Examples and line wrapping in utils/transform.py

Author: npalacioescat

src/liana/utils/transform.py

@@ -5,22 +5,52 @@
 
 def zi_minmax(X: ArrayLike, cutoff: float = 0.5) -> csr_matrix:
     """
-    Zero-inflated min-max scaling, adopted from CiteFuse (Kim et al., 2020; https://academic.oup.com/bioinformatics/article/36/14/4137/5827474).
+    Zero-inflated min-max scaling, adopted from CiteFuse (Kim et al., 2020;
+    https://academic.oup.com/bioinformatics/article/36/14/4137/5827474).
 
-    This function scales the data to the range [0, 1] and sets values below a specified cutoff to 0.
+    This function scales the data to the range [0, 1] for each column of a
+    two-dimensional array and sets values below a specified cutoff to 0 (after
+    scaling).
 
     Parameters
     ----------
     X
         Data to be scaled.
     cutoff
-        Cutoff value for zero-inflation - values less than this are set to 0. Default is 0.5.
+        Cutoff value for zero-inflation - values less than this are set to 0.
+        Default is 0.5.
 
     Returns
     -------
     X
         The scaled data matrix
 
+    Examples
+    --------
+    >>> x = np.array([[0.1, 0.3],
+    ...               [2.0, 4.0],
+    ...               [5.5, 7.1]])
+    >>> print(zi_minmax(x))
+    <Compressed Sparse Row sparse matrix of dtype 'float64'
+            with 6 stored elements and shape (3, 2)>
+    Coords        Values
+    (0, 0)        0.0
+    (0, 1)        0.0
+    (1, 0)        0.0
+    (1, 1)        0.5441176470588236
+    (2, 0)        1.0
+    (2, 1)        1.0
+    >>> print(zi_minmax(x, cutoff=0.1))
+    <Compressed Sparse Row sparse matrix of dtype 'float64'
+            with 6 stored elements and shape (3, 2)>
+    Coords        Values
+    (0, 0)        0.0
+    (0, 1)        0.0
+    (1, 0)        0.3518518518518518
+    (1, 1)        0.5441176470588236
+    (2, 0)        1.0
+    (2, 1)        1.0
+
     """
     X = X.copy()
     if not isspmatrix_csr(X):
@@ -59,6 +89,27 @@ def neg_to_zero(X: ArrayLike, cutoff: float = 0) -> csr_matrix:
     -------
     The modified data matrix
 
+    Examples
+    --------
+    >>> x = np.array([-1, -0.5, 0.1, 0.4, 2])
+    >>> print(neg_to_zero(x))
+    <Compressed Sparse Row sparse matrix of dtype 'float64'
+            with 5 stored elements and shape (1, 5)>
+    Coords        Values
+    (0, 0)        0.0
+    (0, 1)        0.0
+    (0, 2)        0.1
+    (0, 3)        0.4
+    (0, 4)        2.0
+    >>> print(neg_to_zero(x, cutoff=0.5))
+    <Compressed Sparse Row sparse matrix of dtype 'float64'
+            with 5 stored elements and shape (1, 5)>
+    Coords        Values
+    (0, 0)        0.0
+    (0, 1)        0.0
+    (0, 2)        0.0
+    (0, 3)        0.0
+    (0, 4)        2.0
     """
     X = X.copy()
     if not isspmatrix_csr(X):