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Update Plate 4 normalization to standardize to both WT and Null controls #44

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Apr 18, 2024
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Update Plate 4 normalization to standardize to both WT and Null controls #44

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33 changes: 7 additions & 26 deletions 3.processing_features/2.pycytominer_singlecell_pipelines.ipynb
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Expand Up @@ -97,18 +97,9 @@
"name": "stdout",
"output_type": "stream",
"text": [
"{ 'Plate_3': { 'dest_path': 'data/converted_data/Plate_3.parquet',\n",
" 'platemap_path': '/home/jenna/nf1_cellpainting_data/0.download_data/metadata/platemap_NF1_plate3.csv',\n",
" 'source_path': '/home/jenna/nf1_cellpainting_data/2.cellprofiler_analysis/analysis_output/Plate_3/Plate_3_nf1_analysis.sqlite'},\n",
" 'Plate_3_prime': { 'dest_path': 'data/converted_data/Plate_3_prime.parquet',\n",
" 'platemap_path': '/home/jenna/nf1_cellpainting_data/0.download_data/metadata/platemap_NF1_plate3.csv',\n",
" 'source_path': '/home/jenna/nf1_cellpainting_data/2.cellprofiler_analysis/analysis_output/Plate_3_prime/Plate_3_prime_nf1_analysis.sqlite'},\n",
" 'Plate_4': { 'dest_path': 'data/converted_data/Plate_4.parquet',\n",
"{ 'Plate_4': { 'dest_path': 'data/converted_data/Plate_4.parquet',\n",
" 'platemap_path': '/home/jenna/nf1_cellpainting_data/0.download_data/metadata/platemap_NF1_plate4.csv',\n",
" 'source_path': '/home/jenna/nf1_cellpainting_data/2.cellprofiler_analysis/analysis_output/Plate_4/Plate_4_nf1_analysis.sqlite'},\n",
" 'Plate_5': { 'dest_path': 'data/converted_data/Plate_5.parquet',\n",
" 'platemap_path': '/home/jenna/nf1_cellpainting_data/0.download_data/metadata/platemap_NF1_plate5.csv',\n",
" 'source_path': '/home/jenna/nf1_cellpainting_data/2.cellprofiler_analysis/analysis_output/Plate_5/Plate_5_nf1_analysis.sqlite'}}\n"
" 'source_path': '/home/jenna/nf1_cellpainting_data/2.cellprofiler_analysis/analysis_output/Plate_4/Plate_4_nf1_analysis.sqlite'}}\n"
]
}
],
Expand Down Expand Up @@ -164,20 +155,9 @@
"name": "stdout",
"output_type": "stream",
"text": [
"Now performing single-cell pycytominer pipeline for Plate_3\n",
"HET cells have been removed from Plate_3\n",
"Performing normalization for Plate_3 using samples parameter: all\n",
"(11286, 1165)\n",
"Now performing single-cell pycytominer pipeline for Plate_3_prime\n",
"HET cells have been removed from Plate_3_prime\n",
"Performing normalization for Plate_3_prime using samples parameter: all\n",
"(5506, 1140)\n",
"Now performing single-cell pycytominer pipeline for Plate_4\n",
"Performing normalization for Plate_4 using samples parameter: Metadata_Concentration == 0.0 and Metadata_genotype == 'Null'\n",
"(7308, 1157)\n",
"Now performing single-cell pycytominer pipeline for Plate_5\n",
"Performing normalization for Plate_5 using samples parameter: all\n",
"(7759, 1147)\n"
"Performing normalization for Plate_4 using samples parameter: Metadata_Concentration == 0.0 and (Metadata_genotype == 'Null' or Metadata_genotype == 'WT')\n",
"(7308, 1157)\n"
]
}
],
Expand Down Expand Up @@ -240,9 +220,10 @@
" # set default for samples to use in normalization\n",
" samples = \"all\"\n",
"\n",
" # Only for Plate 4, we want to normalize to no siRNA treatment Null cells (controls)\n",
" # Only for Plate 4, we want to normalize to no siRNA treatment Null and WT cells (controls)\n",
" if plate == \"Plate_4\":\n",
" samples = \"Metadata_Concentration == 0.0 and Metadata_genotype == 'Null'\"\n",
" samples = \"Metadata_Concentration == 0.0 and (Metadata_genotype == 'Null' or Metadata_genotype == 'WT')\"\n",
"\n",
"\n",
" print(f\"Performing normalization for {plate} using samples parameter: {samples}\")\n",
"\n",
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4 changes: 2 additions & 2 deletions 3.processing_features/data/single_cell_profiles/Plate_4_bulk_camerons_method.parquet
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4 changes: 2 additions & 2 deletions 3.processing_features/data/single_cell_profiles/Plate_4_sc_feature_selected.parquet
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4 changes: 2 additions & 2 deletions 3.processing_features/data/single_cell_profiles/Plate_4_sc_normalized.parquet
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5 changes: 3 additions & 2 deletions 3.processing_features/scripts/2.pycytominer_singlecell_pipelines.py
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Expand Up @@ -143,9 +143,10 @@
# set default for samples to use in normalization
samples = "all"

# Only for Plate 4, we want to normalize to no siRNA treatment Null cells (controls)
# Only for Plate 4, we want to normalize to no siRNA treatment Null and WT cells (controls)
if plate == "Plate_4":
samples = "Metadata_Concentration == 0.0 and Metadata_genotype == 'Null'"
samples = "Metadata_Concentration == 0.0 and (Metadata_genotype == 'Null' or Metadata_genotype == 'WT')"
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print(f"Performing normalization for {plate} using samples parameter: {samples}")

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