Fix MS7

ddmc/figures/figureMS7.py

@@ -34,29 +34,12 @@ def makeFigure():
         d
     )
 
-    centers_min = pd.DataFrame(model_min.transform()).T
-    centers_min.iloc[:, :] = StandardScaler(with_std=False).fit_transform(
-        centers_min.iloc[:, :]
-    )
-    centers_min = centers_min.T
-    centers_min.columns = np.arange(model_min.n_components) + 1
-    centers_min["Patient_ID"] = X.columns[4:]
-    centers_min = find_patients_with_NATandTumor(
-        centers_min.copy(), "Patient_ID", conc=True
-    )
+    centers_min = reshapePatients(model_min.transform(), X.columns[4:])
 
     # Fit DDMC
     model = DDMC(i, n_components=30, SeqWeight=100, distance_method="Binomial").fit(d)
 
-    # Find and scale centers
-    centers = pd.DataFrame(model.transform()).T
-    centers.iloc[:, :] = StandardScaler(with_std=False).fit_transform(
-        centers.iloc[:, :]
-    )
-    centers = centers.T
-    centers.columns = np.arange(model.n_components) + 1
-    centers["Patient_ID"] = X.columns[4:]
-    centers = find_patients_with_NATandTumor(centers.copy(), "Patient_ID", conc=True)
+    centers = reshapePatients(model.transform(), X.columns[4:])
 
     # Predicting STK11
     lr = LogisticRegressionCV(
@@ -93,7 +76,7 @@ def makeFigure():
     return f
 
 
-def plot_ROCs(ax, centers, centers_min, X, i, y, lr, gene_label):
+def plot_ROCs(ax, centers, centers_min, X, i, y: pd.Series, lr, gene_label):
     """Generate ROC plots using DDMC, unclustered, k-means, and GMM for a particular feature."""
     folds = 7
 
@@ -102,7 +85,7 @@ def plot_ROCs(ax, centers, centers_min, X, i, y, lr, gene_label):
         ax[0],
         lr,
         centers.values,
-        y,
+        y.values,
         cv_folds=folds,
         title="DDMC—Full data set" + gene_label,
     )
@@ -112,52 +95,48 @@ def plot_ROCs(ax, centers, centers_min, X, i, y, lr, gene_label):
         ax[1],
         lr,
         centers_min.values,
-        y,
+        y.values,
         cv_folds=folds,
         title="DDMC—Complete portion" + gene_label,
     )
 
     # Unclustered
     X_f = X.loc[:, centers.index].T
     X_f.index = np.arange(X_f.shape[0])
-    plotROC(ax[2], lr, X_f.values, y, cv_folds=folds, title="Unclustered " + gene_label)
+    plotROC(ax[2], lr, X_f.values, y.values, cv_folds=folds, title="Unclustered " + gene_label)
 
     # Run k-means
-    ncl = 30
     d = X.select_dtypes(include=["float64"]).T.reset_index()
     d.rename(columns={"index": "Patient_ID"}, inplace=True)
     d = d.iloc[:, 1:]
-    x_ = X.copy()
-    x_["Cluster"] = KMeans(n_clusters=ncl).fit(d.T).labels_
-    print(x_)
-    c_kmeans = x_.groupby("Cluster").mean().T
-    c_kmeans["Patient_ID"] = X.columns[4:]
-    c_kmeans.columns = list(np.arange(ncl) + 1) + ["Patient_ID"]
-    c_kmeans.iloc[:, :-1] = StandardScaler(with_std=False).fit_transform(
-        c_kmeans.iloc[:, :-1]
-    )
+
+    kmeans = KMeans(n_clusters=30).fit(d.T)
 
     # Reshape data (Patients vs NAT and tumor sample per cluster)
-    c_kmeansT = find_patients_with_NATandTumor(c_kmeans.copy(), "Patient_ID", conc=True)
+    c_kmeansT = reshapePatients(kmeans.cluster_centers_.T, X.columns[4:])
 
     # Regress k-means clusters against STK11 status
     plotROC(
-        ax[3], lr, c_kmeansT.values, y, cv_folds=folds, title="k-means " + gene_label
+        ax[3], lr, c_kmeansT.values, y.values, cv_folds=folds, title="k-means " + gene_label
     )
 
     # Run GMM
     gmm = DDMC(
         i, n_components=30, SeqWeight=0, distance_method="Binomial", random_state=15
-    ).fit(d, "NA")
-    x_["Cluster"] = gmm.labels()
-    c_gmm = x_.groupby("Cluster").mean().T
-    c_gmm["Patient_ID"] = X.columns[4:]
-    c_gmm.iloc[:, :-1] = StandardScaler(with_std=False).fit_transform(
-        c_gmm.iloc[:, :-1]
-    )
+    ).fit(d)
 
-    # Reshape data (Patients vs NAT and tumor sample per cluster)
-    c_gmmT = find_patients_with_NATandTumor(c_gmm.copy(), "Patient_ID", conc=True)
+    c_gmmT = reshapePatients(gmm.transform(), X.columns[4:])
 
     # Regress GMM clusters against STK11 status
-    plotROC(ax[4], lr, c_gmmT.values, y, cv_folds=folds, title="GMM " + gene_label)
+    plotROC(ax[4], lr, c_gmmT.values, y.values, cv_folds=folds, title="GMM " + gene_label)
+
+
+def reshapePatients(centers, patients):
+    df = pd.DataFrame(centers)
+    df["Patient_ID"] = patients
+    df.iloc[:, :-1] = StandardScaler(with_std=False).fit_transform(
+        df.iloc[:, :-1]
+    )
+
+    # Reshape data (Patients vs NAT and tumor sample per cluster)
+    return find_patients_with_NATandTumor(df.copy(), "Patient_ID", conc=True)