1. Giovanni Marco Dall'Olio
  2. genotype_space

Commits

Giovanni Marco Dall'Olio  committed c108e17

CODING: removing av_closenes

Rscript src/plot_boxplotsBySNPAnnotation_onepageperproperty.R --plot_type pointrange --globa

  • Participants
  • Parent commits 6246f66
  • Branches default

Comments (0)

Files changed (5)

File params/default.yaml

View file
  • Ignore whitespace
     populations: 
         - EUR
         - ASN
-        - AMR
+#        - AMR
         - AFR
     flank_size:
         - 10000

File results/plots/whole_chromosomes/coding_noncoding/chr22_CODING_vs_NONCODING_pointrangeplots.pdf

  • Ignore whitespace
Binary file modified.

File results/tables/whole_chromosomes/coding_nocoding/coding_nocoding_chr22.csv

View file
  • Ignore whitespace
 "glob"	"both"	"n_components"	11597	2.45235836854359	1.22365046284078	0.0113627787452357	0.0222729619030845
 "glob"	"both"	"av_path_length"	11597	2.85246083469863	0.761826865995321	0.0070742997149567	0.0138668200424388
 "glob"	"both"	"av_degree"	11597	2.24957072518755	0.645224671587915	0.00599153549715515	0.0117444196407564
-"glob"	"both"	"av_closeness"	11597	0.193282331637492	0.0899561850965758	0.000835330234456719	0.00163738808135732
 "glob"	"coding"	"n_vertices"	1041	28.5417867435158	26.1185616335295	0.809513119527002	1.58846519733259
 "glob"	"coding"	"n_components"	1041	2.29779058597502	1.14425190473436	0.0354646990873002	0.0695905216050918
 "glob"	"coding"	"av_path_length"	1041	2.93574390009606	0.759493866488986	0.0235395906462879	0.046190505872137
 "glob"	"coding"	"av_degree"	1041	2.39591219980788	0.739600565062931	0.0229230219117208	0.0449806453362196
-"glob"	"coding"	"av_closeness"	1041	0.202086263208453	0.0886934652737898	0.00274894631499442	0.00539411338170245
 "glob"	"no_anno"	"n_vertices"	36439	26.4163670792283	23.044124942132	0.120719379978736	0.236613496604165
 "glob"	"no_anno"	"n_components"	36439	2.72153461950108	1.41092445813262	0.00739129501381905	0.0144871532471482
 "glob"	"no_anno"	"av_path_length"	36439	2.84812138642663	0.856041323226447	0.00448447394012925	0.00878969938042379
 "glob"	"no_anno"	"av_degree"	36439	2.23843414473504	0.696194596831809	0.00364709791693684	0.00714841801487217
-"glob"	"no_anno"	"av_closeness"	36439	0.174716822635089	0.0855898800375507	0.000448372731728106	0.000878823597792135
 "glob"	"noncoding"	"n_vertices"	114274	23.8965381451599	17.688484422579	0.0523259243153893	0.102558013396832
 "glob"	"noncoding"	"n_components"	114274	2.63778287274446	1.33006447590186	0.00393458543072179	0.00771172741990658
 "glob"	"noncoding"	"av_path_length"	114274	2.82446976740116	0.798286081710781	0.00236148310367999	0.0046284708574632
 "glob"	"noncoding"	"av_degree"	114274	2.19215862488405	0.634170851959937	0.00187599882555927	0.00367692907868162
-"glob"	"noncoding"	"av_closeness"	114274	0.181705926982516	0.0876597177001296	0.00025931423203394	0.000508251938802432
 "global_noAMR"	"both"	"n_vertices"	11597	22.7670087091489	16.1743701538395	0.15019467975761	0.294406892476885
 "global_noAMR"	"both"	"n_components"	11597	2.53410364749504	1.2342754314108	0.0114614418608087	0.0224663582424543
 "global_noAMR"	"both"	"av_path_length"	11597	2.77943122359231	0.761811561207837	0.00707415759519359	0.0138665414637443
 "global_noAMR"	"both"	"av_degree"	11597	2.18022072949901	0.633502428323422	0.00588268312414738	0.0115310506390869
-"global_noAMR"	"both"	"av_closeness"	11597	0.191185444511512	0.088762992258449	0.000824250284232568	0.00161566951103542
 "global_noAMR"	"coding"	"n_vertices"	1041	26.5552353506244	23.4717726127359	0.72747910605354	1.42749414911011
 "global_noAMR"	"coding"	"n_components"	1041	2.36503362151777	1.14911639290606	0.0356154679944868	0.0698863675353538
 "global_noAMR"	"coding"	"av_path_length"	1041	2.8684939481268	0.767729855039589	0.0237948551159602	0.0466913979718562
 "global_noAMR"	"coding"	"av_degree"	1041	2.32829548511047	0.719473591839614	0.022299210803389	0.0437565734695728
-"global_noAMR"	"coding"	"av_closeness"	1041	0.200450144092219	0.0873759441595207	0.00270811134704252	0.00531398506276467
 "global_noAMR"	"no_anno"	"n_vertices"	36439	24.5075056944483	20.6192816353431	0.108016550894263	0.21171558206077
 "global_noAMR"	"no_anno"	"n_components"	36439	2.78232113943851	1.39462726754509	0.00730592024918543	0.0143198162248302
 "global_noAMR"	"no_anno"	"av_path_length"	36439	2.76853019566948	0.84265779559832	0.00441436274427117	0.00865227939693812
 "global_noAMR"	"no_anno"	"av_degree"	36439	2.16563270671533	0.678125964642067	0.00355244324549729	0.00696289210525288
-"global_noAMR"	"no_anno"	"av_closeness"	36439	0.174228850956393	0.0850135585572316	0.000445353603340837	0.000872906018323666
 "global_noAMR"	"noncoding"	"n_vertices"	114274	22.2909323205629	15.9832072754466	0.0472813879489096	0.0926707990757638
 "global_noAMR"	"noncoding"	"n_components"	114274	2.70836760767979	1.33266719233414	0.00394228476435583	0.00772681799637166
 "global_noAMR"	"noncoding"	"av_path_length"	114274	2.74566954950382	0.786368655691636	0.00232622907529551	0.0045593734996496
 "global_noAMR"	"noncoding"	"av_degree"	114274	2.12158209128936	0.619236757280099	0.00183182091357612	0.00359034104515347
-"global_noAMR"	"noncoding"	"av_closeness"	114274	0.180352124717784	0.0864900032853748	0.000255853992791569	0.000501469922675275
 "AFR"	"both"	"n_vertices"	11597	15.7470897645943	9.80173062645083	0.0910185545717016	0.178411711070176
 "AFR"	"both"	"n_components"	11597	2.62835216004139	1.23847560279219	0.0115004445168352	0.0225428100234205
 "AFR"	"both"	"av_path_length"	11597	2.41251086487885	0.708218656490415	0.00657649560991977	0.0128910400756472
 "AFR"	"both"	"av_degree"	11597	1.89209425713547	0.571790323469399	0.00530962650818278	0.010407763064642
-"AFR"	"both"	"av_closeness"	11597	0.211140217297577	0.0991317538731246	0.00092053427027882	0.00180440235545382
 "AFR"	"coding"	"n_vertices"	1041	18.1594620557157	13.8821803769448	0.430261332934607	0.8442792792832
 "AFR"	"coding"	"n_components"	1041	2.44092219020173	1.11657818403155	0.0346069856998106	0.0679074755463577
 "AFR"	"coding"	"av_path_length"	1041	2.53558914505283	0.746478749689384	0.0231362028966375	0.0453989592178662
 "AFR"	"coding"	"av_degree"	1041	2.03920864553314	0.636415477349348	0.0197249253466918	0.0387051879424891
-"AFR"	"coding"	"av_closeness"	1041	0.218986071085495	0.102475771376752	0.00317611216601748	0.00623231855895215
 "AFR"	"no_anno"	"n_vertices"	36439	16.5144213617278	11.5809616195714	0.0606682401602556	0.118911515613051
 "AFR"	"no_anno"	"n_components"	36439	2.88685199923159	1.37424031369463	0.00719912077493062	0.0141104861483887
 "AFR"	"no_anno"	"av_path_length"	36439	2.37512314004226	0.758234184168969	0.00397209964888743	0.00778543086411629
 "AFR"	"no_anno"	"av_degree"	36439	1.85324685913444	0.589966333286294	0.00309060856689056	0.00605768269995734
-"AFR"	"no_anno"	"av_closeness"	36439	0.194340097148659	0.0988247065674217	0.000517704939257108	0.00101471674149129
 "AFR"	"noncoding"	"n_vertices"	114274	15.5895479286627	9.71449575051287	0.0287373387826629	0.056324745609794
 "AFR"	"noncoding"	"n_components"	114274	2.81424471008278	1.34461366104328	0.00397762470657907	0.00779608374399855
 "AFR"	"noncoding"	"av_path_length"	114274	2.36563507096977	0.72166453067408	0.00213482188247574	0.00418421832174696
 "AFR"	"noncoding"	"av_degree"	114274	1.83560054868124	0.569019516364684	0.00168326869820862	0.00329918096928055
-"AFR"	"noncoding"	"av_closeness"	114274	0.199940837810876	0.0984157095845462	0.000291132515830063	0.000570615289637064
 "ASN"	"both"	"n_vertices"	11597	9.46330947658877	7.71222468809929	0.0716154697976193	0.140378393897943
 "ASN"	"both"	"n_components"	11597	2.43606105027162	1.16283126444329	0.0107980136298376	0.0211659270675494
 "ASN"	"both"	"av_path_length"	11597	1.7689450375097	0.73406500965282	0.00681650401205269	0.0133614970049761
 "ASN"	"both"	"av_degree"	11597	1.49280324221782	0.697538017516733	0.00647731554077327	0.0126966304201242
-"ASN"	"both"	"av_closeness"	11597	0.29673023195654	0.173899881158211	0.0016148286895885	0.00316533646299266
 "ASN"	"coding"	"n_vertices"	1041	11.3131604226705	10.7099840956487	0.331942959072572	0.651354283540785
 "ASN"	"coding"	"n_components"	1041	2.46013448607109	1.16379501118107	0.0360704139534901	0.0707790841635489
 "ASN"	"coding"	"av_path_length"	1041	1.87223515850144	0.776478234509208	0.0240660005203138	0.0472234523979586
 "ASN"	"coding"	"av_degree"	1041	1.60616685878963	0.756387713898859	0.0234433192164809	0.0460015974875081
-"ASN"	"coding"	"av_closeness"	1041	0.290287992315082	0.195095828918627	0.00604675844292586	0.0118652374020534
 "ASN"	"no_anno"	"n_vertices"	36439	10.5050906995252	9.90759879613285	0.0519021306624009	0.101729685982484
 "ASN"	"no_anno"	"n_components"	36439	2.59002716869288	1.22617159712	0.006423445252253	0.0125901395587745
 "ASN"	"no_anno"	"av_path_length"	36439	1.81300945141195	0.803769338538927	0.00421064095243361	0.00825297875846863
 "ASN"	"no_anno"	"av_degree"	36439	1.50117111611186	0.730134260909667	0.00382489487014962	0.00749690521545796
-"ASN"	"no_anno"	"av_closeness"	36439	0.276684538543868	0.159114659955006	0.000833541006374989	0.00163376462102507
 "ASN"	"noncoding"	"n_vertices"	114274	9.23842693876122	7.56620675797359	0.022382288539483	0.0438689440830182
 "ASN"	"noncoding"	"n_components"	114274	2.57138981745629	1.21750186793768	0.00360160368031485	0.0070590882689324
 "ASN"	"noncoding"	"av_path_length"	114274	1.73074599033901	0.728209029650417	0.00215418176373729	0.00422216339367375
 "ASN"	"noncoding"	"av_degree"	114274	1.43823722019007	0.690356953459652	0.00204220807358835	0.00400269666920328
-"ASN"	"noncoding"	"av_closeness"	114274	0.286573210004025	0.163714023734511	0.000484297433892354	0.00094921558219996
 "EUR"	"both"	"n_vertices"	11597	12.1903940674312	9.40162849233901	0.0873032190543556	0.171129027116683
 "EUR"	"both"	"n_components"	11597	2.70018108131413	1.21131158335091	0.0112482003081206	0.0220483688504521
 "EUR"	"both"	"av_path_length"	11597	2.01677689057515	0.71415081681717	0.00663158145945044	0.0129990176272219
 "EUR"	"both"	"av_degree"	11597	1.65303582823144	0.674323915365625	0.00626175013666272	0.012274085887574
-"EUR"	"both"	"av_closeness"	11597	0.236424359748211	0.121614194433534	0.00112930548844824	0.00221362913818051
 "EUR"	"coding"	"n_vertices"	1041	14.2305475504323	13.8575399008535	0.429497631282611	0.842780707529293
 "EUR"	"coding"	"n_components"	1041	2.6628242074928	1.33324766036733	0.0413223931619772	0.0810847678993118
 "EUR"	"coding"	"av_path_length"	1041	2.11870019212296	0.784398567742756	0.0243114816365232	0.0477051471355668
 "EUR"	"coding"	"av_degree"	1041	1.74438049951969	0.750302018455376	0.0232547004720007	0.045631480803857
-"EUR"	"coding"	"av_closeness"	1041	0.234599039385207	0.115850535252571	0.00359064674031624	0.00704573804343117
 "EUR"	"no_anno"	"n_vertices"	36439	13.3545651636982	12.2798959887006	0.064329690699123	0.126088065184439
 "EUR"	"no_anno"	"n_components"	36439	2.81818930267022	1.30069946318662	0.00681386831259021	0.0133553801148273
 "EUR"	"no_anno"	"av_path_length"	36439	2.0485929471171	0.806875238161013	0.00422691157575283	0.00828486965350277
 "EUR"	"no_anno"	"av_degree"	36439	1.65693644172453	0.711204439879895	0.00372572875889301	0.00730253675255502
-"EUR"	"no_anno"	"av_closeness"	36439	0.227691621614205	0.123302815837869	0.000645936416112949	0.00126605416650889
 "EUR"	"noncoding"	"n_vertices"	114274	11.8053187951765	9.23751617132552	0.0273263418445259	0.0535592131365953
 "EUR"	"noncoding"	"n_components"	114274	2.80650891716401	1.28196006918897	0.00379228338353891	0.00743281757832571
 "EUR"	"noncoding"	"av_path_length"	114274	1.98409159651364	0.720939486624485	0.00213267706332911	0.00418001450893998
 "EUR"	"noncoding"	"av_degree"	114274	1.598006760943	0.653081742131149	0.00193194086017318	0.00378657461309775
-"EUR"	"noncoding"	"av_closeness"	114274	0.23236958975795	0.12362280342032	0.000365699926624059	0.00071676627722561

File results/tables/whole_chromosomes/coding_nocoding/wilcoxon_tests.csv

View file
  • Ignore whitespace
 "av_degree" 2.03920864553314 1.83560054868124 0.636415477349348 0.569019516364684 0.0197249253466918 0.00168326869820862 1041 114274 1.8060131606612 "AFR" 69679036.5 1.37469975904735e-21 "Wilcoxon rank sum test with continuity correction" "value by codingStatus" "both"
 "av_degree" 1.60616685878963 1.43823722019007 0.756387713898859 0.690356953459652 0.0234433192164809 0.00204220807358835 1041 114274 1.40307224136535 "ASN" 66928430.5 3.05776399181482e-12 "Wilcoxon rank sum test with continuity correction" "value by codingStatus" "both"
 "av_degree" 1.74438049951969 1.598006760943 0.750302018455376 0.653081742131149 0.0232547004720007 0.00193194086017318 1041 114274 1.563124710235 "EUR" 65007181.5 2.30282120304574e-07 "Wilcoxon rank sum test with continuity correction" "value by codingStatus" "both"
-"av_closeness" 0.202086263208453 0.181705926982516 0.0886934652737898 0.0876597177001296 0.00274894631499442 0.00025931423203394 1041 114274 0.177582507510024 "glob" 67796797.5 7.31091111365226e-15 "Wilcoxon rank sum test with continuity correction" "value by codingStatus" "both"
-"av_closeness" 0.200450144092219 0.180352124717784 0.0873759441595207 0.0864900032853748 0.00270811134704252 0.000255853992791569 1041 114274 0.17628995769722 "global_noAMR" 67899997 3.39366499223886e-15 "Wilcoxon rank sum test with continuity correction" "value by codingStatus" "both"
-"av_closeness" 0.218986071085495 0.199940837810876 0.102475771376752 0.0984157095845462 0.00317611216601748 0.000291132515830063 1041 114274 0.195176669561849 "AFR" 66461519.5 6.57201337388358e-11 "Wilcoxon rank sum test with continuity correction" "value by codingStatus" "both"
-"av_closeness" 0.290287992315082 0.286573210004025 0.195095828918627 0.163714023734511 0.00604675844292586 0.000484297433892354 1041 114274 0.277503072339637 "ASN" 57686532 0.0935134725961373 "Wilcoxon rank sum test with continuity correction" "value by codingStatus" "both"
-"av_closeness" 0.234599039385207 0.23236958975795 0.115850535252571 0.12362280342032 0.00359064674031624 0.000365699926624059 1041 114274 0.226983619647476 "EUR" 62004800.5 0.0181865300905763 "Wilcoxon rank sum test with continuity correction" "value by codingStatus" "both"

File src/plot_boxplotsBySNPAnnotation_onepageperproperty.R

View file
  • Ignore whitespace
                                                     "av_degree",
 #                                                    "av_w_degree", 
 #                                                    "av_w_degree_inv",
-                                                    "av_closeness",
+#                                                    "av_closeness",
 #                                                    "max_closeness", 
 #                                                    "max_betweenness"
 #                                                    "av_betweenness",
 results_and_annotations.long = melt.data.frame(
                     data = results_and_annotations, 
                     variable_name="network_property",
-                    measure.vars = c("n_vertices", "n_components", "av_path_length", "av_degree", "av_closeness")
+#                    measure.vars = c("n_vertices", "n_components", "av_path_length", "av_degree", "av_closeness")
+                    measure.vars = c("n_vertices", "n_components", "av_path_length", "av_degree")
                     )
 #                    id.vars=c("continent", "chromosome", "central_snp", 
 #                        "n_datapoints",