genelens.enrichment

module documentation

Module for conducting analysis of overrepresentation of gene sets in all signal pathways of Reactome with construction of dendrogram of intersection of overrepresented pathways taking into account weight parameter

Function dendro_reactome_plot The function performs an overrepresentation analysis and draws a dendrogram of signaling pathways taking into account the weight of the genes included in them.
Function _create_similarity_matrix Create a similarity matrix for a given pathway-geneset dataset. :param dict gene_sets: pathway gene set dictionary :rtype: pandas.DataFrame :returns: similarity matrix
Function _dendro_reactome_to_pandas Create DataFrame for dendrogram ploting
Function _get_dendro Undocumented
Function _get_net Graph of pathway construction
Function _reac_pars parsing reactome output
Function _reactome_enrichment the function receives data from Reactome via reactome2py.analysis
def dendro_reactome_plot(gene_set, gene_weights, species='Homo sapiens', out_path='./'):

The function performs an overrepresentation analysis and draws a dendrogram of signaling pathways taking into account the weight of the genes included in them.

Attributes: ----- gene_set : list of genes gene_weights : dict {gene:weights} species : str, species in Reactome out_path : str, where the plot will be saved

def _create_similarity_matrix(gene_sets):

Create a similarity matrix for a given pathway-geneset dataset. :param dict gene_sets: pathway gene set dictionary :rtype: pandas.DataFrame :returns: similarity matrix

def _dendro_reactome_to_pandas(ReactomeRes, G, species='Homo sapiens'):

Create DataFrame for dendrogram ploting

Attributes: ----- ReactomeRes : result of _reac_pars() G : result of _get_net()

def _get_dendro(dt, key_nodes_dict, out_path='./'):

Undocumented

def _get_net(ReactomeRes):

Graph of pathway construction

def _reac_pars(token_result):

parsing reactome output

def _reactome_enrichment(gene_set, species='Homo sapiens'):

the function receives data from Reactome via reactome2py.analysis