Merge pull request #10 from gszep/workspace

workspace
gszep · Sep 29, 2020 · e2ae8a4 · e2ae8a4
2 parents 20c58ba + c5e1a02
commit e2ae8a4
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Showing 17 changed files with 71,803 additions and 10,270 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,4 +1,3 @@
 .*
 !.gitignore
-*.h5ad
 __pycache__
diff --git a/data/390C/390C_unst_022.cleaned.fcs → data/390C/controls/390C_unst_022.cleaned.fcs b/data/390C/390C_unst_022.cleaned.fcs → data/390C/controls/390C_unst_022.cleaned.fcs
diff --git a/data/403C/Donor_unst_021.fcs b/data/403C/Donor_unst_021.fcs
diff --git a/data/403C/donor_unst_021.cleaned.fcs → .../403C/controls/donor_unst_021.cleaned.fcs b/data/403C/donor_unst_021.cleaned.fcs → .../403C/controls/donor_unst_021.cleaned.fcs
diff --git a/data/412C/412C_Unst_022.cleaned.fcs → data/412C/controls/412C_unst_022.cleaned.fcs b/data/412C/412C_Unst_022.cleaned.fcs → data/412C/controls/412C_unst_022.cleaned.fcs
diff --git a/data/423C/Donor_Pre-blood_023.xml b/data/423C/Donor_Pre-blood_023.xml
diff --git a/data/423C/Donor_unst_037.cleaned.fcs → .../423C/controls/Donor_unst_037.cleaned.fcs b/data/423C/Donor_unst_037.cleaned.fcs → .../423C/controls/Donor_unst_037.cleaned.fcs
diff --git a/data/428C/Donor_tLN_027.xml b/data/428C/Donor_tLN_027.xml
diff --git a/data/428C/Donor_unst_032.cleaned.fcs → .../428C/controls/Donor_unst_032.cleaned.fcs b/data/428C/Donor_unst_032.cleaned.fcs → .../428C/controls/Donor_unst_032.cleaned.fcs
diff --git a/data/thresholds.csv b/data/thresholds.csv
@@ -0,0 +1,35 @@
+patient,tissue,CCR10,CCR4,CCR6,CCR7,CD103,CD127,CD25,CD3,CD4,CD45RA,CD69,CD8,CXCR3,CXCR5,Foxp3,HLA-DR,Helios,PD-1
+412C,Blood,400,500,300,1000,400,1000,500,400,800,500,300,1400,400,200,500,600,400,400
+423C,Blood,400,500,300,1000,400,1000,500,400,800,500,300,1400,400,300,400,600,400,400
+428C,Blood,400,500,300,500,400,1000,500,400,800,500,1000,1400,800,200,400,600,200,400
+390C,BM,300,300,300,500,400,1000,500,400,1400,700,1000,1400,1000,200,500,600,400,400
+403C,BM,300,300,300,500,400,1000,300,400,1000,700,700,1400,400,200,500,600,400,400
+412C,BM,400,300,300,500,400,1000,500,400,800,700,1000,1400,600,200,500,600,400,400
+423C,BM,400,400,300,500,400,1000,500,400,800,700,700,1400,600,200,500,700,600,400
+428C,BM,400,400,300,500,400,1000,500,400,800,500,700,1400,600,200,500,400,250,400
+390C,Ileum,300,300,400,300,700,1000,500,400,1200,500,1000,1400,600,400,500,500,400,400
+412C,Ileum,700,300,400,500,900,1000,500,400,600,500,1000,1400,1000,400,700,700,400,400
+423C,Ileum,600,500,500,500,900,1000,500,400,800,500,1000,1400,700,400,700,800,400,400
+428C,Ileum,600,500,300,500,700,1000,500,400,500,200,1000,1400,800,300,200,500,200,400
+390C,Liver,300,400,400,500,400,1000,500,400,1200,600,1000,1400,800,400,500,800,800,800
+403C,Liver,300,400,300,250,400,1000,300,400,800,600,1000,1400,800,200,400,700,800,400
+412C,Liver,300,500,300,250,400,1000,300,400,800,500,1000,1400,800,200,400,700,800,400
+423C,Liver,600,500,300,250,600,1000,300,400,800,500,1000,1400,800,400,700,1500,800,800
+390C,Lung,300,400,300,300,400,1000,500,400,1200,500,1000,1400,700,200,400,700,400,400
+403C,Lung,400,400,300,300,400,1000,300,400,800,500,1000,1400,1000,200,600,1000,400,400
+423C,Lung,500,700,400,500,600,1000,500,400,800,500,1000,1400,1000,400,600,1000,400,800
+428C,Lung,500,400,300,300,600,1000,500,400,800,300,1000,1400,500,200,400,700,250,800
+390C,mLN,300,250,300,1000,400,1000,500,400,1200,500,1000,1400,700,400,500,500,400,400
+403C,mLN,300,300,300,1000,400,1000,500,400,600,500,1000,1400,700,400,500,600,400,400
+412C,mLN,400,300,300,600,400,1000,500,400,400,500,1000,1400,700,400,500,600,400,400
+423C,mLN,600,250,300,1000,400,1000,500,400,800,500,1500,1400,700,400,500,800,400,400
+390C,Spleen,300,400,300,1300,400,1000,500,400,1200,500,1000,1400,700,400,500,700,400,400
+403C,Spleen,300,400,300,500,400,1000,500,400,800,500,1000,1400,700,300,500,600,400,400
+412C,Spleen,300,400,300,500,400,1000,500,400,800,500,1000,1400,700,400,500,600,400,400
+423C,Spleen,400,400,300,500,400,1000,500,400,800,500,1000,1400,700,400,500,800,400,400
+428C,Spleen,400,400,300,500,400,1000,500,400,800,500,1000,1400,700,400,500,700,250,400
+390C,tLN,300,400,300,1000,400,1000,500,400,1200,500,1500,1400,700,400,500,600,400,400
+403C,tLN,300,400,300,1000,400,1000,500,400,800,500,1000,1400,700,400,500,600,400,400
+412C,tLN,300,400,300,1000,400,1000,500,400,800,500,2000,1400,700,400,500,600,400,400
+423C,tLN,400,400,300,1000,400,1000,500,400,800,500,1500,1400,700,400,500,800,400,400
+428C,tLN,300,400,300,1000,400,1000,500,400,800,500,1500,1400,700,400,500,600,250,400
diff --git a/data/workspace.wsp b/data/workspace.wsp
diff --git a/figures/batch-normalisation.png b/figures/batch-normalisation.png
diff --git a/main.ipynb b/main.ipynb
diff --git a/utils/fcs.py b/utils/fcs.py
diff --git a/utils/features.py b/utils/features.py
diff --git a/utils/gates.py b/utils/gates.py