Add correction of factors

meyer-lab · Aug 26, 2024 · 6dcccdd · 6dcccdd
1 parent 465d748
commit 6dcccdd
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Showing 3 changed files with 16 additions and 7 deletions.
diff --git a/pf2/figures/figureA10.py b/pf2/figures/figureA10.py
@@ -27,7 +27,8 @@ def makeFigure():
     subplotLabel(ax)
 
     meta = import_meta()
-    data = read_h5ad("/opt/northwest_bal/full_fitted.h5ad", backed="r")
+    data = read_h5ad("/opt/northwest_bal/full_fitted.h5ad")
+    data.uns["Pf2_A"] = correct_conditions(data)
     conversions = convert_to_patients(data)
 
     patient_factor = pd.DataFrame(
@@ -42,6 +43,13 @@ def makeFigure():
         meta
     )
 
+
+
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+
+
 
 
     names = ["COVID-19", "Non-COVID 19"]

diff --git a/pf2/figures/figureA9.py b/pf2/figures/figureA9.py
@@ -25,10 +25,11 @@ def makeFigure():
     ax, f = getSetup((4, 4), (1, 1))
     subplotLabel(ax)
 
-    X = anndata.read_h5ad("/opt/northwest_bal/full_fitted_uncorrected.h5ad")
+    # X = anndata.read_h5ad("/opt/northwest_bal/full_fitted_uncorrected.h5ad")
 
-    # X = anndata.read_h5ad("/opt/northwest_bal/full_fitted.h5ad")
+    X = anndata.read_h5ad("/opt/northwest_bal/full_fitted.h5ad")
 
+    X.uns["Pf2_A"] = correct_conditions(X)
     # print(np.ravel(X.uns["Pf2_A"]))
     # print(np.ravel(XX.uns["Pf2_A"]))
 

diff --git a/pf2/predict.py b/pf2/predict.py
@@ -35,12 +35,12 @@ def run_plsr(
     data[:] = scale(data)
     plsr = PLSRegression(
         n_components=n_components,
-        scale=True,
+        scale=False,
         max_iter=int(1E15)
     )
-    rfe_cv = RFECV(plsr, step=1, cv=SKF, min_features_to_select=n_components)
-    rfe_cv.fit(data, labels)
-    data = data.loc[:, rfe_cv.support_]
+    # rfe_cv = RFECV(plsr, step=1, cv=SKF, min_features_to_select=n_components)
+    # rfe_cv.fit(data, labels)
+    # data = data.loc[:, rfe_cv.support_]
 
     probabilities = pd.Series(0, dtype=float, index=data.index)
     for train_index, test_index in SKF.split(data, labels):