From 77d93a3a551a438799a97ba57d49b19de0a293ab Mon Sep 17 00:00:00 2001 From: Shantanu Singh Date: Thu, 8 Jun 2023 18:11:27 +0200 Subject: [PATCH] Change variance_threshold default to 0.01 (#286) * Change variance_threshold default to 0.01 * Update feature_select to match variance_threshold default --- pycytominer/feature_select.py | 2 +- pycytominer/operations/variance_threshold.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pycytominer/feature_select.py b/pycytominer/feature_select.py index 16cf9142..755aee3e 100644 --- a/pycytominer/feature_select.py +++ b/pycytominer/feature_select.py @@ -27,7 +27,7 @@ def feature_select( corr_threshold=0.9, corr_method="pearson", freq_cut=0.05, - unique_cut=0.1, + unique_cut=0.01, compression_options=None, float_format=None, blocklist_file=None, diff --git a/pycytominer/operations/variance_threshold.py b/pycytominer/operations/variance_threshold.py index 0eb3186c..0fb93873 100644 --- a/pycytominer/operations/variance_threshold.py +++ b/pycytominer/operations/variance_threshold.py @@ -9,7 +9,7 @@ def variance_threshold( - population_df, features="infer", samples="all", freq_cut=0.05, unique_cut=0.1 + population_df, features="infer", samples="all", freq_cut=0.05, unique_cut=0.01 ): """Exclude features that have low variance (low information content)