Supported by Dr. Osamu Ogasawara and  providing  . |
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Last data update: 2014.03.03 |
DiffusionMap methodsDescriptionGet and set eigenvalues, eigenvectors, and sigma(s) of a DiffusionMap object or print information about a DiffusionMap Usageeigenvalues(dm) eigenvalues(dm) <- value eigenvectors(dm) eigenvectors(dm) <- value sigmas(dm) sigmas(dm) <- value dataset(dm) dataset(dm) <- value ## S4 method for signature 'DiffusionMap' optimal.sigma(object) ## S4 method for signature 'DiffusionMap' print(x) ## S4 method for signature 'DiffusionMap' show(object) Arguments
ValueThe assigned or retrieved value See Also
Examplesdata(guo) dm <- DiffusionMap(guo) eigenvalues(dm) eigenvectors(dm) sigmas(dm) dataset(dm) optimal.sigma(dm) Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(destiny)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/destiny/DiffusionMap-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: DiffusionMap methods
> ### Title: DiffusionMap methods
> ### Aliases: 'DiffusionMap methods' DiffusionMap-methods dataset dataset<-
> ### eigenvalues eigenvalues<- eigenvectors eigenvectors<-
> ### optimal.sigma,DiffusionMap-method print,DiffusionMap-method
> ### show,DiffusionMap-method sigmas sigmas<- values values<- vectors
> ### vectors<-
>
> ### ** Examples
>
> data(guo)
> dm <- DiffusionMap(guo)
> eigenvalues(dm)
[1] 0.9101813 0.8085238 0.7039224 0.6695396 0.6065108 0.5373245 0.4933150
[8] 0.4149055 0.3919145 0.3456990 0.2928573 0.2646238 0.2474504 0.2252171
[15] 0.2041335 0.1940634 0.1824785 0.1764975 0.1604090 0.1508816
> eigenvectors(dm)
DC1 DC2 DC3 DC4 DC5
[1,] 0.158176317 -4.998368e-01 0.2364179396 -0.0812650640 -1.999833e-01
[2,] 0.154033526 -4.692624e-01 0.2107738741 -0.0680103350 -1.734246e-01
[3,] 0.139859917 -3.864763e-01 0.1356620997 -0.0564232453 -1.761489e-01
[4,] 0.124521798 -2.625198e-01 0.1230618285 -0.0689464568 2.334069e-02
[5,] 0.130877998 -2.822391e-01 0.1615624492 -0.0683454343 9.235547e-02
[6,] 0.136323243 -3.143267e-01 0.1511705707 -0.0670114547 5.716043e-02
[7,] 0.113514275 -1.554747e-01 0.0820059437 -0.0379658316 1.972992e-01
[8,] 0.143413364 -3.778506e-01 0.1762231822 -0.0617191561 3.478336e-03
[9,] 0.146680752 -4.096006e-01 0.1916599167 -0.0644975720 -1.100090e-01
[10,] 0.151694902 -4.754728e-01 0.1590298029 -0.0389860759 -2.370580e-01
[11,] 0.153896097 -4.865347e-01 0.1820464690 -0.0525185812 -2.467892e-01
[12,] 0.157911796 -5.041500e-01 0.2176221250 -0.0725340665 -2.447899e-01
[13,] 0.134054422 -3.193797e-01 0.1733231440 -0.0739925048 1.436907e-02
[14,] 0.133940795 -2.942781e-01 0.1648069882 -0.0664525112 8.050361e-02
[15,] 0.140309213 -3.454070e-01 0.1782987564 -0.0746791723 2.169027e-02
[16,] 0.123778948 -2.332334e-01 0.0993186686 -0.0240267582 1.361990e-01
[17,] 0.134193187 -3.142042e-01 0.1278503131 -0.0400720837 4.785831e-02
[18,] 0.148489614 -4.200954e-01 0.1924324385 -0.0650943658 -8.917708e-02
[19,] 0.154418745 -4.765403e-01 0.1916968406 -0.0559579348 -1.980567e-01
[20,] 0.112917973 -2.163430e-01 -0.0128594481 0.0222399948 3.727654e-02
[21,] 0.112199139 -1.848292e-01 -0.0090613248 0.0151481088 1.611568e-01
[22,] 0.099646278 -1.032586e-01 -0.0110734528 0.0055050190 2.229216e-01
[23,] 0.107986583 -1.395371e-01 0.0270673496 -0.0121460429 2.495640e-01
[24,] 0.117107639 -1.988164e-01 0.0417924742 -0.0211060830 1.663581e-01
[25,] 0.100296118 -9.169085e-02 0.0566872121 -0.0162109893 2.462308e-01
[26,] 0.104998050 -1.151976e-01 0.0048784426 0.0005830688 2.127950e-01
[27,] 0.111239392 -1.867857e-01 -0.0562083325 0.0481276721 8.899365e-02
[28,] 0.117095196 -2.393307e-01 -0.0785271973 0.0710830416 4.273642e-03
[29,] 0.111382403 -1.925168e-01 -0.0401227295 0.0382824163 1.313138e-01
[30,] 0.108360669 -1.773010e-01 -0.0809086690 0.0694904501 5.021133e-02
[31,] 0.089868763 -5.850389e-02 0.0043622835 -0.0040548957 2.536727e-01
[32,] 0.103335471 -1.157650e-01 0.0229863316 -0.0073508823 2.663467e-01
[33,] 0.108075681 -1.456841e-01 0.0102106741 0.0082072578 2.035672e-01
[34,] 0.094108562 -8.247242e-02 -0.0251629991 0.0089675307 2.775284e-01
[35,] 0.097510025 -6.588940e-02 0.0040130315 0.0266143861 1.972535e-01
[36,] 0.110623327 -1.434218e-01 -0.0098563760 0.0202724352 7.917022e-02
[37,] 0.113781263 -2.321604e-01 -0.0948078804 0.0839312512 -9.550737e-03
[38,] 0.102851449 -1.508425e-01 -0.1057014914 0.0774083085 7.918005e-02
[39,] 0.127484807 -3.008915e-01 -0.0042372503 0.0398159788 -4.564376e-02
[40,] 0.104858525 -1.275856e-01 -0.0012863428 0.0013280420 2.072398e-01
[41,] 0.098680524 -8.756036e-02 -0.0055761684 -0.0063518560 2.449599e-01
[42,] 0.106119415 -1.369415e-01 -0.0340608201 0.0118472298 1.636258e-01
[43,] 0.062087064 9.763141e-03 0.0417220170 -0.0078806251 2.933280e-01
[44,] 0.069330177 -1.240443e-02 -0.0637389671 0.0266663719 2.422010e-01
[45,] 0.079667858 -4.184569e-02 -0.1353608410 0.0840555759 1.178330e-01
[46,] 0.093861897 -1.189235e-01 -0.1905704993 0.1231016434 3.413440e-02
[47,] 0.086522108 -6.784633e-02 -0.1576839830 0.0992490630 8.299402e-02
[48,] 0.066992814 -6.627522e-02 -0.2905627707 0.1589155462 2.421687e-03
[49,] 0.057553849 1.173046e-02 -0.0755242520 0.0366720976 2.118190e-01
[50,] 0.077314546 -2.663858e-02 -0.0749623037 0.0407636005 2.284616e-01
[51,] 0.069394983 1.984305e-02 0.0664191373 -0.0154893413 2.740088e-01
[52,] 0.071801460 -4.756328e-02 -0.0957727442 0.0410989167 1.974919e-01
[53,] 0.069378292 -1.966662e-02 -0.1431715320 0.0786586245 1.670889e-01
[54,] 0.075892043 -5.235810e-02 -0.2169079910 0.1207767613 1.032391e-01
[55,] 0.081878940 -7.099789e-02 -0.2260677848 0.1296239614 1.080868e-01
[56,] 0.091657235 -8.459323e-02 -0.1166886524 0.0843447373 1.268679e-01
[57,] 0.081540594 -1.931948e-02 -0.0078618884 0.0027841633 2.205268e-01
[58,] 0.088137449 -3.494389e-02 -0.0038758819 -0.0118107847 2.371501e-01
[59,] 0.088735372 -6.611744e-02 -0.0489728205 0.0407367221 1.854067e-01
[60,] 0.082419579 -4.800780e-02 -0.1417878604 0.0756996725 1.118785e-01
[61,] 0.093847381 -6.217103e-02 -0.1028234492 0.0535256151 1.462509e-01
[62,] 0.090213803 -4.086506e-02 -0.0916654783 0.0618814468 1.354520e-01
[63,] 0.078416636 -6.501368e-02 -0.2416745040 0.1345437346 2.000593e-02
[64,] 0.065689028 1.550479e-02 0.0102785584 -0.0664034706 2.382096e-01
[65,] 0.086610022 -8.612944e-02 -0.2080246995 0.1163704281 2.927645e-02
[66,] 0.078671034 -2.424666e-02 -0.0632137360 0.0402693548 1.886913e-01
[67,] 0.050836290 5.678644e-02 0.0818287733 -0.0349377245 3.072087e-01
[68,] 0.096510302 -8.730753e-02 -0.0302978383 0.0382029002 1.854666e-01
[69,] 0.082903177 -6.641788e-02 -0.1214516665 0.0730737593 1.347338e-01
[70,] 0.087563633 -2.218147e-02 -0.1031250830 0.0832388637 6.893687e-02
[71,] 0.081315876 -2.012461e-02 -0.1527283585 0.0820545136 7.162588e-02
[72,] 0.086365766 -9.467886e-02 -0.2636141202 0.1430360652 -2.499715e-03
[73,] 0.071587950 -5.493797e-02 -0.3096018985 0.1579178703 -3.398420e-02
[74,] 0.086451002 -7.759642e-02 -0.2009873766 0.1125233416 1.462659e-02
[75,] 0.074710252 -5.660150e-02 -0.2297372550 0.1242414409 3.250308e-02
[76,] 0.090923057 -4.681560e-02 -0.0532310538 0.0291310029 2.028807e-01
[77,] 0.077800024 -2.455547e-02 -0.0938116165 0.0668378683 1.576172e-01
[78,] 0.078586824 -4.237377e-02 -0.0920303329 0.0535909587 1.689696e-01
[79,] 0.088905338 -3.134677e-02 -0.0511328460 0.0097918337 1.851971e-01
[80,] 0.092862574 -3.704259e-02 -0.0803259867 0.0412365228 1.067358e-01
[81,] 0.094041013 -1.062280e-01 -0.1803979590 0.1099354751 4.870131e-02
[82,] 0.083689576 -7.867672e-02 -0.2075936284 0.1141068950 4.049562e-02
[83,] 0.081147829 -4.296018e-02 -0.2065570615 0.1178930245 2.803284e-02
[84,] 0.084958629 -6.491170e-02 -0.1597977381 0.0848812062 1.044859e-01
[85,] 0.085884970 -4.162230e-02 -0.0382019147 0.0093534672 2.490953e-01
[86,] 0.028628779 5.100199e-02 -0.0011372281 -0.0021311598 2.556183e-01
[87,] 0.062548536 2.434046e-02 -0.1206559342 0.0255236890 1.183069e-01
[88,] 0.033988866 4.347460e-02 -0.0989893718 0.0500735790 1.045172e-01
[89,] -0.003546050 6.546292e-03 -0.2810337222 0.1326828076 -3.412262e-05
[90,] 0.028063467 -3.941086e-03 -0.3514610540 0.1710154590 -6.685844e-02
[91,] -0.006230225 -7.913999e-03 -0.3463815928 0.1754609465 -2.905547e-02
[92,] -0.003381336 -5.979722e-03 -0.3148524400 0.1581724841 -4.622669e-02
[93,] -0.010479506 -1.250146e-03 -0.2454211546 0.1186485874 3.067942e-02
[94,] 0.031395307 2.314019e-02 -0.1419430875 0.0850617829 1.625613e-01
[95,] 0.049743667 5.464870e-03 -0.1924269440 0.0872384004 9.559175e-02
[96,] -0.027966222 2.217320e-02 -0.1412993861 0.0600863238 1.152159e-01
[97,] 0.012731570 1.214551e-02 -0.2546663822 0.1210071837 6.304798e-02
[98,] 0.030189767 -6.839758e-03 -0.2977308825 0.1572672019 2.135303e-02
[99,] 0.014267795 -1.660947e-02 -0.3992841476 0.2053761291 -5.612253e-02
[100,] 0.073784610 -2.066913e-02 -0.2607186433 0.1097867398 -6.755114e-02
[101,] 0.004706213 7.433405e-03 -0.3153857508 0.1544674054 -4.371857e-02
[102,] -0.052518888 4.139850e-02 -0.0079334352 0.0388853835 1.631854e-01
[103,] -0.021962341 3.647290e-02 -0.0848724124 0.0206556415 1.670708e-01
[104,] 0.026757669 3.585786e-02 -0.1294738396 0.0488101029 1.452990e-01
[105,] 0.004249185 4.663746e-02 -0.0868730396 0.0410271014 1.761432e-01
[106,] 0.036491883 -1.099898e-04 -0.2333332387 0.1059949572 8.500879e-02
[107,] 0.029019122 9.967205e-03 -0.3521833929 0.1585521551 -1.008168e-01
[108,] 0.068788513 -2.182972e-02 -0.2713947110 0.1188029899 -7.869716e-03
[109,] 0.039151444 -1.782633e-02 -0.3587098331 0.1887862088 -8.582690e-03
[110,] 0.020944147 1.126278e-02 -0.2717640457 0.0929521622 -6.326376e-02
[111,] 0.055802807 -5.777631e-03 -0.1920797136 0.0869896226 1.034340e-01
[112,] 0.058933783 -1.528737e-03 -0.1385200502 0.0556593544 1.763566e-01
[113,] 0.019300154 2.109896e-02 -0.1679048830 0.0762974694 9.134689e-02
[114,] 0.042437778 4.275355e-02 -0.0743078713 0.0217172856 1.847906e-01
[115,] 0.024372427 2.302395e-03 -0.2091836317 0.0988921705 8.426903e-02
[116,] 0.054734761 -1.995815e-02 -0.2451206831 0.1198858537 6.787593e-02
[117,] 0.036724795 -1.793098e-02 -0.3816428737 0.1896739452 -3.698830e-02
[118,] 0.012810327 4.585564e-03 -0.2641454012 0.1368739014 2.868183e-02
[119,] 0.020609720 3.635502e-03 -0.3071873266 0.1554109597 3.508546e-02
[120,] 0.010233261 2.327447e-02 -0.1611503073 0.0745386317 1.495957e-01
[121,] 0.044695498 3.824384e-02 -0.0557873569 0.0384475565 2.390231e-01
[122,] 0.049330993 1.662420e-02 -0.1464345454 0.0824220356 1.529079e-01
[123,] 0.036325321 3.127693e-02 -0.0746433591 0.0511843734 1.854046e-01
[124,] 0.027965851 2.986784e-02 -0.1207885061 0.0578942194 1.834917e-01
[125,] -0.001885011 2.864279e-02 -0.1335724710 0.0492241367 1.429951e-01
[126,] 0.047897475 1.103970e-02 -0.1682766078 0.0876628522 1.188701e-01
[127,] 0.020265804 2.057082e-03 -0.2867585229 0.1402592326 5.721009e-02
[128,] 0.042399231 2.602169e-02 -0.1526608795 0.1081652743 1.376307e-01
[129,] -0.008213275 4.206218e-02 -0.0796891765 0.0008288007 1.872479e-01
[130,] 0.028121204 3.985066e-02 -0.0696121941 0.0155935876 2.491387e-01
[131,] 0.033692685 1.954857e-02 -0.1625130062 0.0682941500 1.470428e-01
[132,] 0.042948598 3.471826e-02 -0.0940929472 0.0595789258 1.904715e-01
[133,] 0.057602348 2.673366e-02 -0.0919603303 0.0418988601 1.657700e-01
[134,] 0.060191118 -2.762751e-02 -0.2929968616 0.1596705463 5.678264e-02
[135,] 0.057571265 -2.017039e-02 -0.3109671208 0.1625088037 2.005992e-02
[136,] 0.038132616 -2.165173e-02 -0.2751663210 0.1469244996 6.434601e-02
[137,] 0.059076478 -2.393032e-02 -0.2946005780 0.1591759207 5.786116e-02
[138,] 0.044573844 2.392902e-02 -0.1251101499 0.0613961959 1.572824e-01
[139,] 0.045519970 3.941064e-02 -0.0730105634 0.0347437485 1.994553e-01
[140,] 0.022119245 1.557092e-02 -0.1728889173 0.0855338861 1.565833e-01
[141,] 0.048824421 2.690023e-02 -0.0683246072 -0.0022560899 2.329958e-01
[142,] 0.038747927 2.912012e-02 -0.1029820908 0.0591510837 1.898183e-01
[143,] 0.038072455 5.974527e-03 -0.2315855839 0.1319593560 1.089126e-01
[144,] 0.044989126 -4.910186e-03 -0.3051913301 0.1669666544 -3.684836e-03
[145,] 0.052381436 -1.285485e-02 -0.2780623504 0.1399350490 4.700151e-02
[146,] 0.036984318 -1.102322e-02 -0.3130816603 0.1625465444 4.284655e-02
[147,] 0.046085111 1.994112e-02 -0.1099689621 0.0409434478 2.051889e-01
[148,] 0.056213171 2.439124e-02 -0.0984098919 0.0314116004 1.963651e-01
[149,] 0.045917249 1.190326e-02 -0.1785764565 0.0754142840 1.483525e-01
[150,] 0.052658196 1.535481e-02 -0.1333916008 0.0588872992 1.704363e-01
[151,] 0.037044160 2.493688e-02 -0.1328474076 0.0609395702 1.541437e-01
[152,] -0.024686379 -2.087692e-03 -0.2569590012 0.1347380985 -6.030280e-03
[153,] 0.042000118 -1.309777e-02 -0.3865371061 0.1889347085 -4.907774e-02
[154,] 0.073170773 1.722311e-02 -0.1607687518 0.0625862134 4.753473e-02
[155,] 0.047567131 -2.008387e-02 -0.3320016324 0.1644621028 -5.131384e-04
[156,] 0.013843101 3.854576e-02 -0.0810083098 0.0221806418 2.057327e-01
[157,] 0.041029836 2.042077e-02 -0.1629568599 0.0520789817 1.252345e-01
[158,] 0.052060860 2.165498e-02 -0.1282839195 0.0690036464 1.632001e-01
[159,] 0.029766897 9.158013e-03 -0.1729746554 0.0566703878 1.027693e-01
[160,] 0.075218422 4.260202e-03 -0.1435333989 0.0308825574 7.496337e-02
[161,] -0.326785070 -3.599799e-02 0.0166761853 -0.0035179038 -1.252484e-01
[162,] 0.094020926 1.371686e-01 -0.1204346750 -0.1175557053 -4.075374e-01
[163,] -0.335485340 -3.575800e-02 0.0460937950 -0.0175098006 -7.839534e-02
[164,] -0.349271732 -4.017448e-02 0.0399309508 -0.0143208641 -1.359289e-01
[165,] 0.086874093 1.332075e-01 0.0127379941 -0.2955794022 9.370394e-02
[166,] 0.092130592 1.564091e-01 0.0510810503 -0.0673624339 -1.240425e-01
[167,] -0.284817903 -1.939889e-02 0.0538396610 -0.0238060322 5.113798e-02
[168,] 0.092916118 1.316716e-01 -0.0119920234 -0.1682466034 -1.050078e-01
[169,] 0.096199040 1.375933e-01 -0.0497791462 -0.2222631604 -1.827658e-01
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Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and