notebooks_mod

theislab · Dec 18, 2024 · 98e0a84 · 98e0a84
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Showing 14 changed files with 98 additions and 929 deletions.
diff --git a/notebooks/spatialdata_tutorials/1_run_segmentation_free.ipynb b/notebooks/spatialdata_tutorials/1_run_segmentation_free.ipynb
@@ -2,30 +2,17 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 7,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/home/sergio/.local/lib/python3.10/site-packages/dask/dataframe/__init__.py:31: FutureWarning: The legacy Dask DataFrame implementation is deprecated and will be removed in a future version. Set the configuration option `dataframe.query-planning` to `True` or None to enable the new Dask Dataframe implementation and silence this warning.\n",
-      "  warnings.warn(\n",
-      "/home/sergio/.local/lib/python3.10/site-packages/numba/core/decorators.py:246: RuntimeWarning: nopython is set for njit and is ignored\n",
-      "  warnings.warn('nopython is set for njit and is ignored', RuntimeWarning)\n",
-      "/home/sergio/.local/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_text from `anndata` is deprecated. Import anndata.io.read_text instead.\n",
-      "  warnings.warn(msg, FutureWarning)\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import spatialdata_io\n",
     "import spatialdata as sd\n",
-    "import sys\n",
-    "sys.path.append(\"../..\")\n",
-    "import exrna \n",
     "import pandas as pd\n",
-    "import spatialdata_plot"
+    "import spatialdata_plot\n",
+    "import sys\n",
+    "sys.path.append(\"../../src\")\n",
+    "import troutpy \n"
    ]
   },
   {
@@ -209,7 +196,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "spatial_exrna",
    "language": "python",
    "name": "python3"
   },
@@ -223,7 +210,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.8"
+   "version": "3.10.15"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/spatialdata_tutorials/2_process_cells.ipynb b/notebooks/spatialdata_tutorials/2_process_cells.ipynb
@@ -14,6 +14,8 @@
       "/home/sergio/.local/lib/python3.10/site-packages/numba/core/decorators.py:246: RuntimeWarning: nopython is set for njit and is ignored\n",
       "  warnings.warn('nopython is set for njit and is ignored', RuntimeWarning)\n",
       "/home/sergio/.local/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_text from `anndata` is deprecated. Import anndata.io.read_text instead.\n",
+      "  warnings.warn(msg, FutureWarning)\n",
+      "/home/sergio/.local/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_text from `anndata` is deprecated. Import anndata.io.read_text instead.\n",
       "  warnings.warn(msg, FutureWarning)\n"
      ]
     }
@@ -30,8 +32,8 @@
     "\n",
     "# while not pip installable, add path to file \n",
     "import sys\n",
-    "sys.path.append(\"../..\")\n",
-    "import exrna "
+    "sys.path.append(\"../../src\")\n",
+    "import troutpy \n"
    ]
   },
   {

diff --git a/notebooks/spatialdata_tutorials/3_quantify_exRNA.ipynb b/notebooks/spatialdata_tutorials/3_quantify_exRNA.ipynb
@@ -31,8 +31,8 @@
     "\n",
     "# while not pip installable, add path to file \n",
     "import sys\n",
-    "sys.path.append(\"../..\")\n",
-    "import exrna "
+    "sys.path.append(\"../../src\")\n",
+    "import troutpy \n"
    ]
   },
   {

diff --git a/notebooks/spatialdata_tutorials/4_explore_comunication.ipynb b/notebooks/spatialdata_tutorials/4_explore_comunication.ipynb
@@ -2,13 +2,17 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
+      "/home/sergio/.local/lib/python3.10/site-packages/dask/dataframe/__init__.py:31: FutureWarning: The legacy Dask DataFrame implementation is deprecated and will be removed in a future version. Set the configuration option `dataframe.query-planning` to `True` or None to enable the new Dask Dataframe implementation and silence this warning.\n",
+      "  warnings.warn(\n",
+      "/home/sergio/.local/lib/python3.10/site-packages/numba/core/decorators.py:246: RuntimeWarning: nopython is set for njit and is ignored\n",
+      "  warnings.warn('nopython is set for njit and is ignored', RuntimeWarning)\n",
       "/home/sergio/.local/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_text from `anndata` is deprecated. Import anndata.io.read_text instead.\n",
       "  warnings.warn(msg, FutureWarning)\n",
       "/home/sergio/.local/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_text from `anndata` is deprecated. Import anndata.io.read_text instead.\n",
@@ -27,8 +31,8 @@
     "\n",
     "# while not pip installable, add path to file \n",
     "import sys \n",
-    "sys.path.append(\"../..\")\n",
-    "import exrna "
+    "sys.path.append(\"../../src\")\n",
+    "import troutpy "
    ]
   },
   {

diff --git a/notebooks/spatialdata_tutorials/6_identify_patterns.ipynb b/notebooks/spatialdata_tutorials/6_identify_patterns.ipynb
@@ -4,7 +4,22 @@
    "cell_type": "code",
    "execution_count": 1,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/home/sergio/.local/lib/python3.10/site-packages/dask/dataframe/__init__.py:31: FutureWarning: The legacy Dask DataFrame implementation is deprecated and will be removed in a future version. Set the configuration option `dataframe.query-planning` to `True` or None to enable the new Dask Dataframe implementation and silence this warning.\n",
+      "  warnings.warn(\n",
+      "/home/sergio/.local/lib/python3.10/site-packages/numba/core/decorators.py:246: RuntimeWarning: nopython is set for njit and is ignored\n",
+      "  warnings.warn('nopython is set for njit and is ignored', RuntimeWarning)\n",
+      "/home/sergio/.local/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_text from `anndata` is deprecated. Import anndata.io.read_text instead.\n",
+      "  warnings.warn(msg, FutureWarning)\n",
+      "/home/sergio/.local/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_text from `anndata` is deprecated. Import anndata.io.read_text instead.\n",
+      "  warnings.warn(msg, FutureWarning)\n"
+     ]
+    }
+   ],
    "source": [
     "import os\n",
     "import numpy as np\n",
@@ -16,8 +31,8 @@
     "\n",
     "# while not pip installable, add path to file \n",
     "import sys \n",
-    "sys.path.append(\"../..\")\n",
-    "import exrna "
+    "sys.path.append(\"../../src\")\n",
+    "import troutpy "
    ]
   },
   {

diff --git a/notebooks/spatialdata_tutorials/7_image_params.ipynb b/notebooks/spatialdata_tutorials/7_image_params.ipynb
@@ -2,9 +2,18 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 61,
+   "execution_count": 2,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/home/sergio/.local/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_text from `anndata` is deprecated. Import anndata.io.read_text instead.\n",
+      "  warnings.warn(msg, FutureWarning)\n"
+     ]
+    }
+   ],
    "source": [
     "import os\n",
     "import numpy as np\n",
@@ -16,8 +25,8 @@
     "\n",
     "# while not pip installable, add path to file \n",
     "import sys \n",
-    "sys.path.append(\"../..\")\n",
-    "import exrna "
+    "sys.path.append(\"../../src\")\n",
+    "import troutpy "
    ]
   },
   {

diff --git a/notebooks/spatialdata_tutorials/8_exrna_signature.ipynb b/notebooks/spatialdata_tutorials/8_exrna_signature.ipynb
@@ -4,7 +4,20 @@
    "cell_type": "code",
    "execution_count": 1,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/home/sergio/.local/lib/python3.10/site-packages/dask/dataframe/__init__.py:31: FutureWarning: The legacy Dask DataFrame implementation is deprecated and will be removed in a future version. Set the configuration option `dataframe.query-planning` to `True` or None to enable the new Dask Dataframe implementation and silence this warning.\n",
+      "  warnings.warn(\n",
+      "/home/sergio/.local/lib/python3.10/site-packages/numba/core/decorators.py:246: RuntimeWarning: nopython is set for njit and is ignored\n",
+      "  warnings.warn('nopython is set for njit and is ignored', RuntimeWarning)\n",
+      "/home/sergio/.local/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_text from `anndata` is deprecated. Import anndata.io.read_text instead.\n",
+      "  warnings.warn(msg, FutureWarning)\n"
+     ]
+    }
+   ],
    "source": [
     "from gseapy import Biomart\n",
     "import os\n",
@@ -13,7 +26,7 @@
     "import seaborn as sns\n",
     "import matplotlib.pyplot as plt\n",
     "import spatialdata_io\n",
-    "import spatialdata as sd"
+    "import spatialdata as sd\n"
    ]
   },
   {

diff --git a/notebooks/spatialdata_tutorials/9_sender_centric_analysis.ipynb b/notebooks/spatialdata_tutorials/9_sender_centric_analysis.ipynb
@@ -2,9 +2,24 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 60,
+   "execution_count": 1,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/home/sergio/.local/lib/python3.10/site-packages/dask/dataframe/__init__.py:31: FutureWarning: The legacy Dask DataFrame implementation is deprecated and will be removed in a future version. Set the configuration option `dataframe.query-planning` to `True` or None to enable the new Dask Dataframe implementation and silence this warning.\n",
+      "  warnings.warn(\n",
+      "/home/sergio/.local/lib/python3.10/site-packages/numba/core/decorators.py:246: RuntimeWarning: nopython is set for njit and is ignored\n",
+      "  warnings.warn('nopython is set for njit and is ignored', RuntimeWarning)\n",
+      "/home/sergio/.local/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_text from `anndata` is deprecated. Import anndata.io.read_text instead.\n",
+      "  warnings.warn(msg, FutureWarning)\n",
+      "/home/sergio/.local/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_text from `anndata` is deprecated. Import anndata.io.read_text instead.\n",
+      "  warnings.warn(msg, FutureWarning)\n"
+     ]
+    }
+   ],
    "source": [
     "import os\n",
     "import numpy as np\n",
@@ -16,17 +31,9 @@
     "from tqdm import tqdm\n",
     "import scanpy as sc\n",
     "import networkx as nx\n",
-    "import sys \n",
-    "sys.path.append(\"../../exrna\")\n",
-    "from formatting import *\n",
-    "from quantify_overexpression import *\n",
-    "from spatial_variability import *\n",
-    "from compute_target import *\n",
-    "from plotting import *\n",
-    "from compute_source_cell import *\n",
-    "from compute_target import *\n",
-    "from estimate_density import *\n",
-    "from NMF import *"
+    "import sys\n",
+    "sys.path.append(\"../../src\")\n",
+    "import troutpy "
    ]
   },
   {

diff --git a/notebooks/spatialdata_tutorials/DEP_2_filter_transcripts.ipynb b/notebooks/spatialdata_tutorials/DEP_2_filter_transcripts.ipynb