From 26f7be6bb6f60f2d35a0b58c31e99e324464b2e3 Mon Sep 17 00:00:00 2001 From: Nicolas Palacio Date: Fri, 15 Nov 2024 10:05:54 +0100 Subject: [PATCH] Changed default `target_sum` on `preprocessing.sc_trans_normalize_total` --- src/funki/preprocessing.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/funki/preprocessing.py b/src/funki/preprocessing.py index d7e041c..c1ff1f3 100644 --- a/src/funki/preprocessing.py +++ b/src/funki/preprocessing.py @@ -49,7 +49,7 @@ def sc_trans_filter(data, min_genes=None, max_genes=None, mito_pct=None): return DataSet(aux) -def sc_trans_normalize_total(data, target_sum=1e6, log_transform=False): +def sc_trans_normalize_total(data, target_sum=None, log_transform=False): ''' Normalizes the total counts per cell in a single-cell data set. The normaliztion scales the counts so that the sum of all genes in a cell add up @@ -59,8 +59,8 @@ def sc_trans_normalize_total(data, target_sum=1e6, log_transform=False): :param data: A single-cell transcriptomic data set containing raw counts :type data: :class:`funki.input.DataSet` - :param target_sum: The targeted total counts per cell to normalize for, - defaults to ``None``, which is equivalent to CPM normalization + :param target_sum: The targeted total counts per cell to normalize for, e.g. + ``1e6`` is equivalent to CPM normalization, defaults to ``None``. :type target_sum: int | float, optional :param log_transform: Whether to apply log-transformation after normalizing the data, defaults to ``False``