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name_mappings.py
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name_mappings.py
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import seaborn as sns
d_prs_names={
# BCAC
'D_bca_michailidou_2017':'D_bca_michailidou_2017' ,
'UKB_bc_eur':'UKB_bc_eur',
'bcac_onco_eur':'BCAC_eur',
'bcac_onco_eur-minus-outliers':'BCAC_eur-minus-outliers',
'bcac_onco_eur-1pcs':'BCAC_eur-1pcs',
'bcac_onco_eur-2pcs':'BCAC_eur-2pcs',
'bcac_onco_eur-3pcs':'BCAC_eur-3pcs',
'bcac_onco_eur-4pcs':'BCAC_eur-4pcs',
'bcac_onco_eur-5pcs':'BCAC_eur-5pcs',
'bcac_onco_eur-6pcs':'BCAC_eur-6pcs',
'bcac_onco_eur-6pcs':'BCAC_eur-3pcs2',
# UKB
'D2_chol_willer_2013':'Cholesterol',
'D2_sysp_evangelou_2018':'Systolic BP',
'D2_dias_evangelou_2018':'Diastolic BP',
'D2_asth_zhu_2019':'Asthma',
'D_t2d_mahajan_2018':'Type 2 Diabetes (old)',
'D2_ldlp_willer_2013':'LDL levels',
'D2_hdlp_willer_2013':'HDL levels',
'D2_t2di_mahajan_2018':'Type 2 Diabetes',
'D2_gerx_an_2019':'Reflux',
'D2_madd_howard_2019':'Depression',
'GC_utfi_morton_2019':'Uterine Fibroid',
'UKB_t2d_eur':'Type 2 Diabetes (EUR-UKB)',
'UKB_osar_eur':'Osteoarthritis (EUR-UKB)',
'UKB_hfvr_eur':'Hay fever (EUR-UKB)',
'UKB_chol_eur':'Cholesterol levels (EUR-UKB)',
'UKB_ht_eur':'Hypertension (EUR-UKB)',
'UKB_ast_eur':'Asthma (EUR-UKB)',
'UKB_hyty_eur':'Hypotyroidism (EUR-UKB)',
'UKB_gerx_eur':'Reflux (EUR-UKB)',
'UKB_madd_eur':'Depression (EUR-UKB)',
'UKB_angna_eur':'Angina (EUR-UKB)',
'UKB_utfi_eur':'Uterine fibroilds (EUR-UKB)',
'UKB_ctrt_eur':'Cataract (EUR-UKB)',
'UKB_t2d_gbr':'Type 2 Diabetes (GBR-UKB)',
'UKB_osar_gbr':'Osteoarthritis (GBR-UKB)',
'UKB_hfvr_gbr':'Hay fever (GBR-UKB)',
'UKB_chol_gbr':'Cholesterol levels (GBR-UKB)',
'UKB_ht_gbr':'Hypertension (GBR-UKB)',
'UKB_ast_gbr':'Asthma (GBR-UKB)',
'UKB_hyty_gbr':'Hypotyroidism (GBR-UKB)',
'UKB_gerx_gbr':'Reflux (GBR-UKB)',
'UKB_madd_gbr':'Depression (GBR-UKB)',
'UKB_angna_gbr':'Angina (GBR-UKB)',
'UKB_utfi_gbr':'Uterine fibroilds (GBR-UKB)',
'UKB_ctrt_gbr':'Cataract (GBR-UKB)'
}
d_imp_names={
'original':'No imputation',
#AJ
'impute2_1kg_afr2':'African',
'impute2_1kg_sas2':'South-Asian',
'impute2_1kg_eas2':'East-Asian',
'impute2_1kg_eur2':'European',
'impute2_ajkg14_t101':'AJ',
'impute2_1kg_ceu2':'USA',
'impute2_1kg_gbr2':'Britain',
'impute2_1kg_fin2':'Finland',
'impute2_1kg_tsi2':'Italy',
'impute2_1kg_ibs2':'Spain',
'impute2_1kg_eur-ajkg14-t101-merged': "European\n+AJ",
#BCAC
'impX': "impX",
'impX_new': "impX_new",
'impX_313': "impX_313",
'impX2': "impX2",
#UKB
'impute2_1kg_afr':'African',
'impute2_1kg_sas':'South-Asian',
'impute2_1kg_eur':'European', # (500)',
'impute2_1kg_gbr':'Britain',
'impute2_1kg_ibs':'Spain',
'impute2_1kg_eur-minus-gbr':'European-without-British (400)',
'impute2_1kg_eur100-minus-gbr':'European-without-British (100)',
'impute2_1kg_eur100':'European (100)',
'imputeX_new':'UKB',
#GAIN
'PGC2_noAJ':'PGC2_noAJ',
'D_scz_ripke_2011':'Ripke 2011',
'D_scz_ripke_2014':'Ripke 2014',
'D_scz_pardinas_2018':'Pardinas 2018'
}
d_target_names={
'bcac_onco_aj':'AJ',
'ukbb_afr':'African',
'ukbb_sas':'South-Asian',
'ukbb_eur':'European',
'ukbb_gbr':'Britian'
}
eur_pops=["ceu", "gbr", "fin", "tsi", "ibs"]
l_imps=["impute2_1kg_eur2", "impute2_1kg_eas2", "impute2_1kg_afr2", "impute2_ajkg14_t101"] +\
[f"impute2_1kg_{a}2" for a in eur_pops] + ["impute2_1kg_ceu-gbr2", "impute2_1kg_kdv2"] +\
[f"impute2_1kg_eur-minus-{a}2" for a in eur_pops] +\
[f"impute2_1kg_{a}-ajkg14-t101-merged" for a in eur_pops] +\
[f"impute2_1kg_eur-minus-{a}-ajkg14-t101-merged" for a in eur_pops] +["impute2_1kg_eur-ajkg14-t101-merged"] +\
["impX", "impX_new"] + \
["imputeX_new" , "impute2_1kg_eur", "impute2_1kg_sas", "impute2_1kg_afr", "impute2_1kg_gbr", "impute2_1kg_ibs", "impute2_1kg_eur-minus-gbr", "impute2_1kg_eur100", "impute2_1kg_eur100-minus-gbr"]
d_methods={
'pt':'P+T old (EUR LD)',
'pt3':'P+T (EUR LD)',
'pt2':'P+T (target set LD)',
'ls':'Lassosum',
'ld':'LDpred2'
}
d_metrics={
'all':'OR per 1SD',
'or.all':'OR per 1SD',
'99':'top 90% OR'
}
d_phenos_public_to_ukb={
"sysp": "ht",
"dias": "ht",
"t2di": "t2d",
"asth": "ast",
"hdlp": "chol",
"ldlp": "chol"
}
cs = (list(sns.color_palette("bright")) + list(sns.color_palette("pastel"))) * 10