spacr 0.3.64__tar.gz → 0.3.65__tar.gz

{spacr-0.3.64/spacr.egg-info → spacr-0.3.65}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.3.64
+Version: 0.3.65
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson

spacr-0.3.65/notebooks/old/.ipynb_checkpoints/submodule_1_frequency_analysis-checkpoint.ipynb

@@ -0,0 +1,92 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "cf770028",
+   "metadata": {
+    "scrolled": false
+   },
+   "outputs": [],
+   "source": [
+    "from spacr.submodules import analyze_endodyogeny\n",
+    "%matplotlib inline\n",
+    "\n",
+    "settings = {\n",
+    "    'src': 'path',\n",
+    "    'tables': ['cell', 'nucleus', 'pathogen', 'cytoplasm'],\n",
+    "    'cell_types': ['Hela'],\n",
+    "    'cell_plate_metadata': None,\n",
+    "    'pathogen_types': ['nc', 'pc'],\n",
+    "    'pathogen_plate_metadata': [['c1'], ['c2']],\n",
+    "    'treatments': None,\n",
+    "    'treatment_plate_metadata': None,\n",
+    "    'min_area_bin': 500,\n",
+    "    'group_column': 'pathogen',\n",
+    "    'compartment': 'pathogen',\n",
+    "    'pathogen_limit': 1,\n",
+    "    'nuclei_limit': 1000,\n",
+    "    'level': 'well',\n",
+    "    'um_per_px':0.1,\n",
+    "    'max_bins':5,\n",
+    "    'save':True,\n",
+    "    'verbose': True}\n",
+    "\n",
+    "# Run the analysis\n",
+    "output = analyze_endodyogeny(settings)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6657b0db",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from spacr.submodules import analyze_class_proportion\n",
+    "%matplotlib inline\n",
+    "\n",
+    "settings = {\n",
+    "    'src': 'path',\n",
+    "    'tables': ['cell', 'nucleus', 'pathogen', 'cytoplasm'],\n",
+    "    'cell_types': ['cm','infg'],\n",
+    "    'cell_plate_metadata': [['c1', 'c2', 'c3', 'c4', 'c5', 'c6', 'c13', 'c14', 'c15', 'c16', 'c17', 'c18'],['c7', 'c8', 'c9', 'c10', 'c11', 'c12','c18', 'c19', 'c20', 'c21', 'c22', 'c23', 'c24']],\n",
+    "    'pathogen_types': ['nc', 'pc'],\n",
+    "    'pathogen_plate_metadata': [['c1', 'c2', 'c3', 'c4', 'c5', 'c6', 'c7', 'c8', 'c9', 'c10', 'c11', 'c12'], ['c13', 'c14', 'c15', 'c16', 'c17', 'c18', 'c19', 'c20', 'c21', 'c22', 'c23', 'c24']],\n",
+    "    'treatments': ['ub','rnf'],\n",
+    "    'treatment_plate_metadata': [['c1', 'c2','c3', 'c7','c8','c9', 'c13','c14','c15','c19','c20','c21'],['c4','c5','c6','c10','c11','c12','c16','c17','c18','c22','c23','c24']],\n",
+    "    'group_column': 'condition',\n",
+    "    'class_column':'test',\n",
+    "    'pathogen_limit': 1000,\n",
+    "    'nuclei_limit': 1000,\n",
+    "    'level': 'well',\n",
+    "    'save':True,\n",
+    "    'verbose': True}\n",
+    "\n",
+    "# Run the analysis\n",
+    "output = analyze_class_proportion(settings)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "spacr",
+   "language": "python",
+   "name": "spacr"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.19"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

{spacr-0.3.64 → spacr-0.3.65}/notebooks/old/Untitled.ipynb

@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3460bff8",
+   "id": "0582e3fd",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -27,7 +27,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "bc1dc013",
+   "id": "81280b57",
    "metadata": {
     "scrolled": false
    },
@@ -78,12 +78,219 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "id": "dfcc3359",
+   "execution_count": 3,
+   "id": "27e6cd82",
    "metadata": {
     "scrolled": false
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>Key</th>\n",
+       "      <th>Value</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>src</td>\n",
+       "      <td>/nas_mnt/carruthers/Einar/tsg101_screen/TSG101...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>tables</td>\n",
+       "      <td>[cell, nucleus, pathogen, cytoplasm]</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>cell_types</td>\n",
+       "      <td>[Hela]</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3</th>\n",
+       "      <td>cell_plate_metadata</td>\n",
+       "      <td>None</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>4</th>\n",
+       "      <td>pathogen_types</td>\n",
+       "      <td>[nc, pc]</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>5</th>\n",
+       "      <td>pathogen_plate_metadata</td>\n",
+       "      <td>[[c1], [c2]]</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>6</th>\n",
+       "      <td>treatments</td>\n",
+       "      <td>None</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>7</th>\n",
+       "      <td>treatment_plate_metadata</td>\n",
+       "      <td>None</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>8</th>\n",
+       "      <td>min_area_bin</td>\n",
+       "      <td>500</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>9</th>\n",
+       "      <td>group_column</td>\n",
+       "      <td>pathogen</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>10</th>\n",
+       "      <td>compartment</td>\n",
+       "      <td>pathogen</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>11</th>\n",
+       "      <td>pathogen_limit</td>\n",
+       "      <td>1</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>12</th>\n",
+       "      <td>nuclei_limit</td>\n",
+       "      <td>1000</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>13</th>\n",
+       "      <td>level</td>\n",
+       "      <td>well</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>14</th>\n",
+       "      <td>um_per_px</td>\n",
+       "      <td>0.1</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>15</th>\n",
+       "      <td>max_bins</td>\n",
+       "      <td>5</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>16</th>\n",
+       "      <td>save</td>\n",
+       "      <td>True</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>17</th>\n",
+       "      <td>verbose</td>\n",
+       "      <td>True</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "                         Key  \\\n",
+       "0                        src   \n",
+       "1                     tables   \n",
+       "2                 cell_types   \n",
+       "3        cell_plate_metadata   \n",
+       "4             pathogen_types   \n",
+       "5    pathogen_plate_metadata   \n",
+       "6                 treatments   \n",
+       "7   treatment_plate_metadata   \n",
+       "8               min_area_bin   \n",
+       "9               group_column   \n",
+       "10               compartment   \n",
+       "11            pathogen_limit   \n",
+       "12              nuclei_limit   \n",
+       "13                     level   \n",
+       "14                 um_per_px   \n",
+       "15                  max_bins   \n",
+       "16                      save   \n",
+       "17                   verbose   \n",
+       "\n",
+       "                                                Value  \n",
+       "0   /nas_mnt/carruthers/Einar/tsg101_screen/TSG101...  \n",
+       "1                [cell, nucleus, pathogen, cytoplasm]  \n",
+       "2                                              [Hela]  \n",
+       "3                                                None  \n",
+       "4                                            [nc, pc]  \n",
+       "5                                        [[c1], [c2]]  \n",
+       "6                                                None  \n",
+       "7                                                None  \n",
+       "8                                                 500  \n",
+       "9                                            pathogen  \n",
+       "10                                           pathogen  \n",
+       "11                                                  1  \n",
+       "12                                               1000  \n",
+       "13                                               well  \n",
+       "14                                                0.1  \n",
+       "15                                                  5  \n",
+       "16                                               True  \n",
+       "17                                               True  "
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "cell: 60816\n",
+      "nucleus: 80889\n",
+      "pathogen: 111317\n",
+      "cytoplasm: 60816\n",
+      "cells: 60816, cells grouped: 60816\n",
+      "cytoplasms: 60816, cytoplasms grouped: 60816\n",
+      "nucleus: 80889, nucleus grouped: 60816\n",
+      "pathogens: 37541, pathogens grouped: 37541\n",
+      "Generated dataframe with: 791 columns and 37541 rows\n",
+      "Volume bins: [11.18033988749895, 22.3606797749979, 44.7213595499958, 89.4427190999916, 178.8854381999832, 357.7708763999664, 715.5417527999329, 1431.0835055998657]\n",
+      "Volume bin labels: ['11.18-22.36', '22.36-44.72', '44.72-89.44', '89.44-178.89', '178.89-357.77', '357.77-715.54', '715.54-1431.08']\n",
+      "                        pathogen_volume pathogen_volume_bin  bin_index\n",
+      "prcfo                                                                 \n",
+      "pplate1_r10_c1_f10_o10       171.016316        89.44-178.89          4\n",
+      "pplate1_r10_c1_f10_o11        14.112998         11.18-22.36          1\n",
+      "pplate1_r10_c1_f10_o19        36.383419         22.36-44.72          2\n",
+      "pplate1_r10_c1_f10_o24       203.611545             >178.89          5\n",
+      "pplate1_r10_c1_f10_o28       208.128599             >178.89          5\n",
+      "Chi-squared test statistic (raw data): 95.2692\n",
+      "p-value (raw data): 9.9884e-20\n",
+      "\n",
+      "Pairwise Frequency Analysis Results:\n",
+      "Group 1 Group 2                Test Name      p-value  p-value_adj  adj\n",
+      "     nc      pc Pairwise Chi-Square Test 9.988372e-20 9.988372e-20 holm\n",
+      "Chi-squared results saved to /nas_mnt/carruthers/Einar/tsg101_screen/TSG101SCREEN_20240810_132824/plate1/results/analyze_endodyogeny/chi_squared_results.csv\n"
+     ]
+    },
+    {
+     "data": {
+      "image/png": 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",
+      "text/plain": [
+       "<Figure size 1200x800 with 1 Axes>"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
    "source": [
     "from spacr.submodules import analyze_endodyogeny\n",
     "%matplotlib inline\n",
@@ -105,22 +312,28 @@
     "    'level': 'well',\n",
     "    'um_per_px':0.1,\n",
     "    'max_bins':5,\n",
-    "    'save':False,\n",
+    "    'save':True,\n",
     "    'verbose': True}\n",
     "\n",
     "# Run the analysis\n",
-    "chi2, p = analyze_endodyogeny(settings)\n",
-    "print(f\"Chi-squared statistic: {chi2}, p-value: {p}\")\n"
+    "output = analyze_endodyogeny(settings)\n"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
-   "id": "5d6ccf4e",
+   "execution_count": 1,
+   "id": "e6b5835c",
    "metadata": {
     "scrolled": false
    },
    "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Models already downloaded to: /home/carruthers/anaconda3/envs/spacr/lib/python3.9/site-packages/spacr/resources/models\n"
+     ]
+    },
     {
      "data": {
       "text/html": [
@@ -283,8 +496,39 @@
       "Generated dataframe with: 793 columns and 30522 rows\n",
       "Chi-squared test statistic (raw data): 10386.3028\n",
       "p-value (raw data): 0.0000e+00\n",
-      "Chi-squared results saved to /nas_mnt/carruthers/yifan/Yifan_Einar screen/yifanUbtrial11h_20240705_184432/plate1/results/class_chi_squared_results.csv\n",
-      "Annotated data saved to /nas_mnt/carruthers/yifan/Yifan_Einar screen/yifanUbtrial11h_20240705_184432/plate1/results/class_chi_squared_data.csv\n"
+      "\n",
+      "Pairwise Frequency Analysis Results:\n",
+      "    Group 1     Group 2           Test Name       p-value   p-value_adj        adj\n",
+      "  cm_nc_rnf    cm_nc_ub Fisher's Exact Test  0.000000e+00  0.000000e+00 bonferroni\n",
+      "  cm_nc_rnf   cm_pc_rnf Fisher's Exact Test 2.037782e-121 5.705789e-120 bonferroni\n",
+      "  cm_nc_rnf    cm_pc_ub Fisher's Exact Test  0.000000e+00  0.000000e+00 bonferroni\n",
+      "  cm_nc_rnf infg_nc_rnf Fisher's Exact Test  5.556853e-12  1.555919e-10 bonferroni\n",
+      "  cm_nc_rnf  infg_nc_ub Fisher's Exact Test  0.000000e+00  0.000000e+00 bonferroni\n",
+      "  cm_nc_rnf infg_pc_rnf Fisher's Exact Test 3.854386e-239 1.079228e-237 bonferroni\n",
+      "  cm_nc_rnf  infg_pc_ub Fisher's Exact Test  0.000000e+00  0.000000e+00 bonferroni\n",
+      "   cm_nc_ub   cm_pc_rnf Fisher's Exact Test 7.900442e-192 2.212124e-190 bonferroni\n",
+      "   cm_nc_ub    cm_pc_ub Fisher's Exact Test  9.730547e-45  2.724553e-43 bonferroni\n",
+      "   cm_nc_ub infg_nc_rnf Fisher's Exact Test  0.000000e+00  0.000000e+00 bonferroni\n",
+      "   cm_nc_ub  infg_nc_ub Fisher's Exact Test  1.257152e-51  3.520025e-50 bonferroni\n",
+      "   cm_nc_ub infg_pc_rnf Fisher's Exact Test 1.088130e-152 3.046764e-151 bonferroni\n",
+      "   cm_nc_ub  infg_pc_ub Fisher's Exact Test  6.549957e-09  1.833988e-07 bonferroni\n",
+      "  cm_pc_rnf    cm_pc_ub Fisher's Exact Test 7.424495e-300 2.078859e-298 bonferroni\n",
+      "  cm_pc_rnf infg_nc_rnf Fisher's Exact Test 6.909521e-170 1.934666e-168 bonferroni\n",
+      "  cm_pc_rnf  infg_nc_ub Fisher's Exact Test  4.840047e-55  1.355213e-53 bonferroni\n",
+      "  cm_pc_rnf infg_pc_rnf Fisher's Exact Test  6.738680e-08  1.886830e-06 bonferroni\n",
+      "  cm_pc_rnf  infg_pc_ub Fisher's Exact Test 1.721869e-188 4.821232e-187 bonferroni\n",
+      "   cm_pc_ub infg_nc_rnf Fisher's Exact Test  0.000000e+00  0.000000e+00 bonferroni\n",
+      "   cm_pc_ub  infg_nc_ub Fisher's Exact Test 2.077732e-143 5.817650e-142 bonferroni\n",
+      "   cm_pc_ub infg_pc_rnf Fisher's Exact Test 2.926600e-260 8.194479e-259 bonferroni\n",
+      "   cm_pc_ub  infg_pc_ub Fisher's Exact Test  3.393265e-13  9.501141e-12 bonferroni\n",
+      "infg_nc_rnf  infg_nc_ub Fisher's Exact Test  0.000000e+00  0.000000e+00 bonferroni\n",
+      "infg_nc_rnf infg_pc_rnf Fisher's Exact Test 1.202352e-301 3.366584e-300 bonferroni\n",
+      "infg_nc_rnf  infg_pc_ub Fisher's Exact Test  0.000000e+00  0.000000e+00 bonferroni\n",
+      " infg_nc_ub infg_pc_rnf Fisher's Exact Test  8.341849e-29  2.335718e-27 bonferroni\n",
+      " infg_nc_ub  infg_pc_ub Fisher's Exact Test  6.572288e-68  1.840241e-66 bonferroni\n",
+      "infg_pc_rnf  infg_pc_ub Fisher's Exact Test 4.620722e-152 1.293802e-150 bonferroni\n",
+      "Chi-squared results saved to /nas_mnt/carruthers/yifan/Yifan_Einar screen/yifanUbtrial11h_20240705_184432/plate1/results/analyze_class_proportion/class_chi_squared_results.csv\n",
+      "Annotated data saved to /nas_mnt/carruthers/yifan/Yifan_Einar screen/yifanUbtrial11h_20240705_184432/plate1/results/analyze_class_proportion/class_chi_squared_data.csv\n"
      ]
     },
     {
@@ -306,6 +550,14 @@
      },
      "metadata": {},
      "output_type": "display_data"
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Levene's test statistic: 809.1485, p-value: 0.0000e+00\n",
+      "Statistical analysis results saved.\n"
+     ]
     }
    ],
    "source": [
@@ -336,7 +588,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7a990498",
+   "id": "6532d517",
    "metadata": {},
    "outputs": [],
    "source": []

spacr-0.3.65/notebooks/submodules/submodule_1_frequency_analysis.ipynb

@@ -0,0 +1,92 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "cf770028",
+   "metadata": {
+    "scrolled": false
+   },
+   "outputs": [],
+   "source": [
+    "from spacr.submodules import analyze_endodyogeny\n",
+    "%matplotlib inline\n",
+    "\n",
+    "settings = {\n",
+    "    'src': 'path',\n",
+    "    'tables': ['cell', 'nucleus', 'pathogen', 'cytoplasm'],\n",
+    "    'cell_types': ['Hela'],\n",
+    "    'cell_plate_metadata': None,\n",
+    "    'pathogen_types': ['nc', 'pc'],\n",
+    "    'pathogen_plate_metadata': [['c1'], ['c2']],\n",
+    "    'treatments': None,\n",
+    "    'treatment_plate_metadata': None,\n",
+    "    'min_area_bin': 500,\n",
+    "    'group_column': 'pathogen',\n",
+    "    'compartment': 'pathogen',\n",
+    "    'pathogen_limit': 1,\n",
+    "    'nuclei_limit': 1000,\n",
+    "    'level': 'well',\n",
+    "    'um_per_px':0.1,\n",
+    "    'max_bins':5,\n",
+    "    'save':True,\n",
+    "    'verbose': True}\n",
+    "\n",
+    "# Run the analysis\n",
+    "output = analyze_endodyogeny(settings)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6657b0db",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from spacr.submodules import analyze_class_proportion\n",
+    "%matplotlib inline\n",
+    "\n",
+    "settings = {\n",
+    "    'src': 'path',\n",
+    "    'tables': ['cell', 'nucleus', 'pathogen', 'cytoplasm'],\n",
+    "    'cell_types': ['cm','infg'],\n",
+    "    'cell_plate_metadata': [['c1', 'c2', 'c3', 'c4', 'c5', 'c6', 'c13', 'c14', 'c15', 'c16', 'c17', 'c18'],['c7', 'c8', 'c9', 'c10', 'c11', 'c12','c18', 'c19', 'c20', 'c21', 'c22', 'c23', 'c24']],\n",
+    "    'pathogen_types': ['nc', 'pc'],\n",
+    "    'pathogen_plate_metadata': [['c1', 'c2', 'c3', 'c4', 'c5', 'c6', 'c7', 'c8', 'c9', 'c10', 'c11', 'c12'], ['c13', 'c14', 'c15', 'c16', 'c17', 'c18', 'c19', 'c20', 'c21', 'c22', 'c23', 'c24']],\n",
+    "    'treatments': ['ub','rnf'],\n",
+    "    'treatment_plate_metadata': [['c1', 'c2','c3', 'c7','c8','c9', 'c13','c14','c15','c19','c20','c21'],['c4','c5','c6','c10','c11','c12','c16','c17','c18','c22','c23','c24']],\n",
+    "    'group_column': 'condition',\n",
+    "    'class_column':'test',\n",
+    "    'pathogen_limit': 1000,\n",
+    "    'nuclei_limit': 1000,\n",
+    "    'level': 'well',\n",
+    "    'save':True,\n",
+    "    'verbose': True}\n",
+    "\n",
+    "# Run the analysis\n",
+    "output = analyze_class_proportion(settings)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "spacr",
+   "language": "python",
+   "name": "spacr"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.19"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}