improve docs, fix #200

kaizhang · Dec 14, 2023 · e11e051 · e11e051
1 parent e13d69b
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Showing 2 changed files with 4 additions and 5 deletions.
diff --git a/snapatac2-python/snapatac2/tools/_call_peaks.py b/snapatac2-python/snapatac2/tools/_call_peaks.py
@@ -62,10 +62,6 @@ def macs3(
     blacklist
         Path to the blacklist file in BED format. If provided, regions in the blacklist will be
         removed.
-    out_dir
-        If provided, raw peak files from each group will be saved in the directory.
-        Otherwise, they will be stored in a temporary directory which will be removed
-        afterwards.
     key_added
         `.uns` key under which to add the peak information.
     tempdir

diff --git a/snapatac2-python/snapatac2/tools/_embedding.py b/snapatac2-python/snapatac2/tools/_embedding.py
@@ -165,7 +165,7 @@ def spectral(
         `weighted_by_sd` is set to True, as long as it is large enough, e.g. 30.
     features
         Boolean index mask. True means that the feature is kept.
-        False means the feature is removed.
+        False means the feature is removed. If `features=None`, all features are used.
     random_state
         Seed of the random state generator
     sample_size
@@ -184,6 +184,9 @@ def spectral(
         Whether to weight the result eigenvectors by the square root of eigenvalues.
         This parameter is turned on by default. When it is turned on, mannully selecting
         the number of components is usually not necessary.
+    feature_weights
+        Feature weights used in the distance metric. If None, the inverse document
+        frequency (IDF) is used.
     inplace
         Whether to store the result in the anndata object.