       "MuData object with n_obs × n_vars = 1000 × 150 backed at '/var/folders/6f/ht39xtd54tv4n5p35ccnpgf80000gn/T/muon_getting_started_x3o0r9iz.h5mu'\n",
        "  2 modalities\n",
        "    A:\t1000 x 100\n",
        "      uns:\t'misc'\n",
@@ -818,7 +818,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -832,7 +832,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.12.3"
   }
  },
  "nbformat": 4,