# Initialize Notebook
%run ../library/v1.1.4/init.ipy
HTML('''<script> code_show=true;  function code_toggle() {  if (code_show){  $('div.input').hide();  } else {  $('div.input').show();  }  code_show = !code_show }  $( document ).ready(code_toggle); </script> <form action="javascript:code_toggle()"><input type="submit" value="Toggle Code"></form>''')

# Load dataset
dataset = load_dataset(source='upload', uid='ETafDguzb9O')

# Preview expression data
preview_data(dataset)

# Display metadata
display_metadata(dataset)

# Configure signatures
dataset['signature_metadata'] = {
    'Control vs Perturbation': {
        'A': ['I18R026a01_01_R1', 'I18R026a02_01_R1', 'I18R026a03_01_R1'],
        'B': ['I18R026b01_01_R1', 'I18R026b02_01_R1', 'I18R026b03_01_R1']
    }
}

# Generate signatures
for label, groups in dataset['signature_metadata'].items():
    signatures[label] = generate_signature(group_A=groups['A'], group_B=groups['B'], method='limma', dataset=dataset)

# Run analysis
results['pca'] = analyze(dataset=dataset, tool='pca', nr_genes=2500, normalization='logCPM', z_score=True, plot_type='interactive')

# Display results
plot(results['pca'])

# Run analysis
results['library_size_analysis'] = analyze(dataset=dataset, tool='library_size_analysis', plot_type='interactive')

# Display results
plot(results['library_size_analysis'])

# Initialize results
results['enrichr'] = {}

# Loop through signatures
for label, signature in signatures.items():

    # Run analysis
    results['enrichr'][label] = analyze(signature=signature, tool='enrichr', signature_label=label, geneset_size=500, sort_genes_by='logFC')

    # Display results
    plot(results['enrichr'][label])

# Initialize results
results['go_enrichment'] = {}

# Loop through results
for label, enrichr_results in results['enrichr'].items():

    # Run analysis
    results['go_enrichment'][label] = analyze(enrichr_results=enrichr_results['results'], tool='go_enrichment', signature_label=label, plot_type='interactive', go_version=2018, sort_results_by='pvalue')

    # Display results
    plot(results['go_enrichment'][label])

# Initialize results
results['pathway_enrichment'] = {}

# Loop through results
for label, enrichr_results in results['enrichr'].items():

    # Run analysis
    results['pathway_enrichment'][label] = analyze(enrichr_results=enrichr_results['results'], tool='pathway_enrichment', signature_label=label, plot_type='interactive', sort_results_by='pvalue')

    # Display results
    plot(results['pathway_enrichment'][label])

# Initialize results
results['tf_enrichment'] = {}

# Loop through results
for label, enrichr_results in results['enrichr'].items():

    # Run analysis
    results['tf_enrichment'][label] = analyze(enrichr_results=enrichr_results['results'], tool='tf_enrichment', signature_label=label)

    # Display results
    plot(results['tf_enrichment'][label])

# Initialize results
results['kinase_enrichment'] = {}

# Loop through results
for label, enrichr_results in results['enrichr'].items():

    # Run analysis
    results['kinase_enrichment'][label] = analyze(enrichr_results=enrichr_results['results'], tool='kinase_enrichment', signature_label=label)

    # Display results
    plot(results['kinase_enrichment'][label])

# Initialize results
results['mirna_enrichment'] = {}

# Loop through results
for label, enrichr_results in results['enrichr'].items():

    # Run analysis
    results['mirna_enrichment'][label] = analyze(enrichr_results=enrichr_results['results'], tool='mirna_enrichment', signature_label=label)

    # Display results
    plot(results['mirna_enrichment'][label])

# Initialize results
results['l1000cds2'] = {}

# Loop through signatures
for label, signature in signatures.items():

    # Run analysis
    results['l1000cds2'][label] = analyze(signature=signature, tool='l1000cds2', signature_label=label, plot_type='interactive')

    # Display results
    plot(results['l1000cds2'][label])

# Initialize results
results['l1000fwd'] = {}

# Loop through signatures
for label, signature in signatures.items():

    # Run analysis
    results['l1000fwd'][label] = analyze(signature=signature, tool='l1000fwd', signature_label=label)

    # Display results
    plot(results['l1000fwd'][label])