Fix cobra

netZooPy/cobra/cobra.py

@@ -1,9 +1,10 @@
 import pandas as pd
 import numpy as np
 from scipy.linalg import eigh,pinv
+from sklearn.linear_model import LinearRegression, Lasso
 
 
-def cobra(X, expression):
+def cobra(X, expression, cobra='nnls', alpha: np.float64=0.1):
     """
          COBRA decomposes a (partial) gene co-expression matrix as a
          linear combination of covariate-specific components.
@@ -16,6 +17,12 @@ def cobra(X, expression):
                 design matrix of size (n, q), n = number of samples, q = number of covariates
             expression : np.ndarray, pd.DataFrame
                 gene expression as a matrix of size (g, n), g = number of genes
+            cobra : string
+                regression mode
+                nnls: Non-negative least square (default)
+                nnlasso: Non-negative LASSO
+                deprecated: MLE estimate
+            alpha :
     	Returns
         ---------
             psi : array
@@ -55,26 +62,32 @@ def cobra(X, expression):
     Q = c_eigenvectors[:, indices_nonzero].T[::-1].T
 
     #
-    gtq = np.matmul(g.T, Q)
     d = c_eigenvalues[indices_nonzero][::-1]
 
-    #
-    xtx_inv = np.linalg.pinv(
-        np.dot(X.T, X)
-    )
-    xtx_inv_xt = np.dot(
-        xtx_inv, X.T
-    )
+    if cobra=='nnls':
+        model = LinearRegression(positive=True).fit(X, np.diag(d) )
+        psi = np.transpose(model.coef_)
+    elif cobra=='nnlasso':
+        model == Lasso(alpha=alpha, positive=True).fit(X, np.diag(d) )
+        psi = np.transpose(model.coef_)
+    elif cobra=='deprecated':
+        gtq = np.matmul(g.T, Q)
+        xtx_inv = np.linalg.pinv(
+            np.dot(X.T, X)
+        )
+        xtx_inv_xt = np.dot(
+            xtx_inv, X.T
+        )
 
-    #
-    psi = np.zeros((q, n))
+        #
+        psi = np.zeros((q, n))
 
-    for i in range(q):
-        for h in range(n):
-            psi[i, h] = n * np.sum([
-                (
-                        xtx_inv_xt[i, k] * gtq[k, h] ** 2
-                ) for k in range(n)
-            ])
+        for i in range(q):
+            for h in range(n):
+                psi[i, h] = n * np.sum([
+                    (
+                            xtx_inv_xt[i, k] * gtq[k, h] ** 2
+                    ) for k in range(n)
+                ])
 
     return psi, Q, d, g

requirements.txt

@@ -7,3 +7,4 @@ igraph
 joblib
 statsmodels
 click
+scikit-learn

tests/test_cobra.py

@@ -23,7 +23,7 @@ def test_cobra():
     G_gt = pd.read_csv(G_gt_path, index_col=0)
 
     # Call COBRA
-    psi, Q, D, G = cobra.cobra(X, expression)
+    psi, Q, D, G = cobra.cobra(X, expression, cobra='deprecated')
 
     # Cast output to pandas
     psi = pd.DataFrame(psi, index=psi_gt.index, columns=psi_gt.columns)