oncoprintjs 5.0.2 → 6.0.0

package/test/generate_data.py

@@ -0,0 +1,108 @@
+import json
+import numpy as np
+import pandas as pd
+
+
+def generate_heatmap_data():
+	hm_df = pd.DataFrame(
+		columns=['TCGA-{0:02d}'.format(n) for n in range(50)],
+		index=['GENE{0}'.format(n) for n in range(5)])
+	
+	hm_df.ix[:, :] = np.random.randn(*hm_df.values.shape)
+	hm_df.ix[:3, :12] = np.random.randn(3, 12) + 1
+	hm_df.ix[3:, :12] = np.random.randn(2, 12) - 0.5
+	hm_df.ix[:2, 12:28] = np.random.randn(2, 28-12) - 2
+	hm_df.ix[2:, 28:35] = np.random.randn(3, 35-28) + 3
+	hm_df.ix[:, 45:] = 0
+	
+	data = []
+	for gene in hm_df.index:
+		datum = {'gene': gene, 'data': []}
+		for samp in hm_df.columns:
+			datum['data'].append({'sample': samp, 'vaf': hm_df.ix[gene, samp]})
+		data.append(datum)
+	
+	json_str = json.dumps(data, indent=4)
+	
+	with open('heatmap-data.js', 'w') as f:
+		f.write('var hm_data = ' + json_str + ';')
+	return
+
+
+def generate_glyphmap_data():
+	ga_df = pd.DataFrame(
+		columns=['TCGA-{0:02d}'.format(n) for n in range(50)],
+		index=['GENE{0}'.format(n) for n in range(5)])
+	
+	data = []
+	for gene in ga_df.index:
+		datum = {
+			'gene': gene, 
+			'desc': 'Annotation for ' + gene, 
+			'data': []
+		}
+		for samp in ga_df.columns:
+			sample = {'sample': samp}
+			
+			dice_1 = np.random.random()
+			if dice_1 < 0.3:
+				sample['disp_cna'] = None
+				dice_2 = np.random.random()
+				if dice_2 < 0.2:
+					sample['disp_cna'] = 'amp'
+				elif dice_2 < 0.4:
+					sample['disp_cna'] = 'homdel'
+				elif dice_2 < 0.6:
+					sample['disp_cna'] = 'gain'
+				elif dice_2 < 0.8:
+					sample['disp_cna'] = 'hetloss'
+				else:
+					sample['disp_cna'] = 'diploid'
+			
+			dice_1 = np.random.random()
+			if dice_1 < 0.3:
+				sample['disp_mut'] = None
+				dice_2 = np.random.random()
+				if dice_2 < 0.25:
+					sample['disp_mut'] = 'trunc'
+				elif dice_2 < 0.5:
+					sample['disp_mut'] = 'inframe'
+				elif dice_2 < 0.75:
+					sample['disp_mut'] = 'promoter'
+				else:
+					sample['disp_mut'] = 'missense'
+			
+			dice_1 = np.random.random()
+			if dice_1 < 0.2:
+				sample['disp_mrna'] = None
+				dice_2 = np.random.random()
+				if dice_2 < 0.6:
+					sample['disp_mrna'] = 'up'
+				else:
+					sample['disp_mrna'] = 'down'
+			
+			dice_1 = np.random.random()
+			if dice_1 < 0.2:
+				sample['disp_prot'] = None
+				dice_2 = np.random.random()
+				if dice_2 < 0.6:
+					sample['disp_prot'] = 'up'
+				else:
+					sample['disp_prot'] = 'down'
+			
+			datum['data'].append(sample)
+			
+		data.append(datum)
+	
+	json_str = json.dumps(data, indent=4)
+	
+	with open('glyphmap-data.js', 'w') as f:
+		f.write('var ga_data = ' + json_str + ';')
+	return
+
+if __name__ == "__main__":
+	np.random.seed(0)
+	generate_heatmap_data()
+	generate_glyphmap_data()
+
+