diff --git a/docs/source/api/index.rst b/docs/source/api/index.rst index b9f387b..f8f9b3d 100644 --- a/docs/source/api/index.rst +++ b/docs/source/api/index.rst @@ -40,15 +40,6 @@ preprocess preprocess -connectivity --------------- -.. currentmodule:: spycone.connectivity - -.. autosummary:: - :template: ./_templates/class.rst - :toctree: generated/ - - connectivity iso_function ------------- @@ -108,4 +99,17 @@ visualize spycone.visualize.vis_all_clusters spycone.visualize.switch_plot spycone.visualize.gsea_plot + + +iso_function +------------- +.. currentmodule:: spycone.splicingfactor + +.. autosummary:: + :template: ./_templates/class.rst + :toctree: generated/ + + spycone.splicingfactor.SF_coexpression + spycone.splicingfactor.SF_motifsearch + \ No newline at end of file diff --git a/spycone/BioNetwork.py b/spycone/BioNetwork.py index e461610..01774dc 100644 --- a/spycone/BioNetwork.py +++ b/spycone/BioNetwork.py @@ -68,7 +68,7 @@ def __init__( """ if self.path == "human": #print("Reading edge list and removing loops") - path = os.path.join(dir_path,f'data/network/9606_biogrid_entrez.tab') + path = os.path.join(dir_path,f'data/network/9606_ddi_weighted_biogrid_entrez.tab') g = nx.read_edgelist(path=path, **self.kwargs) tmp = 0 for gene in g: diff --git a/spycone/DOMINO/src/core/preprocess_slices.py b/spycone/DOMINO/src/core/preprocess_slices.py index 9139e42..9047c3c 100755 --- a/spycone/DOMINO/src/core/preprocess_slices.py +++ b/spycone/DOMINO/src/core/preprocess_slices.py @@ -2,7 +2,7 @@ sys.path.insert(0, "../") import networkx as nx import pandas as pd -import community as community_louvain +import community.community_louvain as community_louvain import numpy as np def create_slices(network_file, output_file_name, resolution=0.15):