diff --git a/Makefile b/Makefile index 546aac8a29691a838dadca0672afe3c067337894..8e4713f587c00d375f8d151a3a26de66df8c6709 100644 --- a/Makefile +++ b/Makefile @@ -1,2 +1,2 @@ init: - pip install -r requirements.txt + pip install -r requirements.txt diff --git a/README.md b/README.md index dca98c32d3d02986e3e530a1d4ef14a58b94f86b..72a8fa00560a36734998e1b373129b86ba4ddadd 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,22 @@ -# Group Factor Analysis Code -Decomposes a set of expressions into a group expression -and calculates how it is regulated via an ANOVA that is -relating it to the observables in the journal file. The -final p values are then fdr corrected and the resulting -q values are also calculated. +# Simple Group Factor Analysis +Decomposes a set of expressions into a group expression. +The expression regulation can be studied via an ANOVA that +relates it to the observables in the journal file. The +final p values are then FDR corrected and the resulting +q values are produced. The journal and analyte expression file must be ordered the same way with respect to the samples that are positioned on the columns. +Install with: +pip install --index-url https://test.pypi.org/simple/ impetuous-gfa + +Visit the active code via: +https://github.com/richardtjornhammar/impetuous + +Visit the published code: +https://doi.org/10.5281/zenodo.2594691 + +Cite using +DOI: 10.5281/zenodo.2594691 diff --git a/requirements.txt b/requirements.txt index 8c799548dc9131531b973b07d3dfe7212fa6b398..6d747bdc5aca9335f11be3d7eefc892ba93215cd 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,6 +1,6 @@ pandas==0.23.4 numpy==1.13.3 statsmodels==0.9.0 -sklearn==0.19.0 +scikit-learn==0.19.0 scipy==0.19.1 patsy==0.5.0 diff --git a/setup.py b/setup.py index dec8b7e61a9bc2e14449a0a9b91abfd7de9d374f..1b90a3fb830ca55d15ca928f694f9fc0cf37126b 100644 --- a/setup.py +++ b/setup.py @@ -5,7 +5,7 @@ with open("README.md", "r") as fh: setuptools.setup( name="impetuous-gfa", - version="0.1.0", + version="0.1.2", author="Richard Tjörnhammar", author_email="richard.tjornhammar@gmail.com", description="Impetuous Group Factor Analysis", @@ -15,8 +15,7 @@ setuptools.setup( packages=setuptools.find_packages(), classifiers=[ "Programming Language :: Python :: 3", - "License :: OSI Approved :: Apache License 2.0", + "License :: OSI Approved :: Apache Software License", "Operating System :: OS Independent", - "Domain :: Group Factor Analysis", ], ) diff --git a/src/impetuous.py b/src/impetuous.py index 17fd94344e3ece2ceca0fa852b7e6a0b3eb8cec1..d0ce467b07fa3cceb4f5f20bb6f6d0e2da9cea7d 100644 --- a/src/impetuous.py +++ b/src/impetuous.py @@ -109,5 +109,6 @@ if __name__ == '__main__' : analyte_df = pd.read_csv(analyte_file,'\t' , index_col=0 ) journal_df = prune_journal( pd.read_csv(journal_file,'\t', index_col=0 ) ) + print ( quantify_groups( analyte_df, journal_df, 'Group ~ Var + C(Cat) ', grouping_file ) )