From e11e0512976f044feda13d62456061580b0d9689 Mon Sep 17 00:00:00 2001 From: Kai Zhang Date: Thu, 14 Dec 2023 16:14:10 +0800 Subject: [PATCH] improve docs, fix #200 --- snapatac2-python/snapatac2/tools/_call_peaks.py | 4 ---- snapatac2-python/snapatac2/tools/_embedding.py | 5 ++++- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/snapatac2-python/snapatac2/tools/_call_peaks.py b/snapatac2-python/snapatac2/tools/_call_peaks.py index 8d172dbe8..9cbd8f228 100644 --- 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 index 7deb85fc1..dd71467f1 100644 --- 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.