lmds: Landmark MDS
In lmds: Landmark Multi-Dimensional Scaling
Description
Usage
Arguments
Value
Examples
Description
A fast dimensionality reduction method scaleable to large numbers of samples.
Landmark Multi-Dimensional Scaling (LMDS) is an extension of classical 'Torgerson MDS',
but rather than calculating a complete distance matrix between all pairs of samples,
only the distances between a set of landmarks and the samples are calculated.
A fast dimensionality reduction method scaleable to large numbers of samples.
Landmark Multi-Dimensional Scaling (LMDS) is an extension of classical Torgerson MDS´,
but rather than calculating a complete distance matrix between all pairs of samples,
only the distances between a set of landmarks and the samples are calculated.
Usage
1
2
3
Arguments
x
A matrix, optionally sparse.
ndim
The number of dimensions
distance_method
The distance metric to use. Options are "euclidean" (default), "pearson", "spearman", "cosine", "manhattan".
landmark_method
The landmark selection method to use. Options are "sample" (default).
num_landmarks
The number of landmarks to use,
Value
The dimensionality reduction in the form of a nrow(x) by ndim matrix.
Examples
1
2
3
Example output
comp_1 comp_2 comp_3
[1,] -0.146491076 4.219631e-02 0.166807798
[2,] -0.182706004 7.446980e-02 0.074999373
[3,] -0.100892711 1.495415e-02 0.122063923
[4,] -0.161003265 4.128150e-02 0.173400141
[5,] -0.142148774 2.850009e-02 0.171421137
[6,] -0.165281596 5.290190e-02 0.179187576
[7,] -0.146223357 3.209290e-02 0.168891461
[8,] -0.169528251 6.140979e-02 0.187336448
[9,] -0.141784336 3.313490e-02 0.160210572
[10,] -0.116498657 2.794373e-02 0.174860783
[11,] -0.147243842 3.247395e-02 0.163240731
[12,] -0.044354400 -1.620196e-01 0.309631942
[13,] -0.166025755 5.268247e-02 0.181426054
[14,] -0.144497395 1.137605e-01 0.141143812
[15,] -0.162291371 4.500289e-02 0.157546814
[16,] -0.161907433 5.027023e-02 0.194041378
[17,] -0.151977987 6.361986e-02 0.150051439
[18,] -0.120981265 -6.155727e-03 0.129143141
[19,] -0.146721458 -2.564249e-02 0.104197816
[20,] -0.137924776 3.408264e-02 0.143757445
[21,] -0.148274440 5.739240e-02 0.134909723
[22,] -0.147120347 6.057807e-02 0.189884295
[23,] -0.135145373 2.742848e-02 0.160557793
[24,] -0.141019360 3.326589e-02 0.169932534
[25,] -0.169259835 5.184096e-02 0.185571797
[26,] -0.144723202 3.629392e-02 0.174667582
[27,] -0.168156011 5.180980e-02 0.188242465
[28,] -0.144021233 1.993126e-02 0.154687033
[29,] -0.137548865 3.291563e-02 0.178338271
[30,] -0.158484441 4.612448e-02 0.167965786
[31,] -0.171118490 -9.619855e-03 0.145843428
[32,] -0.160473133 4.486213e-02 0.172026794
[33,] -0.183826394 6.238580e-02 0.197373417
[34,] -0.142131756 6.323890e-02 0.172308906
[35,] -0.152951809 5.736377e-02 0.166158726
[36,] -0.145619907 2.174754e-02 0.176922320
[37,] -0.152929955 3.691416e-02 0.159339155
[38,] -0.167515662 5.432955e-02 0.187598204
[39,] -0.176327102 8.355221e-03 0.136164581
[40,] -0.159694258 6.643748e-02 0.165264442
[41,] -0.074178975 3.584687e-02 0.215085757
[42,] -0.152846986 4.888412e-02 0.208115425
[43,] -0.141891873 3.985578e-02 0.166009573
[44,] -0.159462287 5.444816e-02 0.178853778
[45,] -0.158715561 4.292146e-02 0.177310218
[46,] -0.156082754 4.319227e-02 0.165715935
[47,] -0.122871402 2.245238e-02 0.144746766
[48,] -0.167491046 9.046903e-02 0.169384673
[49,] -0.172876436 4.360728e-02 0.183690496
[50,] -0.165022218 1.515998e-02 0.152781871
[51,] -0.124740477 -3.247868e-02 0.165806568
[52,] -0.167592094 1.105755e-02 0.199242267
[53,] -0.151462730 4.170003e-02 0.171040749
[54,] -0.144295252 2.612502e-02 0.156917423
[55,] -0.116615063 2.298325e-02 0.127934129
[56,] -0.157732930 4.836978e-02 0.178065651
[57,] -0.162009068 4.585564e-02 0.192702659
[58,] -0.167194267 4.605688e-02 0.175292497
[59,] -0.229176259 -1.807532e-02 0.189102813
[60,] -0.181488183 5.144078e-02 0.180207050
[61,] -0.111253255 -1.805006e-01 -0.110958702
[62,] -0.140653595 2.812871e-02 0.148856532
[63,] -0.162781543 -3.223590e-02 0.207584366
[64,] -0.161570156 7.224109e-02 0.169858480
[65,] -0.136593180 4.432723e-02 0.157210306
[66,] -0.162260090 4.491010e-02 0.161529749
[67,] -0.153691052 3.830571e-02 0.177082410
[68,] -0.154142614 4.088749e-02 0.180005514
[69,] -0.128382896 5.261555e-02 0.161255292
[70,] -0.174392980 3.271504e-02 0.202708854
[71,] -0.166383548 2.561491e-02 0.178513409
[72,] -0.175097520 6.001380e-02 0.203252992
[73,] -0.135221195 -7.016180e-02 0.025123202
[74,] -0.145199593 3.242216e-02 0.165297231
[75,] -0.257577218 1.115395e-01 0.130713831
[76,] -0.143134987 3.954627e-02 0.159770284
[77,] -0.158994999 3.806054e-02 0.172777739
[78,] -0.155894065 4.084216e-02 0.177038119
[79,] -0.136160409 1.554597e-02 0.155744883
[80,] -0.182671082 2.058888e-02 0.181786564
[81,] 0.048017902 1.486510e-01 0.108398858
[82,] -0.160946047 4.726803e-02 0.183222408
[83,] -0.156908898 5.007176e-02 0.152335593
[84,] -0.174771898 5.007399e-02 0.186112984
[85,] -0.152837185 4.206293e-03 0.176927576
[86,] -0.157838642 -1.653564e-03 0.167701892
[87,] -0.165879120 -2.694060e-02 0.239800436
[88,] -0.164537244 5.433231e-02 0.184074631
[89,] -0.171924973 6.230610e-02 0.215370570
[90,] -0.160163048 4.459817e-02 0.179350706
[91,] -0.171190513 7.087657e-02 0.218761631
[92,] -0.169280670 3.852616e-02 0.154684096
[93,] -0.168165348 5.827686e-02 0.155953855
[94,] -0.174938369 5.714916e-02 0.187200227
[95,] -0.152272731 4.427233e-02 0.174392388
[96,] -0.138232138 1.001604e-01 0.121202339
[97,] -0.168550231 3.753008e-02 0.160464809
[98,] -0.120629946 2.419728e-02 0.161153324
[99,] -0.147440861 3.214688e-02 0.161037182
[100,] -0.129510099 2.000678e-02 0.182330061
[101,] -0.135679631 2.959471e-02 0.174820865
[102,] -0.174670104 -7.632670e-03 0.213951719
[103,] -0.145973908 3.514066e-02 0.183569242
[104,] -0.131031056 -1.467965e-01 0.269121980
[105,] -0.152536556 3.996409e-02 0.157585164
[106,] -0.171884194 3.238828e-02 0.175367842
[107,] -0.159150875 4.755613e-02 0.179234989
[108,] -0.182602830 6.913114e-02 0.200897143
[109,] -0.165551749 3.990540e-02 0.167584362
[110,] -0.144706519 4.314174e-02 0.167704282
[111,] -0.150581196 3.694528e-02 0.160624105
[112,] -0.158629488 4.127708e-02 0.175966163
[113,] -0.138392735 4.643119e-02 0.164863717
[114,] -0.168823227 2.441535e-03 0.199498014
[115,] -0.121565535 1.808948e-02 0.169117258
[116,] -0.152393115 3.918009e-02 0.178660558
[117,] -0.150439477 2.662832e-02 0.164317171
[118,] -0.158490980 7.601531e-02 0.212731360
[119,] -0.147727430 4.354792e-02 0.167414694
[120,] -0.213905974 1.607444e-01 0.312151950
[121,] -0.143964449 -8.264399e-03 0.117014388
[122,] -0.168408715 3.414518e-02 0.307424957
[123,] -0.158166766 5.986416e-02 0.165441867
[124,] -0.167109630 4.476924e-02 0.168001584
[125,] -0.145031621 3.513256e-02 0.155035291
[126,] -0.211016027 6.060014e-02 0.154001697
[127,] -0.147346936 3.427756e-02 0.159599040
[128,] -0.188240311 4.741420e-02 0.159158020
[129,] -0.143925345 2.551550e-02 0.161121737
[130,] -0.155075413 5.266236e-02 0.168862306
[131,] -0.127020866 3.969389e-02 0.136890691
[132,] -0.171102981 5.142901e-02 0.184509063
[133,] -0.157697494 4.612010e-02 0.184771696
[134,] -0.148997155 -1.013087e-02 0.130059911
[135,] -0.144254131 5.883930e-02 0.213814123
[136,] -0.148012153 9.956160e-02 0.183274847
[137,] -0.145949130 5.370636e-02 0.153969863
[138,] -0.143079495 3.941801e-02 0.178857817
[139,] -0.166959785 6.484646e-02 0.168172594
[140,] -0.127068354 3.101841e-03 0.160881108
[141,] -0.178417093 5.050191e-02 0.186328600
[142,] -0.151433906 3.110283e-02 0.181685160
[143,] -0.159248561 5.363325e-02 0.182255723
[144,] -0.152516243 4.684020e-02 0.172212564
[145,] -0.106281366 6.283001e-02 0.143896297
[146,] -0.161824232 3.392577e-02 0.159072526
[147,] -0.123539647 3.858826e-02 0.178063900
[148,] -0.135591529 2.919151e-02 0.157745217
[149,] -0.158050341 3.863846e-02 0.161619291
[150,] -0.138075775 3.332166e-02 0.154500408
[151,] -0.129209523 3.017463e-02 0.154332210
[152,] -0.151641348 4.077486e-02 0.175994689
[153,] -0.129516390 2.108079e-02 0.164882571
[154,] -0.104146466 3.503229e-02 0.172319039
[155,] -0.167735163 5.712239e-02 0.186106001
[156,] -0.172550779 5.001271e-02 0.181146946
[157,] -0.196633813 6.245122e-02 0.169417916
[158,] -0.149906585 3.881779e-02 0.176359488
[159,] -0.147588001 4.832196e-02 0.144797969
[160,] -0.181997358 5.576501e-02 0.186160060
[161,] -0.150589676 5.140404e-02 0.134057208
[162,] -0.164843824 5.012518e-02 0.183563301
[163,] -0.331912456 9.047939e-02 0.041158960
[164,] -0.144264455 3.036096e-03 0.102921690
[165,] -0.125554554 3.251832e-02 0.145577461
[166,] -0.187448501 6.646321e-02 0.158734452
[167,] -0.174660474 6.375285e-02 0.199334532
[168,] -0.143506468 4.024924e-02 0.156775102
[169,] -0.134781517 6.308310e-02 0.138627746
[170,] -0.182723286 6.232170e-02 0.150444110
[171,] -0.145446754 2.191039e-02 0.154993152
[172,] 0.154364640 1.342932e-02 0.130234479
[173,] -0.174122026 4.555385e-02 0.179402571
[174,] -0.133383740 1.784596e-02 0.151886990
[175,] -0.174330497 5.512036e-02 0.199272164
[176,] -0.156771382 3.705750e-02 0.183593797
[177,] -0.100209361 3.060724e-02 0.146876843
[178,] -0.176283718 5.594027e-02 0.186304574
[179,] -0.146131056 4.410532e-02 0.177423110
[180,] -0.144401028 3.945207e-02 0.176501660
[181,] -0.032892450 -3.125305e-01 -0.418850235
[182,] -0.157381971 7.325620e-02 0.167969807
[183,] -0.148189745 2.169886e-02 0.186469723
[184,] -0.125650076 6.415526e-04 0.153829480
[185,] -0.208360063 5.560265e-02 0.165008944
[186,] -0.161212090 -6.364242e-03 0.199471731
[187,] -0.136724424 2.458988e-02 0.157607085
[188,] -0.159021359 4.888885e-02 0.187487517
[189,] -0.156037395 2.355556e-02 0.168833458
[190,] -0.140944662 3.764433e-02 0.173864748
[191,] -0.171031364 4.409998e-02 0.183881276
[192,] -0.182644456 3.785164e-02 0.197755002
[193,] -0.174679118 3.434302e-02 0.188287220
[194,] -0.168055570 9.482341e-02 0.138533866
[195,] -0.159517743 5.703043e-02 0.173625836
[196,] -0.243306624 7.453427e-02 0.160685668
[197,] -0.130135745 -1.051370e-02 0.163139691
[198,] -0.027606486 4.243607e-02 0.172416891
[199,] -0.158034858 5.200346e-02 0.164054811
[200,] -0.151114563 3.313238e-02 0.175979841
[201,] 0.500000000 -3.572069e-02 0.307695927
[202,] -0.173499937 5.214684e-02 0.195429951
[203,] -0.156959565 3.252067e-02 0.173654048
[204,] -0.160343486 2.869572e-02 0.177059115
[205,] -0.142334075 3.505638e-02 0.147724278
[206,] -0.111707010 5.932032e-02 0.158902969
[207,] -0.179009354 5.129983e-02 0.196678234
[208,] -0.162477308 4.614789e-02 0.179455656
[209,] -0.155359127 3.964757e-02 0.181990075
[210,] -0.142632886 2.386089e-02 0.183402868
[211,] -0.197224419 -2.012158e-02 0.110630034
[212,] -0.118203959 -1.825675e-02 0.178296252
[213,] -0.150413141 4.878952e-02 0.177726979
[214,] -0.198149973 4.336494e-02 0.179430583
[215,] -0.147663188 3.380124e-02 0.162382975
[216,] -0.151130925 4.606187e-02 0.174479210
[217,] -0.178660720 5.811688e-02 0.193604627
[218,] -0.159384133 3.237182e-02 0.178443934
[219,] -0.149520634 4.659995e-02 0.171776286
[220,] -0.159341612 3.633388e-02 0.182879027
[221,] -0.158464841 4.749387e-02 0.179974358
[222,] -0.188283052 4.475016e-02 0.194421195
[223,] -0.316370065 1.287006e-01 0.116647462
[224,] -0.116929414 3.917508e-02 0.140546003
[225,] -0.115751418 2.870128e-02 0.174908242
[226,] -0.181686216 3.289818e-02 0.183039712
[227,] -0.158193298 4.173254e-02 0.162931907
[228,] -0.166528460 3.987825e-02 0.202767733
[229,] -0.147926497 4.518798e-03 0.205898435
[230,] -0.131248508 2.480962e-02 0.182102358
[231,] -0.168128151 6.263817e-02 0.161500171
[232,] -0.158158126 5.320075e-02 0.189423287
[233,] -0.111676676 1.358962e-01 0.093860247
[234,] -0.142463784 3.460451e-02 0.166743861
[235,] -0.132826028 4.000991e-02 0.142546334
[236,] -0.174559103 5.088471e-02 0.193936448
[237,] -0.089804355 -1.449320e-01 -0.193307484
[238,] -0.155342126 3.115731e-02 0.164583616
[239,] -0.143304026 6.073636e-02 0.155151348
[240,] -0.133297499 2.284075e-02 0.160225053
[241,] -0.157209517 3.141798e-02 0.185141086
[242,] -0.147630623 3.705421e-02 0.168063364
[243,] -0.179255721 4.370841e-02 0.167194752
[244,] -0.164582654 4.143695e-02 0.165903005
[245,] -0.167276381 5.159731e-02 0.180265821
[246,] -0.173179752 7.705958e-02 0.175095066
[247,] -0.141335635 3.526658e-02 0.154797770
[248,] -0.111490103 1.581681e-02 0.192274580
[249,] -0.147414736 4.911245e-02 0.165315775
[250,] -0.194335304 5.614812e-02 0.166257890
[251,] -0.152623689 -8.923584e-03 0.112854367
[252,] -0.133670773 3.953795e-02 0.164118779
[253,] -0.132225687 1.133355e-01 0.125084696
[254,] -0.159349644 3.576319e-02 0.156264803
[255,] -0.143518404 3.181909e-02 0.161487787
[256,] -0.159571531 4.404605e-02 0.170556339
[257,] -0.145501530 4.416277e-02 0.172270259
[258,] -0.152636653 2.929900e-02 0.157431826
[259,] -0.161574602 4.441181e-02 0.172028558
[260,] -0.161372035 6.411202e-02 0.174525761
[261,] -0.161440398 4.287986e-02 0.175769848
[262,] -0.146193672 9.657104e-02 0.106025844
[263,] -0.118493908 4.025151e-04 0.188471396
[264,] -0.120622569 3.519309e-02 0.181014105
[265,] -0.114030547 5.783164e-02 0.213437585
[266,] -0.140544556 -3.434039e-02 0.087840010
[267,] -0.061396918 2.517389e-02 0.169306046
[268,] -0.091352782 4.588471e-02 0.177801757
[269,] -0.152811657 4.689125e-02 0.170837211
[270,] -0.147066216 4.628609e-02 0.170266935
[271,] -0.132658004 2.556501e-03 0.185010845
[272,] -0.182242618 6.219572e-02 0.199996587
[273,] -0.110846979 1.019271e-02 0.169086505
[274,] -0.160119781 4.378157e-02 0.175952726
[275,] -0.136551055 1.467960e-02 0.149362213
[276,] -0.171843001 6.967293e-02 0.166124140
[277,] -0.124119363 2.506520e-02 0.181613493
[278,] -0.171210973 5.556069e-02 0.181224487
[279,] -0.149115725 2.996695e-02 0.133513774
[280,] -0.374460889 1.873486e-02 0.114181373
[281,] -0.157459854 4.329019e-02 0.172881414
[282,] -0.143209353 1.908660e-02 0.154367362
[283,] -0.152233050 2.847989e-02 0.173359050
[284,] -0.159239083 5.475929e-02 0.175802384
[285,] -0.165199851 7.065062e-02 0.154865958
[286,] -0.169097970 5.713704e-02 0.192668566
[287,] -0.142455223 6.100607e-02 0.200928029
[288,] -0.159104802 5.546565e-02 0.179944692
[289,] -0.164365600 5.505430e-02 0.189607771
[290,] -0.114535306 1.788824e-02 0.166150338
[291,] -0.116422368 2.434864e-02 0.150696935
[292,] -0.155267987 3.686131e-02 0.166092842
[293,] -0.156856105 7.806349e-02 0.220907320
[294,] -0.185547466 3.618847e-02 0.170213453
[295,] -0.160298765 3.387871e-02 0.179561066
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[912,] -0.136912641 1.822375e-02 0.178068439
[913,] -0.129520772 4.534823e-02 0.139210134
[914,] -0.174552741 6.353626e-02 0.187540263
[915,] -0.145484979 2.698149e-02 0.194027626
[916,] -0.117863965 7.207952e-02 0.133389415
[917,] -0.115982959 -1.968808e-01 0.201502577
[918,] -0.191787765 5.480256e-02 0.193336355
[919,] -0.144572400 6.127967e-02 0.140334658
[920,] -0.183932377 5.428782e-02 0.158547525
[921,] -0.148334078 3.499869e-02 0.162348660
[922,] -0.156104756 4.532652e-02 0.179788312
[923,] -0.135642942 5.853786e-02 0.175069387
[924,] -0.169096463 5.572619e-02 0.178634909
[925,] -0.170160052 4.767798e-02 0.189291722
[926,] -0.142891683 3.201495e-02 0.167139979
[927,] -0.177806140 5.772021e-02 0.194884781
[928,] -0.150918689 4.983850e-03 0.129972138
[929,] -0.098333000 -7.084750e-02 -0.001251716
[930,] -0.152291853 4.939362e-02 0.177501884
[931,] -0.144912825 4.446629e-02 0.171991732
[932,] -0.167157051 4.655501e-02 0.163521749
[933,] -0.160882906 4.585922e-02 0.176212760
[934,] -0.171934508 8.507191e-02 0.202940977
[935,] -0.167007282 4.904018e-02 0.187170672
[936,] -0.171657045 5.330404e-02 0.183572338
[937,] -0.154283451 6.047266e-02 0.180869708
[938,] -0.151842389 4.879085e-02 0.155529719
[939,] -0.088466558 1.116694e-02 0.190339606
[940,] -0.146202792 4.034218e-02 0.156076145
[941,] -0.135104969 3.992991e-02 0.170140551
[942,] -0.160438934 4.321960e-02 0.174092288
[943,] -0.131007922 3.855985e-02 0.172471438
[944,] -0.155902921 3.020639e-02 0.169420069
[945,] -0.164995862 5.864914e-02 0.183612412
[946,] -0.151359457 2.741704e-02 0.164179292
[947,] -0.172857160 5.282603e-02 0.197648631
[948,] -0.174906167 4.943299e-02 0.184307732
[949,] -0.146586069 3.141093e-02 0.161204307
[950,] -0.135060428 6.125859e-02 0.145759815
[951,] -0.120450334 -7.043409e-03 0.178683309
[952,] -0.097447006 -5.529352e-02 0.100802352
[953,] -0.163951133 4.461123e-02 0.181812260
[954,] -0.178735797 4.094525e-02 0.185970953
[955,] -0.179893278 3.719421e-02 0.175584596
[956,] -0.176917061 4.568165e-02 0.146029750
[957,] -0.118249661 -4.366339e-03 0.164592634
[958,] -0.146325991 4.815551e-02 0.181381555
[959,] -0.121034471 -5.170259e-03 0.177516064
[960,] -0.157999707 2.090296e-02 0.208832501
[961,] -0.176083068 6.700010e-02 0.193453028
[962,] -0.188507731 7.093492e-02 0.161379956
[963,] -0.164723177 5.427376e-02 0.183935937
[964,] -0.149848258 4.236156e-02 0.185672207
[965,] -0.180205785 6.154280e-02 0.167450531
[966,] -0.134595741 3.501525e-02 0.180631416
[967,] -0.161462990 4.967157e-02 0.178895794
[968,] -0.181688854 8.202682e-02 0.200725947
[969,] -0.140958811 6.305286e-02 0.167228136
[970,] -0.151653278 -7.217085e-03 0.194888491
[971,] -0.176293019 4.674906e-02 0.200919168
[972,] -0.136047432 8.271848e-03 0.163676846
[973,] -0.140056519 2.992694e-02 0.161823245
[974,] -0.141619925 3.736374e-02 0.160452188
[975,] -0.161877260 4.203731e-02 0.173437209
[976,] 0.033056722 1.099650e-01 0.095912205
[977,] -0.154816699 3.872803e-02 0.190567532
[978,] -0.144438278 3.973731e-02 0.180831781
[979,] -0.154672574 4.679587e-02 0.184699870
[980,] -0.170881612 5.238252e-02 0.183784402
[981,] -0.138996542 3.067968e-02 0.178738174
[982,] -0.138445220 2.903005e-02 0.150488496
[983,] -0.160430284 5.873051e-02 0.185755689
[984,] -0.165396203 5.068988e-02 0.189443686
[985,] -0.169120868 4.753590e-02 0.181707241
[986,] -0.139346593 9.250484e-02 0.116301596
[987,] -0.140528737 2.946820e-02 0.155311872
[988,] -0.159909528 4.708024e-02 0.182622602
[989,] -0.146126404 7.068098e-02 0.175871868
[990,] -0.135700391 3.486882e-02 0.169452270
[991,] -0.101817955 -5.269720e-03 0.188146779
[992,] -0.157221668 -2.277858e-02 0.175515143
[993,] -0.162717573 5.715204e-02 0.185599049
[994,] -0.117507410 2.458216e-02 0.174065496
[995,] -0.181980028 6.506868e-02 0.153809352
[996,] -0.137085069 4.351504e-02 0.140907378
[997,] 0.060827029 -3.008082e-02 0.219637873
[998,] -0.145468944 3.740228e-02 0.170141454
[999,] -0.134082229 4.378387e-03 0.145218077
[1000,] -0.176928405 5.673468e-02 0.191806334
attr(,"addend")
[1] -0.02702665 -0.03254517 0.05789632
attr(,"multiplier")
[1] 1.496685
lmds documentation built on Sept. 27, 2019, 5:03 p.m.
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Description Usage Arguments Value Examples
Description
A fast dimensionality reduction method scaleable to large numbers of samples. Landmark Multi-Dimensional Scaling (LMDS) is an extension of classical 'Torgerson MDS', but rather than calculating a complete distance matrix between all pairs of samples, only the distances between a set of landmarks and the samples are calculated.
A fast dimensionality reduction method scaleable to large numbers of samples. Landmark Multi-Dimensional Scaling (LMDS) is an extension of classical Torgerson MDS´, but rather than calculating a complete distance matrix between all pairs of samples, only the distances between a set of landmarks and the samples are calculated.
Usage
1 2 3 |
Arguments
x |
A matrix, optionally sparse. |
ndim |
The number of dimensions |
distance_method |
The distance metric to use. Options are "euclidean" (default), "pearson", "spearman", "cosine", "manhattan". |
landmark_method |
The landmark selection method to use. Options are "sample" (default). |
num_landmarks |
The number of landmarks to use, |
Value
The dimensionality reduction in the form of a nrow(x) by ndim matrix.
Examples
1 2 3 |
Example output
comp_1 comp_2 comp_3
[1,] -0.146491076 4.219631e-02 0.166807798
[2,] -0.182706004 7.446980e-02 0.074999373
[3,] -0.100892711 1.495415e-02 0.122063923
[4,] -0.161003265 4.128150e-02 0.173400141
[5,] -0.142148774 2.850009e-02 0.171421137
[6,] -0.165281596 5.290190e-02 0.179187576
[7,] -0.146223357 3.209290e-02 0.168891461
[8,] -0.169528251 6.140979e-02 0.187336448
[9,] -0.141784336 3.313490e-02 0.160210572
[10,] -0.116498657 2.794373e-02 0.174860783
[11,] -0.147243842 3.247395e-02 0.163240731
[12,] -0.044354400 -1.620196e-01 0.309631942
[13,] -0.166025755 5.268247e-02 0.181426054
[14,] -0.144497395 1.137605e-01 0.141143812
[15,] -0.162291371 4.500289e-02 0.157546814
[16,] -0.161907433 5.027023e-02 0.194041378
[17,] -0.151977987 6.361986e-02 0.150051439
[18,] -0.120981265 -6.155727e-03 0.129143141
[19,] -0.146721458 -2.564249e-02 0.104197816
[20,] -0.137924776 3.408264e-02 0.143757445
[21,] -0.148274440 5.739240e-02 0.134909723
[22,] -0.147120347 6.057807e-02 0.189884295
[23,] -0.135145373 2.742848e-02 0.160557793
[24,] -0.141019360 3.326589e-02 0.169932534
[25,] -0.169259835 5.184096e-02 0.185571797
[26,] -0.144723202 3.629392e-02 0.174667582
[27,] -0.168156011 5.180980e-02 0.188242465
[28,] -0.144021233 1.993126e-02 0.154687033
[29,] -0.137548865 3.291563e-02 0.178338271
[30,] -0.158484441 4.612448e-02 0.167965786
[31,] -0.171118490 -9.619855e-03 0.145843428
[32,] -0.160473133 4.486213e-02 0.172026794
[33,] -0.183826394 6.238580e-02 0.197373417
[34,] -0.142131756 6.323890e-02 0.172308906
[35,] -0.152951809 5.736377e-02 0.166158726
[36,] -0.145619907 2.174754e-02 0.176922320
[37,] -0.152929955 3.691416e-02 0.159339155
[38,] -0.167515662 5.432955e-02 0.187598204
[39,] -0.176327102 8.355221e-03 0.136164581
[40,] -0.159694258 6.643748e-02 0.165264442
[41,] -0.074178975 3.584687e-02 0.215085757
[42,] -0.152846986 4.888412e-02 0.208115425
[43,] -0.141891873 3.985578e-02 0.166009573
[44,] -0.159462287 5.444816e-02 0.178853778
[45,] -0.158715561 4.292146e-02 0.177310218
[46,] -0.156082754 4.319227e-02 0.165715935
[47,] -0.122871402 2.245238e-02 0.144746766
[48,] -0.167491046 9.046903e-02 0.169384673
[49,] -0.172876436 4.360728e-02 0.183690496
[50,] -0.165022218 1.515998e-02 0.152781871
[51,] -0.124740477 -3.247868e-02 0.165806568
[52,] -0.167592094 1.105755e-02 0.199242267
[53,] -0.151462730 4.170003e-02 0.171040749
[54,] -0.144295252 2.612502e-02 0.156917423
[55,] -0.116615063 2.298325e-02 0.127934129
[56,] -0.157732930 4.836978e-02 0.178065651
[57,] -0.162009068 4.585564e-02 0.192702659
[58,] -0.167194267 4.605688e-02 0.175292497
[59,] -0.229176259 -1.807532e-02 0.189102813
[60,] -0.181488183 5.144078e-02 0.180207050
[61,] -0.111253255 -1.805006e-01 -0.110958702
[62,] -0.140653595 2.812871e-02 0.148856532
[63,] -0.162781543 -3.223590e-02 0.207584366
[64,] -0.161570156 7.224109e-02 0.169858480
[65,] -0.136593180 4.432723e-02 0.157210306
[66,] -0.162260090 4.491010e-02 0.161529749
[67,] -0.153691052 3.830571e-02 0.177082410
[68,] -0.154142614 4.088749e-02 0.180005514
[69,] -0.128382896 5.261555e-02 0.161255292
[70,] -0.174392980 3.271504e-02 0.202708854
[71,] -0.166383548 2.561491e-02 0.178513409
[72,] -0.175097520 6.001380e-02 0.203252992
[73,] -0.135221195 -7.016180e-02 0.025123202
[74,] -0.145199593 3.242216e-02 0.165297231
[75,] -0.257577218 1.115395e-01 0.130713831
[76,] -0.143134987 3.954627e-02 0.159770284
[77,] -0.158994999 3.806054e-02 0.172777739
[78,] -0.155894065 4.084216e-02 0.177038119
[79,] -0.136160409 1.554597e-02 0.155744883
[80,] -0.182671082 2.058888e-02 0.181786564
[81,] 0.048017902 1.486510e-01 0.108398858
[82,] -0.160946047 4.726803e-02 0.183222408
[83,] -0.156908898 5.007176e-02 0.152335593
[84,] -0.174771898 5.007399e-02 0.186112984
[85,] -0.152837185 4.206293e-03 0.176927576
[86,] -0.157838642 -1.653564e-03 0.167701892
[87,] -0.165879120 -2.694060e-02 0.239800436
[88,] -0.164537244 5.433231e-02 0.184074631
[89,] -0.171924973 6.230610e-02 0.215370570
[90,] -0.160163048 4.459817e-02 0.179350706
[91,] -0.171190513 7.087657e-02 0.218761631
[92,] -0.169280670 3.852616e-02 0.154684096
[93,] -0.168165348 5.827686e-02 0.155953855
[94,] -0.174938369 5.714916e-02 0.187200227
[95,] -0.152272731 4.427233e-02 0.174392388
[96,] -0.138232138 1.001604e-01 0.121202339
[97,] -0.168550231 3.753008e-02 0.160464809
[98,] -0.120629946 2.419728e-02 0.161153324
[99,] -0.147440861 3.214688e-02 0.161037182
[100,] -0.129510099 2.000678e-02 0.182330061
[101,] -0.135679631 2.959471e-02 0.174820865
[102,] -0.174670104 -7.632670e-03 0.213951719
[103,] -0.145973908 3.514066e-02 0.183569242
[104,] -0.131031056 -1.467965e-01 0.269121980
[105,] -0.152536556 3.996409e-02 0.157585164
[106,] -0.171884194 3.238828e-02 0.175367842
[107,] -0.159150875 4.755613e-02 0.179234989
[108,] -0.182602830 6.913114e-02 0.200897143
[109,] -0.165551749 3.990540e-02 0.167584362
[110,] -0.144706519 4.314174e-02 0.167704282
[111,] -0.150581196 3.694528e-02 0.160624105
[112,] -0.158629488 4.127708e-02 0.175966163
[113,] -0.138392735 4.643119e-02 0.164863717
[114,] -0.168823227 2.441535e-03 0.199498014
[115,] -0.121565535 1.808948e-02 0.169117258
[116,] -0.152393115 3.918009e-02 0.178660558
[117,] -0.150439477 2.662832e-02 0.164317171
[118,] -0.158490980 7.601531e-02 0.212731360
[119,] -0.147727430 4.354792e-02 0.167414694
[120,] -0.213905974 1.607444e-01 0.312151950
[121,] -0.143964449 -8.264399e-03 0.117014388
[122,] -0.168408715 3.414518e-02 0.307424957
[123,] -0.158166766 5.986416e-02 0.165441867
[124,] -0.167109630 4.476924e-02 0.168001584
[125,] -0.145031621 3.513256e-02 0.155035291
[126,] -0.211016027 6.060014e-02 0.154001697
[127,] -0.147346936 3.427756e-02 0.159599040
[128,] -0.188240311 4.741420e-02 0.159158020
[129,] -0.143925345 2.551550e-02 0.161121737
[130,] -0.155075413 5.266236e-02 0.168862306
[131,] -0.127020866 3.969389e-02 0.136890691
[132,] -0.171102981 5.142901e-02 0.184509063
[133,] -0.157697494 4.612010e-02 0.184771696
[134,] -0.148997155 -1.013087e-02 0.130059911
[135,] -0.144254131 5.883930e-02 0.213814123
[136,] -0.148012153 9.956160e-02 0.183274847
[137,] -0.145949130 5.370636e-02 0.153969863
[138,] -0.143079495 3.941801e-02 0.178857817
[139,] -0.166959785 6.484646e-02 0.168172594
[140,] -0.127068354 3.101841e-03 0.160881108
[141,] -0.178417093 5.050191e-02 0.186328600
[142,] -0.151433906 3.110283e-02 0.181685160
[143,] -0.159248561 5.363325e-02 0.182255723
[144,] -0.152516243 4.684020e-02 0.172212564
[145,] -0.106281366 6.283001e-02 0.143896297
[146,] -0.161824232 3.392577e-02 0.159072526
[147,] -0.123539647 3.858826e-02 0.178063900
[148,] -0.135591529 2.919151e-02 0.157745217
[149,] -0.158050341 3.863846e-02 0.161619291
[150,] -0.138075775 3.332166e-02 0.154500408
[151,] -0.129209523 3.017463e-02 0.154332210
[152,] -0.151641348 4.077486e-02 0.175994689
[153,] -0.129516390 2.108079e-02 0.164882571
[154,] -0.104146466 3.503229e-02 0.172319039
[155,] -0.167735163 5.712239e-02 0.186106001
[156,] -0.172550779 5.001271e-02 0.181146946
[157,] -0.196633813 6.245122e-02 0.169417916
[158,] -0.149906585 3.881779e-02 0.176359488
[159,] -0.147588001 4.832196e-02 0.144797969
[160,] -0.181997358 5.576501e-02 0.186160060
[161,] -0.150589676 5.140404e-02 0.134057208
[162,] -0.164843824 5.012518e-02 0.183563301
[163,] -0.331912456 9.047939e-02 0.041158960
[164,] -0.144264455 3.036096e-03 0.102921690
[165,] -0.125554554 3.251832e-02 0.145577461
[166,] -0.187448501 6.646321e-02 0.158734452
[167,] -0.174660474 6.375285e-02 0.199334532
[168,] -0.143506468 4.024924e-02 0.156775102
[169,] -0.134781517 6.308310e-02 0.138627746
[170,] -0.182723286 6.232170e-02 0.150444110
[171,] -0.145446754 2.191039e-02 0.154993152
[172,] 0.154364640 1.342932e-02 0.130234479
[173,] -0.174122026 4.555385e-02 0.179402571
[174,] -0.133383740 1.784596e-02 0.151886990
[175,] -0.174330497 5.512036e-02 0.199272164
[176,] -0.156771382 3.705750e-02 0.183593797
[177,] -0.100209361 3.060724e-02 0.146876843
[178,] -0.176283718 5.594027e-02 0.186304574
[179,] -0.146131056 4.410532e-02 0.177423110
[180,] -0.144401028 3.945207e-02 0.176501660
[181,] -0.032892450 -3.125305e-01 -0.418850235
[182,] -0.157381971 7.325620e-02 0.167969807
[183,] -0.148189745 2.169886e-02 0.186469723
[184,] -0.125650076 6.415526e-04 0.153829480
[185,] -0.208360063 5.560265e-02 0.165008944
[186,] -0.161212090 -6.364242e-03 0.199471731
[187,] -0.136724424 2.458988e-02 0.157607085
[188,] -0.159021359 4.888885e-02 0.187487517
[189,] -0.156037395 2.355556e-02 0.168833458
[190,] -0.140944662 3.764433e-02 0.173864748
[191,] -0.171031364 4.409998e-02 0.183881276
[192,] -0.182644456 3.785164e-02 0.197755002
[193,] -0.174679118 3.434302e-02 0.188287220
[194,] -0.168055570 9.482341e-02 0.138533866
[195,] -0.159517743 5.703043e-02 0.173625836
[196,] -0.243306624 7.453427e-02 0.160685668
[197,] -0.130135745 -1.051370e-02 0.163139691
[198,] -0.027606486 4.243607e-02 0.172416891
[199,] -0.158034858 5.200346e-02 0.164054811
[200,] -0.151114563 3.313238e-02 0.175979841
[201,] 0.500000000 -3.572069e-02 0.307695927
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[1] 1.496685
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