def run(enrichr_results, signature_label):
# Libraries
libraries = {
'KEA_2015': '### A. KEA (experimentally validated targets)',
'ARCHS4_Kinases_Coexp': '### B. ARCHS4 (coexpressed genes)'
}
# Initialize results
results = []
# Loop through genesets
for geneset in ['upregulated', 'downregulated']:
# Append ChEA results
enrichment_dataframe = s.get_enrichr_results(
enrichr_results[geneset]['userListId'],
gene_set_libraries=libraries,
geneset=geneset)
results.append(enrichment_dataframe)
# Concatenate results
enrichment_dataframe = pd.concat(results)
return {
'enrichment_dataframe': enrichment_dataframe,
'signature_label': signature_label
}
def run(enrichr_results, signature_label):
# Libraries
libraries = {
'TargetScan_microRNA_2017':
'### A. TargetScan (experimentally validated targets)',
'miRTarBase_2017':
'### B. miRTarBase (experimentally validated targets)'
}
# Initialize results
results = []
# Loop through genesets
for geneset in ['upregulated', 'downregulated']:
# Append ChEA results
enrichment_dataframe = s.get_enrichr_results(
enrichr_results[geneset]['userListId'],
gene_set_libraries=libraries,
geneset=geneset)
results.append(enrichment_dataframe)
# Concatenate results
enrichment_dataframe = pd.concat(results)
return {
'enrichment_dataframe': enrichment_dataframe,
'signature_label': signature_label
}
def run(enrichr_results,
signature_label,
plot_type='interactive',
sort_results_by='pvalue'):
# Libraries
libraries = {
'KEGG_2016': 'KEGG Pathways',
'WikiPathways_2016': 'WikiPathways',
'Reactome_2016': 'Reactome Pathways'
}
# Get Enrichment Results
enrichment_results = {
geneset: s.get_enrichr_results(enrichr_results[geneset]['userListId'],
gene_set_libraries=libraries,
geneset=geneset)
for geneset in ['upregulated', 'downregulated']
}
enrichment_results['signature_label'] = signature_label
enrichment_results['plot_type'] = plot_type
enrichment_results['sort_results_by'] = sort_results_by
# Return
return enrichment_results
def run(enrichr_results,
signature_label,
plot_type='interactive',
go_version='2018',
sort_results_by='pvalue'):
# Libraries
go_version = str(go_version)
libraries = {
'GO_Biological_Process_' + go_version:
'Gene Ontology Biological Process (' + go_version + ' version)',
'GO_Molecular_Function_' + go_version:
'Gene Ontology Molecular Function (' + go_version + ' version)',
'GO_Cellular_Component_' + go_version:
'Gene Ontology Cellular Component (' + go_version + ' version)'
}
# Get Enrichment Results
enrichment_results = {
geneset: s.get_enrichr_results(enrichr_results[geneset]['userListId'],
gene_set_libraries=libraries,
geneset=geneset)
for geneset in ['upregulated', 'downregulated']
}
enrichment_results['signature_label'] = signature_label
enrichment_results['plot_type'] = plot_type
enrichment_results['sort_results_by'] = sort_results_by
# Return
return enrichment_results
def run(enrichr_results, signature_label, plot_type='interactive'):
# Libraries
libraries = {
'GO_Biological_Process_2017b': 'Gene Ontology Biological Process',
'GO_Molecular_Function_2017b': 'Gene Ontology Molecular Function',
'GO_Cellular_Component_2017b': 'Gene Ontology Cellular Component'
}
# Get Enrichment Results
enrichment_results = {
geneset: s.get_enrichr_results(enrichr_results[geneset]['userListId'],
gene_set_libraries=libraries,
geneset=geneset)
for geneset in ['upregulated', 'downregulated']
}
enrichment_results['signature_label'] = signature_label
enrichment_results['plot_type'] = plot_type
# Return
return enrichment_results