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Update LM and UMAPs #37

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Mar 7, 2024
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Update LM and UMAPs #37

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cf9738f
update LM and UMAPs
jenna-tomkinson Mar 7, 2024
c442a6d
update scripts
jenna-tomkinson Mar 7, 2024
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141 changes: 81 additions & 60 deletions 4.analyze_data/notebooks/UMAP/0.UMAP_coordinates.ipynb
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Expand Up @@ -65,10 +65,11 @@
{
"data": {
"text/plain": [
"['../../../3.processing_features/data/single_cell_profiles/Plate_4_sc_feature_selected.parquet',\n",
" '../../../3.processing_features/data/single_cell_profiles/Plate_1_sc_feature_selected.parquet',\n",
" '../../../3.processing_features/data/single_cell_profiles/Plate_2_sc_feature_selected.parquet',\n",
"['../../../3.processing_features/data/single_cell_profiles/Plate_1_sc_feature_selected.parquet',\n",
" '../../../3.processing_features/data/single_cell_profiles/Plate_3_prime_sc_feature_selected.parquet',\n",
" '../../../3.processing_features/data/single_cell_profiles/Plate_4_sc_feature_selected.parquet',\n",
" '../../../3.processing_features/data/single_cell_profiles/Plate_5_sc_feature_selected.parquet',\n",
" '../../../3.processing_features/data/single_cell_profiles/Plate_2_sc_feature_selected.parquet',\n",
" '../../../3.processing_features/data/single_cell_profiles/Plate_3_sc_feature_selected.parquet']"
]
},
Expand Down Expand Up @@ -98,13 +99,18 @@
"name": "stdout",
"output_type": "stream",
"text": [
"dict_keys(['Plate_4_sc_feature_selected.parquet', 'Plate_1_sc_feature_selected.parquet', 'Plate_2_sc_feature_selected.parquet', 'Plate_3_prime_sc_feature_selected.parquet', 'Plate_3_sc_feature_selected.parquet'])\n"
"dict_keys(['Plate_1_sc_feature_selected.parquet', 'Plate_3_prime_sc_feature_selected.parquet', 'Plate_4_sc_feature_selected.parquet', 'Plate_5_sc_feature_selected.parquet', 'Plate_2_sc_feature_selected.parquet', 'Plate_3_sc_feature_selected.parquet'])\n"
]
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{
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"execution_count": 4,
Expand Down Expand Up @@ -139,75 +145,90 @@
"name": "stderr",
"output_type": "stream",
"text": [
"/Users/tomkinsj/miniconda3/envs/python_analysis_nf1/lib/python3.9/site-packages/umap/umap_.py:1943: UserWarning: n_jobs value -1 overridden to 1 by setting random_state. Use no seed for parallelism.\n",
"/home/jenna/mambaforge/envs/python_analysis_nf1/lib/python3.9/site-packages/umap/umap_.py:1943: UserWarning: n_jobs value -1 overridden to 1 by setting random_state. Use no seed for parallelism.\n",
" warn(f\"n_jobs value {self.n_jobs} overridden to 1 by setting random_state. Use no seed for parallelism.\")\n"
]
},
{
"name": "stdout",
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"text": [
"(7502, 2)\n"
"(241, 2)\n"
]
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{
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"text": [
"/Users/tomkinsj/miniconda3/envs/python_analysis_nf1/lib/python3.9/site-packages/umap/umap_.py:1943: UserWarning: n_jobs value -1 overridden to 1 by setting random_state. Use no seed for parallelism.\n",
"/home/jenna/mambaforge/envs/python_analysis_nf1/lib/python3.9/site-packages/umap/umap_.py:1943: UserWarning: n_jobs value -1 overridden to 1 by setting random_state. Use no seed for parallelism.\n",
" warn(f\"n_jobs value {self.n_jobs} overridden to 1 by setting random_state. Use no seed for parallelism.\")\n"
]
},
{
"name": "stdout",
"output_type": "stream",
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"(241, 2)\n"
"(7300, 2)\n"
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"/Users/tomkinsj/miniconda3/envs/python_analysis_nf1/lib/python3.9/site-packages/umap/umap_.py:1943: UserWarning: n_jobs value -1 overridden to 1 by setting random_state. Use no seed for parallelism.\n",
"/home/jenna/mambaforge/envs/python_analysis_nf1/lib/python3.9/site-packages/umap/umap_.py:1943: UserWarning: n_jobs value -1 overridden to 1 by setting random_state. Use no seed for parallelism.\n",
" warn(f\"n_jobs value {self.n_jobs} overridden to 1 by setting random_state. Use no seed for parallelism.\")\n"
]
},
{
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"text": [
"(1714, 2)\n"
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{
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"/Users/tomkinsj/miniconda3/envs/python_analysis_nf1/lib/python3.9/site-packages/umap/umap_.py:1943: UserWarning: n_jobs value -1 overridden to 1 by setting random_state. Use no seed for parallelism.\n",
"/home/jenna/mambaforge/envs/python_analysis_nf1/lib/python3.9/site-packages/umap/umap_.py:1943: UserWarning: n_jobs value -1 overridden to 1 by setting random_state. Use no seed for parallelism.\n",
" warn(f\"n_jobs value {self.n_jobs} overridden to 1 by setting random_state. Use no seed for parallelism.\")\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
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"text": [
"/Users/tomkinsj/miniconda3/envs/python_analysis_nf1/lib/python3.9/site-packages/umap/umap_.py:1943: UserWarning: n_jobs value -1 overridden to 1 by setting random_state. Use no seed for parallelism.\n",
"/home/jenna/mambaforge/envs/python_analysis_nf1/lib/python3.9/site-packages/umap/umap_.py:1943: UserWarning: n_jobs value -1 overridden to 1 by setting random_state. Use no seed for parallelism.\n",
" warn(f\"n_jobs value {self.n_jobs} overridden to 1 by setting random_state. Use no seed for parallelism.\")\n"
]
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"/home/jenna/mambaforge/envs/python_analysis_nf1/lib/python3.9/site-packages/umap/umap_.py:1943: UserWarning: n_jobs value -1 overridden to 1 by setting random_state. Use no seed for parallelism.\n",
" warn(f\"n_jobs value {self.n_jobs} overridden to 1 by setting random_state. Use no seed for parallelism.\")\n"
]
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"(18038, 2)\n"
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],
Expand Down Expand Up @@ -293,68 +314,68 @@
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>9684</th>\n",
" <td>C8</td>\n",
" <td>2</td>\n",
" <td>640</td>\n",
" <td>HET</td>\n",
" <td>0.044605</td>\n",
" <td>1.602842</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4861</th>\n",
" <td>F4</td>\n",
" <td>3</td>\n",
" <td>361</td>\n",
" <th>980</th>\n",
" <td>B3</td>\n",
" <td>23</td>\n",
" <td>297</td>\n",
" <td>WT</td>\n",
" <td>0.316304</td>\n",
" <td>3.236223</td>\n",
" <td>1.599025</td>\n",
" <td>5.475614</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7331</th>\n",
" <td>C7</td>\n",
" <td>13</td>\n",
" <td>331</td>\n",
" <td>HET</td>\n",
" <td>1.450350</td>\n",
" <td>2.152666</td>\n",
" <th>15023</th>\n",
" <td>B12</td>\n",
" <td>6</td>\n",
" <td>531</td>\n",
" <td>Null</td>\n",
" <td>-1.793289</td>\n",
" <td>0.987861</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6033</th>\n",
" <td>B6</td>\n",
" <td>6</td>\n",
" <td>141</td>\n",
" <td>HET</td>\n",
" <td>2.589996</td>\n",
" <td>2.678065</td>\n",
" <th>4946</th>\n",
" <td>G4</td>\n",
" <td>23</td>\n",
" <td>386</td>\n",
" <td>WT</td>\n",
" <td>0.444975</td>\n",
" <td>-2.371571</td>\n",
" </tr>\n",
" <tr>\n",
" <th>13543</th>\n",
" <td>G10</td>\n",
" <td>17</td>\n",
" <td>115</td>\n",
" <th>17693</th>\n",
" <td>G12</td>\n",
" <td>1</td>\n",
" <td>481</td>\n",
" <td>Null</td>\n",
" <td>1.953981</td>\n",
" <td>0.519260</td>\n",
" <td>0.670747</td>\n",
" <td>2.854921</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7156</th>\n",
" <td>D7</td>\n",
" <td>16</td>\n",
" <td>235</td>\n",
" <td>HET</td>\n",
" <td>0.737558</td>\n",
" <td>5.601034</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" Metadata_Well Metadata_Site Metadata_number_of_singlecells \\\n",
"9684 C8 2 640 \n",
"4861 F4 3 361 \n",
"7331 C7 13 331 \n",
"6033 B6 6 141 \n",
"13543 G10 17 115 \n",
"980 B3 23 297 \n",
"15023 B12 6 531 \n",
"4946 G4 23 386 \n",
"17693 G12 1 481 \n",
"7156 D7 16 235 \n",
"\n",
" Metadata_genotype UMAP0 UMAP1 \n",
"9684 HET 0.044605 1.602842 \n",
"4861 WT 0.316304 3.236223 \n",
"7331 HET 1.450350 2.152666 \n",
"6033 HET 2.589996 2.678065 \n",
"13543 Null 1.953981 0.519260 "
"980 WT 1.599025 5.475614 \n",
"15023 Null -1.793289 0.987861 \n",
"4946 WT 0.444975 -2.371571 \n",
"17693 Null 0.670747 2.854921 \n",
"7156 HET 0.737558 5.601034 "
]
},
"execution_count": 6,
Expand Down
10 changes: 7 additions & 3 deletions 4.analyze_data/notebooks/UMAP/1.vis_UMAP.ipynb
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Expand Up @@ -28,13 +28,13 @@
"output_type": "stream",
"text": [
"Warning message:\n",
"\"package 'ggplot2' was built under R version 4.2.3\"\n"
"“package ‘ggplot2’ was built under R version 4.2.3”\n"
]
}
],
"source": [
"suppressPackageStartupMessages(library(ggplot2)) #plotting\n",
"suppressPackageStartupMessages(library(dplyr)) #work with data frames\n"
"suppressPackageStartupMessages(library(dplyr)) #work with data frames"
]
},
{
Expand Down Expand Up @@ -62,6 +62,7 @@
"[3] \"results/UMAP_Plate_3_prime_sc_feature_selected.tsv\"\n",
"[4] \"results/UMAP_Plate_3_sc_feature_selected.tsv\" \n",
"[5] \"results/UMAP_Plate_4_sc_feature_selected.tsv\" \n",
"[6] \"results/UMAP_Plate_5_sc_feature_selected.tsv\" \n",
"$Plate_1\n",
"[1] \"figures/UMAP_Plate_1\"\n",
"\n",
Expand All @@ -76,6 +77,9 @@
"\n",
"$Plate_4\n",
"[1] \"figures/UMAP_Plate_4\"\n",
"\n",
"$Plate_5\n",
"[1] \"figures/UMAP_Plate_5\"\n",
"\n"
]
}
Expand Down Expand Up @@ -212,7 +216,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": null,
"metadata": {
"vscode": {
"languageId": "r"
Expand Down
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