Merge pull request #2 from lli-rice/master

add code for paper figure generation

paper/data/drug_info/DO_slim.txt

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+DOID:104	bacterial_infectious_disease
+DOID:1564	fungal_infectious_disease
+DOID:1398	parasitic_infectious_disease
+DOID:934	viral_infectious_disease
+DOID:13241	behcet's_disease
+DOID:176	cardiovascular_cancer
+DOID:0050700	cardiomyopathy
+DOID:6000	congestive_heart_failure
+DOID:326	ischemia
+DOID:3953	adrenal_gland_cancer
+DOID:12361	graves'_disease
+DOID:9744	type_1_diabetes_mellitus
+DOID:2394	ovarian_cancer
+DOID:2998	testicular_cancer
+DOID:1793	pancreatic_cancer
+DOID:1785	pituitary_cancer
+DOID:1781	thyroid_gland_cancer
+DOID:7998	hyperthyroidism
+DOID:1459	hypothyroidism
+DOID:10608	celiac_disease
+DOID:8577	ulcerative_colitis
+DOID:13250	diarrhea
+DOID:5041	esophageal_cancer
+DOID:4607	biliary_tract_cancer
+DOID:3571	liver_cancer
+DOID:0050589	inflammatory_bowel_disease
+DOID:10155	intestinal_cancer
+DOID:403	mouth_disease
+DOID:2355	anemia
+DOID:1247	blood_coagulation_disease
+DOID:4960	bone_marrow_cancer
+DOID:1240	leukemia
+DOID:0060058	lymphoma
+DOID:3277	thymus_cancer
+DOID:672	spleen_cancer
+DOID:1909	melanoma
+DOID:2723	dermatitis
+DOID:7147	ankylosing_spondylitis
+DOID:986	alopecia_areata
+DOID:8893	psoriasis
+DOID:8857	lupus_erythematosus
+DOID:848	arthritis
+DOID:184	bone_cancer
+DOID:0060249	scoliosis
+DOID:0080006	bone_development_disease
+DOID:14696	Ehlers-Danlos_syndrome
+DOID:1115	sarcoma
+DOID:4045	muscle_cancer
+DOID:423	myopathy
+DOID:10595	Charcot-Marie-Tooth_disease
+DOID:2377	multiple_sclerosis
+DOID:12842	Guillain-Barre_syndrome
+DOID:437	myasthenia_gravis
+DOID:1969	cerebral_palsy
+DOID:9588	encephalitis
+DOID:1826	epilepsy
+DOID:1307	dementia
+DOID:3070	high_grade_glioma
+DOID:0080829	low_grade_glioma
+DOID:649	prion_disease
+DOID:9471	meningitis
+DOID:12858	Huntington's_disease
+DOID:0050951	hereditary_ataxia
+DOID:231	motor_neuron_disease
+DOID:14330	Parkinson's_disease
+DOID:10652	Alzheimer's_disease
+DOID:2174	ocular_cancer
+DOID:5101	ear_cancer
+DOID:0050563	nonsyndromic_deafness
+DOID:13399	color_blindness
+DOID:1686	glaucoma
+DOID:83	cataract
+DOID:4448	macular_degeneration
+DOID:0050572	cone-rod_dystrophy
+DOID:10584	retinitis_pigmentosa
+DOID:289	endometriosis
+DOID:2394	ovarian_cancer
+DOID:363	uterine_cancer
+DOID:11612	polycystic_ovary_syndrome
+DOID:10283	prostate_cancer
+DOID:2998	testicular_cancer
+DOID:2841	asthma
+DOID:1324	lung_cancer
+DOID:1612	breast_cancer
+DOID:11054	urinary_bladder_cancer
+DOID:263	kidney_cancer
+DOID:1074	kidney_failure
+DOID:9352	type_2_diabetes_mellitus
+DOID:1485	cystic_fibrosis
+DOID:1935	Bardet-Biedl_syndrome
+DOID:11934	head_and_neck_cancer
+DOID:5419	schizophrenia
+DOID:2237	hepatitis
+DOID:9351	diabetes_mellitus
+DOID:10763	hypertension
+DOID:0060041	autism_spectrum_disorder
+DOID:4990	essential_tremor
+DOID:769	neuroblastoma
+DOID:10534	stomach_cancer
+DOID:9778	irritable_bowel_syndrome
+DOID:9970	obesity
+DOID:3312	bipolar_disorder
+DOID:326	ischemia
+DOID:1596	mental_depression
+DOID:2030	anxiety_disorder
+DOID:114	heart_disease
+DOID:0050828	artery_disease
+DOID:3770	pulmonary_fibrosis
+DOID:3083	chronic obstructive pulmonary disease
+DOID:3382	liposarcoma

paper/data/geo2kegg.txt

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+GSE14924_CD4 Acute myeloid leukemia LAML
+GSE14924_CD8 Acute myeloid leukemia LAML
+GSE9476 Acute myeloid leukemia LAML
+GSE1297 Alzheimer disease ALZ
+GSE16759 Alzheimer disease ALZ
+GSE5281_EC Alzheimer disease ALZ
+GSE5281_HIP Alzheimer disease ALZ
+GSE5281_VCX Alzheimer disease ALZ
+GSE24739_G0 Chronic myeloid leukemia CML
+GSE24739_G1 Chronic myeloid leukemia CML
+GSE23878 Colorectal cancer CRC
+GSE4107 Colorectal cancer CRC
+GSE4183 Colorectal cancer CRC
+GSE8671 Colorectal cancer CRC
+GSE9348 Colorectal cancer CRC
+GSE19420 Diabetes mellitus type 2 DMND
+GSE1145 Dilated cardiomyopathy DCM
+GSE3585 Dilated cardiomyopathy DCM
+GSE7305 Endometrial cancer UCEC
+GSE19728 Glioma GBM
+GSE21354 Glioma LGG
+GSE8762 Huntington disease HUNT
+GSE30153 Lupus erythematosus systemic LES
+GSE18842 Non small cell lung cancer LUAD
+GSE19188 Non small cell lung cancer LUAD
+GSE38666_epithelia Ovarian neoplasms OV
+GSE38666_stroma Ovarian neoplasms OV
+GSE15471 Pancreatic cancer PAAD
+GSE16515 Pancreatic cancer PAAD
+GSE22780 Pancreatic neoplasms PAAD
+GSE32676 Pancreatic cancer PAAD
+GSE20153 Parkinson disease PARK
+GSE20164 Parkinson disease PARK
+GSE20291 Parkinson disease PARK
+GSE6956AA Prostate cancer PRAD
+GSE6956C Prostate cancer PRAD
+GSE11906 Pulmonary disease chronic obstructive PDCO
+GSE42057 Pulmonary disease chronic obstructive PDCO
+GSE14762 Renal cancer KIRC
+GSE781 Renal cancer KIRC
+GSE3467 Thyroid cancer THCA
+GSE3678 Thyroid cancer THCA