From b40881a290015c628f9bc81bd1a5e309147197d6 Mon Sep 17 00:00:00 2001 From: Avrohom Gottlieb Date: Wed, 14 Aug 2024 16:52:07 -0400 Subject: [PATCH] update skip-quantile-normalization documentation to improve clarity --- docs/cli.rst | 2 +- docs/quickstart.rst | 2 +- pyrefinebio/high_level_functions.py | 3 ++- pyrefinebio/script.py | 2 +- 4 files changed, 5 insertions(+), 4 deletions(-) diff --git a/docs/cli.rst b/docs/cli.rst index 638f8d8..6d0bc38 100644 --- a/docs/cli.rst +++ b/docs/cli.rst @@ -88,7 +88,7 @@ You can also pass in other optional command options to alter the Dataset itself * **transformation** - Can be used to change the transformation of the Dataset. The default is "NONE", and the other available choices are "MINMAX" and "STANDARD". For more information on Dataset transformation check out `Gene transformations`_. -* **skip-quantile-normalization** - Can be used to choose whether or not quantile normalization is skipped for RNA-seq Samples. For more information check out `Quantile normalization`_. +* **skip-quantile-normalization** - Can be used to disable quantile normalization for RNA-seq Samples, which is performed by default. For more information check out `Quantile normalization`_. * **extract** - Can be used to choose whether the downloaded zip file should be automatically extracted. It will automatically extract to the same location that you passed in as :code:`path`. So if :code:`path` is a zip file: :code:`./path/to/dataset.zip` it will be extracted to the dir :code:`./path/to/dataset/`, if :code:`path` is a dir: :code:`./path/to/dir/` it will be extracted to :code:`./path/to/dir/[generated-file-name]/`. By default, :code:`extract` is False. diff --git a/docs/quickstart.rst b/docs/quickstart.rst index 12c4e79..3fcd828 100644 --- a/docs/quickstart.rst +++ b/docs/quickstart.rst @@ -109,7 +109,7 @@ You can also pass in other optional parameters to alter the Dataset itself and t * **transformation** `(str)` - Can be used to change the transformation of the Dataset. The default is "NONE", and the other available choices are "MINMAX" and "STANDARD". For more information on Dataset transformation check out `Gene transformations`_. -* **skip_quantile_normalization** `(bool)` - Can be used to choose whether or not quantile normalization is skipped for RNA-seq Samples. For more information check out `Quantile normalization`_. +* **skip_quantile_normalization** `(bool)` - Can be used to disable quantile normalization for RNA-seq Samples, which is performed by default. For more information check out `Quantile normalization`_. * **extract** `(bool)` - Can be used to choose whether the downloaded zip file should be automatically extracted. It will automatically extract to the same location that you passed in as :code:`path`. So if :code:`path` is a zip file: :code:`./path/to/dataset.zip` it will be extracted to the dir :code:`./path/to/dataset/`, if :code:`path` is a dir: :code:`./path/to/dir/` it will be extracted to :code:`./path/to/dir/[generated-file-name]/`. By default, :code:`extract` is False. diff --git a/pyrefinebio/high_level_functions.py b/pyrefinebio/high_level_functions.py index b2a0c86..a1507a5 100644 --- a/pyrefinebio/high_level_functions.py +++ b/pyrefinebio/high_level_functions.py @@ -93,7 +93,8 @@ def download_dataset( transformation (str): the transformation for the dataset - `NONE`, `MINMAX`, or `STANDARD` skip_quantile_normalization (bool): control whether or not the dataset should skip quantile - normalization for RNA-seq Samples + normalization for RNA-seq Samples. Quantile normalization + is performed by default. quant_sf_only (bool): include only quant.sf files in the generated dataset. diff --git a/pyrefinebio/script.py b/pyrefinebio/script.py index 7ab27c0..db76366 100644 --- a/pyrefinebio/script.py +++ b/pyrefinebio/script.py @@ -106,7 +106,7 @@ def describe(entity=None): "--skip-quantile-normalization", default=False, type=click.BOOL, - help="Control whether the Dataset should skip quantile normalization for RNA-seq Samples", + help="Control whether the Dataset should skip quantile normalization for RNA-seq Samples. Quantile normalization is performed by default.", ) @click.option( "--timeout",