背景：酵母会在一定的时期发生diauxic shift，有一些基因的表达上升，有一些基因表达被抑制，通过聚类算法，将基因表达的变化模式聚成6类。
ORF Name R1.Ratio R2.Ratio R3.Ratio R4.Ratio R5.Ratio R6.Ratio R7.Ratio 1 YDR025W RPS18A 0.136061549576028 -0.111031312388744 -0.189033824390017 -0.782408564927373 -0.75702324650746 -0.855989697308481 -2.30451104180995 2 YDR031w -0.286881147788162 -0.0840642647884746 0.184424571137428 0.136061549576028 0.535331732996556 2.32192809488736 1.25153876699596 3 YDR060w -0.0426443374084937 -0.0976107966264223 -0.0143552929770701 -0.799087306074004 -0.839959587489532 -2.24792751344359 -2.38681094647222 4 YDR064W YS15 -0.0565835283663676 -0.124328135002202 -0.070389327891398 -0.545968369105293 -0.55581615506164 -2.10433665981474 -2.36737106564853 5 YDR070c 0.0144995696951152 0.0740005814437768 0.0588936890535686 0.0144995696951152 0.251538766995964 2.39592867633114 1.68965987938785 6 YDR144C MKC7 0.136061549576028 -0.0426443374084937 -0.298658315564515 -0.871843648509318 -1.14404636961671 -2.42223300068305 -2.72246602447109 7 YDR171W HSP42 0.0740005814437768 0.136061549576028 0.434402824145775 0.836501267717121 0.943416471633632 3.64385618977472 3.32192809488736 8 YDR178W SDH4 -0.189033824390017 -0.028569152196771 0.599462070416271 0.888968687611256 0.836501267717121 2.55639334852439 2.64385618977472 9 YDR258C HSP78 -0.250961573533219 0.136061549576028 -0.22650852980868 0.862496476250065 0.62148837674627 2.55639334852439 2.39592867633114 10 YBL015W ACH1 -0.111031312388744 0.0588936890535686 0.0144995696951152 0.104697378666693 0.3040061868901 2.73696559416621 3.32192809488736 11 YDR272W GLO2 -0.028569152196771 -0.0976107966264223 0.358453970912476 0.434402824145775 0.377069649079823 2.55639334852439 1.25153876699596 12 YDR272W 0.0740005814437768 0.3040061868901 0.494109070270043 0.473931188332412 0.377069649079823 2.32192809488736 1.47393118833241 13 YDR342C HXT7 0.184424571137428 0.434402824145775 0.943416471633632 1.51457317282976 1.64385618977472 2.32192809488736 1.59946207041627 14 YDR343C HXT6 0.15200309344505 0.761213140412884 1.28630418515664 1.94341647163363 1.51457317282976 2.18442457113743 2.64385618977472 15 YBL027W RPL19A 0.0439433475875972 0.0144995696951152 0.395928676331139 -0.16349873228288 -0.27500704749987 -1.11103131238874 -2.44360665147561 16 YDR382W RPLA4 0.104697378666693 0.15200309344505 0.104697378666693 0.0588936890535686 0.0439433475875972 -0.604071323668861 -2.36457243229586 17 YDR398W -0.0143552929770701 -0.0840642647884746 -0.124328135002202 -1.03562390973072 -1.1243281350022 -2.02147972741045 -2.799087306074 18 YDR417C 0.321928094887362 0.120294233717712 0.0892673380970873 -0.344828496997441 -0.250961573533219 -1.64616265715789 -2.54596836910529 19 YDR418W RPL15A 0.200912693925996 0.168122758808327 0.286304185156641 -0.20163386116965 -0.20163386116965 -1.75274859140713 -2.99638874644762 20 YDR516C -0.137503523749935 0.2688167584278 0.415037499278844 0.785875194647153 0.713118852211838 2.32192809488736 1.02914634565952 21 YBL043W -0.516015147003665 0.0740005814437768 0 -0.214124805352847 -0.53605290024021 1.94341647163363 2.32192809488736 22 YDR529C QCR7 0.168122758808327 0.0291463456595165 0.377069649079823 0.862496476250065 0.810966175609983 2.18442457113743 2.55639334852439 23 YDR533C -0.070389327891398 0.0588936890535686 0.577766999316952 0.415037499278844 0.0144995696951152 2.73696559416621 2.39592867633114 24 YBL045C COR1 0.0740005814437768 0 0.68965987938785 0.514573172829758 0.15200309344505 1.68965987938785 2.47393118833241 25 YEL011w GLC3 -0.286881147788162 0.120294233717712 0.494109070270043 0.836501267717121 0.494109070270043 2.64385618977472 2.83650126771712 26 YEL012w UBC8 -0.0840642647884746 -0.298658315564515 0.0740005814437768 0.0740005814437768 -0.356143810225275 1.32192809488736 2.32192809488736 27 YEL024w RIP1 0.0892673380970873 0.2688167584278 0.556393348524385 0.888968687611256 0.943416471633632 1.94341647163363 2.32192809488736 28 YBL048W -0.250961573533219 0.104697378666693 -0.150559676575381 -0.22650852980868 -0.356143810225275 2.55639334852439 2.18442457113743 29 YBL049W -0.584962500721156 0.168122758808327 0.184424571137428 -0.150559676575381 -0.823749360308273 2.47393118833241 2.64385618977472 30 YEL054c RPL15A 0.200912693925996 0.0892673380970873 0.321928094887362 -0.321928094887362 -0.475084882948783 -1.64154602908752 -2.46466826700344 31 YER024w -0.27500704749987 -0.150559676575381 0.168122758808327 -0.356143810225275 -0.495695162624069 1.12029423371771 3.18442457113743 32 YER053c -0.189033824390017 0.358453970912476 1.02914634565952 1.51457317282976 1.64385618977472 2.18442457113743 2.64385618977472 33 YER065c ICL1 0.120294233717712 0.168122758808327 0.535331732996556 0.0892673380970873 -0.150559676575381 0.535331732996556 3.64385618977472 34 YER067w -0.070389327891398 0.15200309344505 0.761213140412884 1.02914634565952 0.377069649079823 3.18442457113743 2.55639334852439 35 YBL064C 0.377069649079823 0.0439433475875972 0.736965594166206 0.888968687611256 0.761213140412884 3.47393118833241 2.83650126771712 36 YER131w RPS26B 0.358453970912476 0.136061549576028 0.473931188332412 0.0439433475875972 -0.0143552929770701 -1.36737106564853 -2.48800077083407 37 YER150w -0.0143552929770701 0.184424571137428 1.15200309344505 1.51457317282976 1.59946207041627 3.47393118833241 3.32192809488736 38 YAL003W TEF5 0.234465253637023 0 -0.0426443374084937 -0.641546029087524 -0.933572638261024 -1.53605290024021 -2.33342373372519 39 YFL014W HSP12 -0.150559676575381 0.377069649079823 0.62148837674627 1.59946207041627 2.25153876699596 3.64385618977472 3.47393118833241 40 YFL054C -0.678071905112638 -0.36737106564853 -0.137503523749935 -0.27500704749987 -0.176322772640463 2.47393118833241 0.971430847803229 41 YBL078C -0.400537929583729 -0.16349873228288 0.136061549576028 0.234465253637023 0.321928094887362 2.32192809488736 2.12029423371771 42 YFR015C GSY1 -0.22650852980868 0.0439433475875972 0.415037499278844 1.55639334852439 1.02914634565952 2.73696559416621 2.73696559416621 43 YFR033C QCR6 0.0588936890535686 -0.111031312388744 0.0291463456595165 0.321928094887362 0.62148837674627 2.39592867633114 1.88896868761126 44 YFR053C HXK1 0.184424571137428 0.321928094887362 0.395928676331139 1 1.47393118833241 2.55639334852439 0.377069649079823 45 YGL031C RPL30A 0.0291463456595165 0 0.0439433475875972 -0.137503523749935 0 -0.669026765509631 -2.31324585178756 46 YGL037C 0.200912693925996 0.377069649079823 0.286304185156641 1.15200309344505 1.47393118833241 2.83650126771712 1.83650126771712 47 YGL076C RPL6A 0.0740005814437768 -0.411426245726465 -0.028569152196771 -0.790772037862 -0.839959587489532 -1.6959938131099 -2.78868571061353 48 YGL078C -0.0143552929770701 -0.250961573533219 0.321928094887362 -0.831877241191673 -0.831877241191673 -1.46988597627446 -2.4594316186373 49 YGL102C 0.0291463456595165 -0.0976107966264223 0.168122758808327 0 -0.028569152196771 -1.39506279951758 -2.55090066464752 50 YBL100C 0.136061549576028 0.217591435072627 0.415037499278844 0.577766999316952 0.888968687611256 1.28630418515664 2.39592867633114 51 YGL191W COX13 0.0439433475875972 -0.070389327891398 0.0291463456595165 0.0291463456595165 0.888968687611256 2.47393118833241 2.32192809488736 52 YBL108W 0.0439433475875972 0.0892673380970873 0.395928676331139 0.217591435072627 0.971430847803229 0.888968687611256 2.39592867633114 53 YGL259W -0.137503523749935 -0.070389327891398 0.473931188332412 0.643856189774725 0.377069649079823 1.68965987938785 2.83650126771712 54 YGR008C STF2 -0.0565835283663676 0.0439433475875972 0.494109070270043 1.12029423371771 1.05889368905357 2.73696559416621 2.05889368905357 55 YGR043C -0.432959407276106 -0.7311832415722 -0.0565835283663676 -0.111031312388744 -0.16349873228288 3.47393118833241 2.64385618977472 56 YGR067C 0.0439433475875972 -0.0976107966264223 0.168122758808327 -0.344828496997441 -0.37851162325373 0.599462070416271 2.39592867633114 57 YGR088W CTT1 0.15200309344505 0.0588936890535686 0.217591435072627 0.736965594166206 0.971430847803229 3.64385618977472 2.94341647163363 58 YGR103W 0.15200309344505 -0.0565835283663676 0.321928094887362 -0.903038270112912 -1.10433665981474 -1.64154602908752 -2.56315813040281 59 YGR148C RPL30B 0.200912693925996 0.104697378666693 0.0588936890535686 -0.286881147788162 -0.27500704749987 -1.81966818349646 -2.61588707391606 60 YGR160W 0.321928094887362 0.104697378666693 -0.250961573533219 -1.48542682717024 -1.48026512205446 -2.50842865253186 -3.21412480535285 61 YGR214W NAB1A 0.2688167584278 0.15200309344505 0.454031630894707 -0.36737106564853 -0.286881147788162 -1.66902676550963 -2.45154083301783 62 YGR236C -0.124328135002202 -0.189033824390017 -0.298658315564515 -0.495695162624069 -0.641546029087524 3.47393118833241 2.83650126771712 63 YGR243W -0.344828496997441 -0.27500704749987 -0.37851162325373 -0.20163386116965 -0.411426245726465 3.18442457113743 2.47393118833241 64 YGR244C 0.0439433475875972 0.2688167584278 0.761213140412884 0.943416471633632 1.47393118833241 2.39592867633114 2.05889368905357 65 YGR248W -0.298658315564515 -0.389566811762726 0.434402824145775 0.666576266274808 1.39592867633114 4.05889368905357 2.47393118833241 66 YGR264C MES1 0.415037499278844 0.434402824145775 0 -0.722466024471091 -0.815575428862572 -2.55581615506164 -2.08746284125034 67 YHL015W URP2 0.168122758808327 0.321928094887362 0.104697378666693 -0.0840642647884746 -0.176322772640463 -1.80322703643493 -2.85598969730848 68 YHL021C -0.443606651475615 0.120294233717712 0.643856189774725 1 0.785875194647153 2.94341647163363 2.47393118833241 69 YHL033C RPL4A 0.340075441597622 0.217591435072627 0.184424571137428 -0.176322772640463 -0.505890929729957 -1.56559717585423 -2.51349074558812 70 YBR032W 0 0.15200309344505 0.395928676331139 0.136061549576028 -0.0565835283663676 -1.09761079662642 -2.39780296186249 71 YAL012W CYS3 0.104697378666693 -0.0143552929770701 0.556393348524385 -0.575312330687437 -0.7311832415722 -1.25096157353322 -2.52105073690096 72 YHR051W COX6 0.200912693925996 0.0291463456595165 0.200912693925996 0.415037499278844 0.761213140412884 2.18442457113743 2.47393118833241 73 YHR087W -0.411426245726465 -0.422233000683048 -0.111031312388744 0.104697378666693 0.888968687611256 2.94341647163363 0.971430847803229 74 YHR089C GAR1 -0.20163386116965 -0.333423733725192 -0.137503523749935 -0.713695814843359 -0.464668267003444 -2.16992500144231 -2.63459326844576 75 YHR096C HXT5 -0.124328135002202 -0.0426443374084937 0.666576266274808 0.321928094887362 -0.321928094887362 1.43440282414577 3.05889368905357 76 YHR104W 0.286304185156641 0.2688167584278 0.556393348524385 0.643856189774725 0.577766999316952 2.39592867633114 1.25153876699596 77 YHR128W FUR1 0.234465253637023 0.0740005814437768 0.234465253637023 -0.713695814843359 -0.669026765509631 -1.87184364850932 -2.34482849699744 78 YBR048W RPS18B 0.120294233717712 0.200912693925996 0.0740005814437768 -0.411426245726465 -0.992768430768924 -1.51601514700366 -2.48026512205446 79 YBR051W -0.150559676575381 0.200912693925996 0 -0.400537929583729 -0.941106310946431 0.321928094887362 2.64385618977472 80 YIL018W RPL5A 0.3040061868901 0.0892673380970873 0.2688167584278 -0.214124805352847 -0.176322772640463 -1.37295209791183 -2.33913738491959 81 YIL053W GPP1 0.2688167584278 -0.0143552929770701 -0.22650852980868 -0.941106310946431 -1.23878685958712 -2.32768736417605 -2.95791459863299 82 YIL069C RP50B -0.0565835283663676 -0.495695162624069 -0.411426245726465 -0.641546029087524 -0.704871964456353 -1.9560566524124 -2.44625622988956 83 YIL111W COX5B -0.0840642647884746 0.136061549576028 0.666576266274808 1.08926733809709 1.47393118833241 2.94341647163363 1.08926733809709 84 YIL113W -0.333423733725192 -0.356143810225275 -0.298658315564515 0.0439433475875972 -0.0840642647884746 2.39592867633114 1.28630418515664 85 YIL125W KGD1 0.234465253637023 0.556393348524385 0.377069649079823 0.120294233717712 0.494109070270043 1.43440282414577 2.94341647163363 86 YIL136W OM45 -0.978195629681652 -0.263034405833794 0.217591435072627 -0.250961573533219 1.32192809488736 3.47393118833241 1.78587519464715 87 YIL162W SUC2 0.0588936890535686 0.377069649079823 0.785875194647153 0.377069649079823 0.0439433475875972 2.73696559416621 1.35845397091248 88 YBR072W HSP26 -0.0143552929770701 0.395928676331139 0.358453970912476 1 1.43440282414577 3.47393118833241 2.83650126771712 89 YJL045W -0.333423733725192 -0.189033824390017 0.415037499278844 -0.0840642647884746 -0.485426827170242 1 2.32192809488736 90 YJL089W SIP4 -0.632268215499513 -0.344828496997441 -0.238786859587116 -0.189033824390017 -0.250961573533219 1.12029423371771 3.05889368905357 91 YJL109C -0.0840642647884746 0.0291463456595165 -0.111031312388744 -1.17632277264046 -1.08406426478847 -3.23419472295381 -1.98913900736823 92 YJL136C RPS25B 0.184424571137428 -0.0840642647884746 0.340075441597622 -0.070389327891398 -0.475084882948783 -1.46466826700344 -2.35895882583233 93 YJL148W 0.0892673380970873 -0.20163386116965 0.168122758808327 -0.75702324650746 -0.678071905112638 -1.29278174922785 -2.41413553298445 94 YJL177W RPL20B 0.340075441597622 0.136061549576028 0.136061549576028 -0.422233000683048 -0.622930350920177 -1.93357263826102 -2.38956681176273 95 YJL190C RPS24A 0.120294233717712 -0.189033824390017 0.340075441597622 0.0892673380970873 -0.0840642647884746 -1.4594316186373 -2.32481060342048 96 YJR095W ACR1 -0.613531652917927 -0.464668267003444 1.08926733809709 -0.124328135002202 -0.176322772640463 1.35845397091248 3.64385618977472 97 YJR096W -0.411426245726465 0.217591435072627 0.200912693925996 0.340075441597622 0.943416471633632 2.83650126771712 1.43440282414577 98 YJR123W RPS5 0.104697378666693 0.0892673380970873 0.168122758808327 -0.37851162325373 -0.411426245726465 -1.85598969730848 -2.48026512205446 99 YJR145C RPS7B 0.0740005814437768 0.0588936890535686 -0.250961573533219 -0.565597175854225 -0.422233000683048 -1.53605290024021 -2.61353165291793 100 YKL009W -0.150559676575381 -0.443606651475615 -0.0976107966264223 -0.790772037862 -1.07724299893246 -2.03913839390696 -2.52105073690096 101 YKL026C -0.189033824390017 -0.150559676575381 0.0291463456595165 0.2688167584278 0.535331732996556 3.64385618977472 2.73696559416621 102 YBR116C -0.16349873228288 0.184424571137428 0.0439433475875972 -0.22650852980868 -0.422233000683048 1.78587519464715 2.39592867633114 103 YBR117C TKL2 0.358453970912476 0.643856189774725 0.68965987938785 0.0439433475875972 -0.27500704749987 1.64385618977472 2.47393118833241 104 YKL081W TEF4 0.0740005814437768 -0.150559676575381 -0.0143552929770701 -0.925999418556223 -0.722466024471091 -2.15704371014558 -2.43562859405209 105 YKL085W MDH1 0.0439433475875972 0.0144995696951152 0.286304185156641 0.915935735211525 1.35845397091248 2.83650126771712 2.55639334852439 106 YKL103C LAP4 -0.070389327891398 0.377069649079823 0.473931188332412 0.888968687611256 1.32192809488736 2.39592867633114 1.68965987938785 107 YKL109W HAP4 0.234465253637023 0.577766999316952 1.02914634565952 0.666576266274808 0.62148837674627 2.55639334852439 3.18442457113743 108 YKL141W SDH3 0.358453970912476 0.168122758808327 0.643856189774725 0.785875194647153 1.15200309344505 1.94341647163363 2.64385618977472 109 YKL142W MRP8 -0.070389327891398 0.217591435072627 0.234465253637023 0.494109070270043 1.02914634565952 2.47393118833241 1.15200309344505 110 YKL151C -0.124328135002202 0.234465253637023 0.577766999316952 0.62148837674627 0.251538766995964 2.55639334852439 1.78587519464715 111 YKL187C 0.0439433475875972 0.0740005814437768 0.200912693925996 -0.16349873228288 -0.400537929583729 2.12029423371771 3.32192809488736 112 YKL193C SDS22 -0.0565835283663676 -0.124328135002202 -0.263034405833794 0.184424571137428 0.514573172829758 2.47393118833241 1.43440282414577 113 YKL217W JEN1 -0.485426827170242 -0.070389327891398 0.0439433475875972 -0.333423733725192 0.120294233717712 3.47393118833241 3.83650126771712 114 YKR059W TIF1 0.217591435072627 0.0740005814437768 0.473931188332412 -0.27500704749987 -0.505890929729957 -1.44360665147561 -2.3305584000308 115 YBR139W 0.120294233717712 0.514573172829758 0.434402824145775 1.08926733809709 0.888968687611256 2 2.39592867633114 116 YKR097W PCK1 -0.124328135002202 -0.176322772640463 0.434402824145775 -0.0840642647884746 -0.250961573533219 0.415037499278844 3.83650126771712 117 YLL026w HSP104 0.0144995696951152 0.0144995696951152 -0.189033824390017 0.836501267717121 1 2.39592867633114 2.64385618977472 118 YBR147W -0.0976107966264223 0.340075441597622 -0.028569152196771 0.0740005814437768 0.251538766995964 3.05889368905357 2.47393118833241 119 YLL041c SDH2 -0.0565835283663676 -0.0976107966264223 0.494109070270043 1.05889368905357 1.43440282414577 2.55639334852439 2.64385618977472 120 YLL044W 0.286304185156641 0.0144995696951152 -0.16349873228288 -0.443606651475615 -0.713695814843359 -2.09085343045111 -2.53356334821451 121 YLL045c RPL4B 0.184424571137428 -0.176322772640463 -0.0840642647884746 -0.111031312388744 -0.111031312388744 -1.94860084749336 -3.06522762277562 122 YLR048w 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0.2688167584278 2.55639334852439 1.51457317282976 215 YPL131W RPL1 0.0588936890535686 0.0892673380970873 0.15200309344505 -0.823749360308273 -0.22650852980868 -1.65535182861255 -2.53356334821451 216 YPL220W SSM1A 0.0439433475875972 -0.0143552929770701 0.395928676331139 -0.356143810225275 -0.0426443374084937 -1.60407132366886 -2.76765479823735 217 YPL226W 0.0439433475875972 0.0740005814437768 -0.0976107966264223 -0.839959587489532 -1.17632277264046 -1.88752527074159 -2.45680614923047 218 YPR137W 0.0740005814437768 -0.176322772640463 -0.20163386116965 -0.887525270741588 -0.918386234446348 -1.6959938131099 -2.95419631038688 219 YPR149W NCE2 0.15200309344505 0.120294233717712 0.395928676331139 0.810966175609983 0.915935735211525 2.05889368905357 2.32192809488736 220 YPR184W GDE -0.238786859587116 -0.0840642647884746 -0.27500704749987 0.200912693925996 0.556393348524385 1.51457317282976 2.64385618977472 221 YDL215C GDH2 -0.070389327891398 0.0439433475875972 0.0439433475875972 -0.464668267003444 -0.0565835283663676 0.3040061868901 2.32192809488736 222 YDR258C HSP78 -0.214124805352847 -0.0840642647884746 -0.263034405833794 0.666576266274808 0.915935735211525 2.18442457113743 2.47393118833241 223 YCR010C -0.485426827170242 -0.36737106564853 0.234465253637023 -0.36737106564853 -0.422233000683048 0.535331732996556 2.64385618977472 224 YCR021c HSP30 -0.790772037862 0.0144995696951152 1.88896868761126 1.55639334852439 0.862496476250065 3.64385618977472 3.32192809488736 225 YDL083C 0.104697378666693 -0.286881147788162 -0.189033824390017 -0.650764559116902 -0.799087306074004 -1.17632277264046 -2.40053792958373 226 YDL085w -0.111031312388744 1 0.0588936890535686 -0.124328135002202 -0.27500704749987 2.05889368905357 2.83650126771712 227 YDL136w -0.070389327891398 -0.0143552929770701 -0.0426443374084937 -0.36737106564853 -0.214124805352847 -1.55090066464752 -2.56315813040281 228 YDL199c -0.0426443374084937 0.494109070270043 0.415037499278844 0.184424571137428 -0.344828496997441 1.73696559416621 2.32192809488736 229 YDL204w -0.36737106564853 0.915935735211525 -0.505890929729957 0.2688167584278 0.0892673380970873 4.05889368905357 3.05889368905357 230 YDL208W NHP2 0.0439433475875972 -0.150559676575381 0.0439433475875972 -0.575312330687437 -0.485426827170242 -2.14404636961671 -2.63691458035588
算法1 Lloyd Algorithm k_mean clustering * Centers to Clusters: After centers have been selected, assign each data point to the cluster corresponding to its nearest center; ties are broken arbitrarily. * Clusters to Centers: After data points have been assigned to clusters, assign each cluster’s center of gravity to be the cluster’s new center.
程序利用Lloyd算法，随机选取起始的Centers，并进行2000次迭代，选取最佳结果。
python源码
1 from os.path import dirname 2 import numpy as np 3 import math 4 import random 5 import matplotlib.pyplot as plt 6 7 def square_EuclideanDistance(vId,wId,Centers): 8 s = 0 9 for i in range(m): 10 s += (points[vId][i]-Centers[wId][i])**2 11 return s 12 13 def Centers_to_Clusters(Centers): 14 global Cluster 15 Cluster = [[] for i in range(k)] 16 Distortion = 0 17 for i in range(len(points)): 18 minVal = INF 19 minId = -1 20 for c in range(k): 21 tmp = square_EuclideanDistance(i, c,Centers) 22 if tmp < minVal: 23 minVal = tmp 24 minId = c 25 Cluster[minId].append(i) 26 Distortion += minVal 27 return Distortion/points_num 28 29 def Clusters_to_Centers(): 30 #print(Cluster) 31 Centers = [] 32 for i in range(k): 33 coordinate = [0 for i in range(m)] 34 for pId in Cluster[i]: 35 for j in range(m): 36 coordinate[j] += points[pId][j] 37 if len(Cluster[i])==0: 38 coordinate = [0.5 for item in coordinate] 39 else: 40 coordinate = [item/len(Cluster[i]) for item in coordinate] 41 Centers.append(coordinate) 42 #print(Centers) 43 return Centers 44 45 def LloydClustering(): 46 global Cluster 47 Centers = random.sample(points,k) 48 minDistortion = INF 49 Distortion = Centers_to_Clusters(Centers) 50 i = 0 51 while(Distortion < minDistortion): 52 i += 1 53 #print('*%d iteration*...'%i) 54 minDistortion = Distortion 55 Centers = Clusters_to_Centers() 56 Distortion = Centers_to_Clusters(Centers) 57 return [Centers,Distortion] 58 59 if __name__ == '__main__': 60 INF = 999999 61 dataset = open(dirname(__file__)+'230genes_log_expression.txt').read().strip().split(' ') 62 dataset = [line.split() for line in dataset] 63 name = [item[1] for item in dataset[1:]] 64 k = 6 # 分成 6 类 65 m = 7 # 数据的维度 66 #print(m) 67 # print(m,k) 68 points = [] 69 for line in dataset[1:]: 70 if(len(line)==10): 71 points.append(list(map(float,line[3:]))) 72 elif(len(line)==9): 73 points.append(list(map(float,line[2:]))) 74 75 points_num = len(points) 76 out_Distortion = INF 77 out_Centers = [] 78 out_i = -1 79 for i in range(2000): 80 [Centers,Distortion] = LloydClustering() #Distortion 精确度 81 if Distortion<out_Distortion: 82 out_Distortion = Distortion 83 out_Centers = Centers 84 out_i = i 85 86 print(out_i,out_Distortion) 87 88 for c in out_Centers: 89 for i in range(len(c)): 90 if i != 0: 91 print(' ',end='') 92 print('%.3f'%c[i],end='') 93 print('') 94 95 x = [i for i in range(1,8)] 96 97 plt.rcParams['figure.figsize']=(12,8) 98 for i in range(len(points)): 99 plt.plot(x,points[i],color='#C0C0C0',linewidth=1.5,linestyle='-',marker='.') 100 101 for i in range(k): 102 plt.plot(x,Centers[i],linewidth=1.5,linestyle='-',marker='.') 103 plt.show()
运行结果：
