From 7dacfbccdf6a82f08993d37b0ee2dea5aa9f8983 Mon Sep 17 00:00:00 2001 From: simonvh Date: Fri, 13 Apr 2018 10:21:18 +0200 Subject: [PATCH 1/2] typo, missing import --- README.rst | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.rst b/README.rst index 32216f3..fb2759c 100644 --- a/README.rst +++ b/README.rst @@ -135,6 +135,7 @@ First we import the necessary modules and declare some constants: .. code-block:: python import os + import glob import pandas as pd import numpy as np @@ -222,7 +223,7 @@ for the co-expression module inference is used. .. code-block:: python N_SAMPLES = ex_matrix.shape[1] # Full dataset - adjancencies = grnboost2(expression_data=ex_matrix.T.sample(n=N_SAMPLES, replace=False), + adjacencies = grnboost2(expression_data=ex_matrix.T.sample(n=N_SAMPLES, replace=False), tf_names=tf_names, verbose=True) Derive potential regulons from these co-expression modules From 35a81616e0aa9c6703df25bb961170518d4fc324 Mon Sep 17 00:00:00 2001 From: simonvh Date: Fri, 13 Apr 2018 10:21:40 +0200 Subject: [PATCH 2/2] fix error --- src/pyscenic/transform.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/pyscenic/transform.py b/src/pyscenic/transform.py index e986c46..6ba1e45 100644 --- a/src/pyscenic/transform.py +++ b/src/pyscenic/transform.py @@ -228,7 +228,7 @@ def module2df(db: Type[RankingDatabase], module: Regulon, motif_annotations: pd. def modules2df(db: Type[RankingDatabase], modules: Sequence[Regulon], motif_annotations: pd.DataFrame, - weighted_recovery=False, module2features_func=module2features) -> pd.DataFrame: + weighted_recovery=False, return_recovery_curves=False, module2features_func=module2features) -> pd.DataFrame: # Make sure return recovery curves is always set to false because the metadata for the distributed dataframe needs # to be fixed for the dask framework. #TODO: Remove this restriction.