diff --git a/perturbation-count-summary.ipynb b/perturbation-count-summary.ipynb index 77cfeb8..ce32067 100644 --- a/perturbation-count-summary.ipynb +++ b/perturbation-count-summary.ipynb @@ -64,7 +64,7 @@ "There are a total of 52,223 image-based profiles assayed in 2016_04_01_a549_48hr_batch1\n", "There are a total of 10,752 image-based consensus profiles assayed in 2016_04_01_a549_48hr_batch1\n", "There are 1,571 unique compounds assayed in 2016_04_01_a549_48hr_batch1\n", - "There are 1 unique time points assayed in 2016_04_01_a549_48hr_batch1\n", + "There are 1 unique time points assayed in 2016_04_01_a549_48hr_batch1 (['48H'])\n", "There are 7 unique doses assayed in 2016_04_01_a549_48hr_batch1\n", "There are 1 unique cell lines assayed in 2016_04_01_a549_48hr_batch1 (['A549'])\n", "There is a total of 9,395 unique perturbations assayed in 2016_04_01_a549_48hr_batch1\n", @@ -72,7 +72,7 @@ "There are a total of 51,447 image-based profiles assayed in 2017_12_05_Batch2\n", "There are a total of 10,368 image-based consensus profiles assayed in 2017_12_05_Batch2\n", "There are 349 unique compounds assayed in 2017_12_05_Batch2\n", - "There are 3 unique time points assayed in 2017_12_05_Batch2\n", + "There are 3 unique time points assayed in 2017_12_05_Batch2 (['24H' '48H' '6H'])\n", "There are 6 unique doses assayed in 2017_12_05_Batch2\n", "There are 3 unique cell lines assayed in 2017_12_05_Batch2 (['A549' 'MCF7' 'U2OS'])\n", "There is a total of 9,369 unique perturbations assayed in 2017_12_05_Batch2\n", @@ -94,8 +94,8 @@ " num_compounds = len(consensus_df.Metadata_broad_sample.unique())\n", " print(f\"There are {num_compounds:,} unique compounds assayed in {batch}\")\n", " \n", - " time_points = len(consensus_df.Metadata_time_point.unique())\n", - " print(f\"There are {time_points} unique time points assayed in {batch}\")\n", + " time_points = consensus_df.Metadata_time_point.unique()\n", + " print(f\"There are {len(time_points)} unique time points assayed in {batch} ({time_points})\")\n", " \n", " doses = len(consensus_df.Metadata_dose_recode.unique())\n", " print(f\"There are {doses} unique doses assayed in {batch}\")\n", @@ -197,8 +197,10 @@ " print(f\"In batch {batch}, we profiled {batch_cell_count:,} cells\")\n", " \n", " output_cell_count_summary_file = cell_count_dir / f\"{batch}_metadata_cell_count_summary.tsv.gz\"\n", - " batch_metadata_df.to_csv(output_cell_count_summary_file, index=False)\n", - " \n", + " batch_metadata_df.to_csv(\n", + " output_cell_count_summary_file, index=False, compression={\"method\": \"gzip\", \"mtime\": 0}\n", + " )\n", + " \n", " total_cells += batch_cell_count\n", " \n", "print(f\"\\nWe profiled a total of {total_cells:,} cells in the LINCS Cell Painting dataset\")" diff --git a/profiles/cell_count/2016_04_01_a549_48hr_batch1_metadata_cell_count_summary.tsv.gz b/profiles/cell_count/2016_04_01_a549_48hr_batch1_metadata_cell_count_summary.tsv.gz index b65e015..58cc638 100644 --- a/profiles/cell_count/2016_04_01_a549_48hr_batch1_metadata_cell_count_summary.tsv.gz +++ b/profiles/cell_count/2016_04_01_a549_48hr_batch1_metadata_cell_count_summary.tsv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:6929a0c4f09ee3b97f4b794f5ab338dc01208bb6f0dfd8347220107181a8a748 +oid sha256:28a429d4bf68c014278886cb66f838338a60532334c214f1a8649956afc35ad2 size 1058707 diff --git a/profiles/cell_count/2017_12_05_Batch2_metadata_cell_count_summary.tsv.gz b/profiles/cell_count/2017_12_05_Batch2_metadata_cell_count_summary.tsv.gz index ffea6b7..157068f 100644 --- a/profiles/cell_count/2017_12_05_Batch2_metadata_cell_count_summary.tsv.gz +++ b/profiles/cell_count/2017_12_05_Batch2_metadata_cell_count_summary.tsv.gz @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:c15b968c5bc457484dc131fba6fc410e374ccbbc4c4624160df951e1045e5d32 +oid sha256:6aaceed38cad4f050b64324859c087e31dae13babd02b5a53942a0a454ec1e4f size 950856