Related
I cannot figure out a precise value of a tick location because I do not know how the scale works. For example, in the following scenario:
> dput(df_partial_2)
structure(list(v = 8:400, Tv_partial = c(7.98105946849764, 8.73878705524418,
9.47352664242238, 10.1859798998468, 10.8768274522901, 11.546729501371,
12.1963264293038, 12.826239385031, 13.4370708532459, 14.0294052067967,
14.6038092429507, 15.1608327039841, 15.7010087825473, 16.2248546122473,
16.7328717438707, 17.2255466076639, 17.7033509620725, 18.1667423293303,
18.6161644182794, 19.0520475347892, 19.4748089801349, 19.8848534376828,
20.2825733482202, 20.6683492742624, 21.0425502536523, 21.405534142766,
21.7576479496252, 22.0992281572083, 22.4306010372483, 22.7520829547891,
23.0639806637737, 23.3665915939217, 23.6602041291518, 23.9450978777947,
24.2215439348345, 24.489805136414, 24.7501363068249, 25.0027844982076,
25.2479892231676, 25.4859826805202, 25.7169899743615, 25.941229326661,
26.1589122835664, 26.3702439156033, 26.5754230119487, 26.7746422689521,
26.9680884730723, 27.1559426783938, 27.3383803788816, 27.515571675528,
27.6876814385425, 27.8548694647289, 28.0172906301918, 28.1750950385095,
28.3284281645058, 28.4774309937505, 28.6222401579151, 28.7629880661037,
28.8998030322791, 29.0328093988977, 29.1621276568663, 29.2878745619276,
29.4101632475811, 29.5291033346404, 29.6448010375253, 29.7573592673884,
29.8668777321649, 29.9734530336404, 30.0771787616219, 30.1781455852996,
30.2764413418811, 30.3721511225791, 30.4653573560312, 30.5561398892264,
30.6445760660137, 30.7307408032637, 30.8147066647521, 30.8965439328325,
30.9763206779655, 31.0541028261659, 31.1299542244299, 31.2039367042032,
31.2761101429469, 31.3465325238588, 31.4152599938029, 31.4823469195027,
31.5478459420476, 31.611808029764, 31.6742825294991, 31.7353172163643,
31.7949583419839, 31.8532506812946, 31.9102375779375, 31.9659609882845,
32.0204615241418, 32.0737784941661, 32.1259499440361, 32.1770126954122,
32.227002383724, 32.2759534948179, 32.3238994005003, 32.3708723930087,
32.4169037184423, 32.4620236091842, 32.5062613153437, 32.5496451352497,
32.5922024450215, 32.6339597272468, 32.674942598791, 32.715175837766,
32.7546834096823, 32.7934884928088, 32.8316135027644, 32.8690801163648,
32.9059092947446, 32.9421213057798, 32.9777357458282, 33.0127715608099,
33.0472470666478, 33.0811799690861, 33.1145873829068, 33.14748585056,
33.1798913602291, 33.2118193633436, 33.2432847915594, 33.2743020732209,
33.3048851493212, 33.3350474889736, 33.3648021044129, 33.3941615655357,
33.4231380139978, 33.4517431768788, 33.4799883799295, 33.5078845604127,
33.5354422795497, 33.5626717345866, 33.5895827704883, 33.6161848912738,
33.642487271004, 33.6684987644302, 33.6942279173145, 33.7196829764334,
33.7448718992726, 33.7698023634215, 33.7944817756786, 33.8189172808753,
33.843115770427, 33.8670838906179, 33.8908280506314, 33.9143544303296,
33.937668987792, 33.9607774666199, 33.9836854030141, 34.0063981326306,
34.0289207972252, 34.0512583510889, 34.0734155672827, 34.0953970436786,
34.1172072088102, 34.138850327541, 34.1603305065546, 34.1816516996727,
34.2028177130061, 34.2238322099433, 34.2446987159822, 34.2654206234098,
34.2860011958333, 34.3064435725688, 34.3267507728909, 34.346925700147,
34.3669711457419, 34.3868897929958, 34.4066842208781, 34.4263569076246,
34.4459102342371, 34.4653464878726, 34.484667865123, 34.5038764751908,
34.5229743429622, 34.541963411981, 34.5608455473279, 34.5796225384059,
34.5982961016364, 34.6168678830676, 34.6353394608986, 34.6537123479216,
34.6719879938843, 34.6901677877762, 34.708253060039, 34.7262450847056,
34.7441450814691, 34.761954217683, 34.7796736102968, 34.7973043277266,
34.8148473916649, 34.8323037788297, 34.8496744226562, 34.8669602149322,
34.8841620073785, 34.901280613177, 34.9183168084477, 34.9352713336757,
34.9521448950907, 34.9689381660001, 34.9856517880761, 35.0022863726003,
35.0188425016658, 35.0353207293377, 35.0517215827748, 35.0680455633125,
35.0842931475085, 35.1004647881526, 35.1165609152417, 35.1325819369209,
35.1485282403922, 35.1644001927908, 35.1801981420321, 35.1959224176277,
35.2115733314733, 35.2271511786088, 35.2426562379515, 35.2580887730034,
35.2734490325325, 35.288737251231, 35.3039536503486, 35.3190984383043,
35.3341718112745, 35.3491739537616, 35.3641050391398, 35.3789652301832,
35.3937546795724, 35.4084735303836, 35.4231219165597, 35.437699963363,
35.4522077878117, 35.4666454990999, 35.4810131990013, 35.4953109822585,
35.5095389369564, 35.5236971448821, 35.537785681871, 35.5518046181384,
35.5657540186003, 35.5796339431791, 35.5934444470997, 35.6071855811722,
35.6208573920644, 35.6344599225624, 35.6479932118224, 35.66145729561,
35.6748522065322, 35.6881779742576, 35.7014346257297, 35.7146221853696,
35.7277406752709, 35.7407901153869, 35.7537705237088, 35.7666819164374,
35.7795243081463, 35.792297711939, 35.8050021395982, 35.81763760173,
35.8302041078994, 35.8427016667617, 35.8551302861874, 35.8674899733808,
35.8797807349937, 35.8920025772338, 35.9041555059675, 35.9162395268184,
35.9282546452606, 35.9402008667078, 35.9520781965976, 35.963886640472,
35.9756262040536, 35.9872968933178, 35.9988987145614, 36.0104316744679,
36.0218957801686, 36.0332910393006, 36.0446174600623, 36.0558750512647,
36.0670638223806, 36.0781837835905, 36.0892349458256, 36.1002173208092,
36.111130921094, 36.1219757600986, 36.1327518521402, 36.1434592124663,
36.1540978572838, 36.1646678037854, 36.1751690701755, 36.1856016756927,
36.1959656406317, 36.2062609863626, 36.2164877353493, 36.2266459111657,
36.2367355385108, 36.2467566432224, 36.2567092522888, 36.2665933938604,
36.2764090972585, 36.2861563929844, 36.2958353127264, 36.3054458893661,
36.3149881569836, 36.3244621508616, 36.3338679074887, 36.3432054645623,
36.352474860989, 36.3616761368869, 36.3708093335841, 36.3798744936191,
36.3888716607389, 36.3978008798968, 36.4066621972502, 36.4154556601571,
36.4241813171723, 36.4328392180434, 36.4414294137055, 36.4499519562765,
36.4584068990513, 36.4667942964954, 36.4751142042391, 36.4833666790704,
36.4915517789274, 36.499669562892, 36.507720091181, 36.5157034251392,
36.5236196272302, 36.5314687610289, 36.5392508912119, 36.5469660835497,
36.5546144048966, 36.5621959231825, 36.5697107074028, 36.5771588276094,
36.584540354901, 36.5918553614133, 36.5991039203094, 36.6062861057698,
36.6134019929824, 36.620451658133, 36.6274351783945, 36.6343526319172,
36.6412040978187, 36.6479896561739, 36.6547093880043, 36.6613633752684,
36.667951700851, 36.6744744485537, 36.6809317030839, 36.6873235500453,
36.6936500759276, 36.6999113680962, 36.7061075147822, 36.7122386050729,
36.7183047289007, 36.7243059770343, 36.7302424410682, 36.7361142134128,
36.7419213872849, 36.7476640566979, 36.7533423164519, 36.7589562621244,
36.7645059900605, 36.7699915973636, 36.7754131818859, 36.7807708422192,
36.7860646776854, 36.7912947883274, 36.7964612749003, 36.8015642388619,
36.8066037823638, 36.811580008243, 36.8164930200124, 36.8213429218528,
36.8261298186035, 36.8308538157543, 36.8355150194369, 36.8401135364163,
36.8446494740827, 36.849122940443, 36.853534044113, 36.8578828943088,
36.8621696008394, 36.8663942740982, 36.8705570250556, 36.8746579652508,
36.8786972067844, 36.8826748623109, 36.8865910450307), upper = c(8.03359225925823,
8.80857834632081, 9.5612639540498, 10.2924319542762, 11.0027615088121,
11.6928792116129, 12.3633783233509, 13.0148273942128, 13.6477746695034,
14.2627505985141, 14.8602694075212, 15.4408301755264, 16.0049176292822,
16.5530027709442, 17.085543401016, 17.6029845727229, 18.1057589993884,
18.5942874281687, 19.0689789887631, 19.5302315225719, 19.9784318961527,
20.4139563015338, 20.8371705451927, 21.2484303270819, 21.6480815106972,
22.0364603848133, 22.4138939176628, 22.7807000039433, 23.1371877048629,
23.483657481973, 23.8204014245163, 24.1477034710795, 24.4658396252724,
24.7750781659481, 25.0756798521194, 25.3678981224866, 25.6519792899843,
25.9281627314614, 26.1966810723811, 26.4577603670466, 26.7116202742093,
26.9584742281375, 27.1985296055078, 27.4319878880867, 27.6590448211454,
27.8798905679742, 28.0947098605409, 28.303682146198, 28.5069817307874,
28.7047779179796, 28.8972351451356, 29.0845131157104, 29.2667669283157,
29.4441472022976, 29.6168002003046, 29.7848679474905, 29.9484883479501,
30.1077952978449, 30.2629187955558, 30.4139850494996, 30.5611165825133,
30.7044323337553, 30.8440477582857, 30.9800749232191, 31.1126226023811,
31.2417963677869, 31.3676986784984, 31.4904289682926, 31.610083729402,
31.7267565955176, 31.8405384216734, 31.9515173620422, 32.0597789462855,
32.1654061533981, 32.2684794831148, 32.3690770267303, 32.4672745344442,
32.5631454822052, 32.6567611359263, 32.7481906140996, 32.837500949199,
32.924757146882, 33.0100222434937, 33.0933573629117, 33.1748217705806,
33.2544729270661, 33.3323665397096, 33.4085566127212, 33.4830954965083,
33.5560339350466, 33.6274211119235, 33.6973046960334, 33.7657308845263,
33.8327444461067, 33.8983887619512, 33.9627058662137, 34.0257364851272,
34.0875200750857, 34.1480948594313, 34.2074978650149, 34.2657649565552,
34.3229308710607, 34.3790292508966, 34.4340926756696, 34.4881526941562,
34.5412398538176, 34.5933837311924, 34.6446129601967, 34.6949552603321,
34.7444374635548, 34.7930855410287, 34.8409246284613, 34.8879790518782,
34.9342723507123, 34.9798273022007, 35.0246659442585, 35.0688095978648,
35.1122788884366, 35.155093766912, 35.1972735304098, 35.2388368426575,
35.2798017523627, 35.3201857126241, 35.3600055990019, 35.3992777278467,
35.4380178729083, 35.4762412824328, 35.5139626950424, 35.5511963569724,
35.5879560358473, 35.6242550362788, 35.660106214586, 35.6955219932856,
35.7305143739968, 35.7650949511975, 35.799274924944, 35.8330651144483,
35.8664759690332, 35.8995175805539, 35.9321996949078, 35.9645317237364,
35.9965227545901, 36.0281815616323, 36.0595166157857, 36.0905360958059,
36.1212478965051, 36.1516596385052, 36.181778677794, 36.2116121145547,
36.2411668014046, 36.2704493514818, 36.2994661468907, 36.3282233466523,
36.3567268944537, 36.3849825252517, 36.4129957724961, 36.4407719758422,
36.4683162877621, 36.4956336789202, 36.5227289452774, 36.5496067144771,
36.576271451485, 36.6027274639768, 36.6289789077896, 36.6550297930879,
36.680883989219, 36.7065452293272, 36.7320171152315, 36.7573031227545,
36.7824066060878, 36.8073308017407, 36.8320788325874, 36.8566537133383,
36.8810583533731, 36.9052955606898, 36.9293680454236, 36.9532784242442,
36.9770292236016, 37.0006228824751, 37.0240617555395, 37.0473481170782,
37.0704841638112, 37.0934720175169, 37.1163137271682, 37.1390112728497,
37.1615665679841, 37.1839814617295, 37.2062577405082, 37.2283971318262,
37.2504013057289, 37.2722718773406, 37.2940104076643, 37.3156184070184,
37.3370973368792, 37.358448611312, 37.3796735974135, 37.4007736195177,
37.421749959301, 37.4426038580381, 37.4633365164149, 37.4839490983855,
37.5044427309976, 37.5248185065204, 37.5450774822177, 37.5652206837748,
37.5852491045726, 37.6051637081801, 37.6249654278839, 37.6446551690956,
37.6642338095978, 37.6837022011351, 37.703061169198, 37.7223115139911,
37.741454012788, 37.7604894191547, 37.7794184641224, 37.7982418559697,
37.8169602831027, 37.8355744125794, 37.8540848919306, 37.872492348051,
37.8907973901634, 37.9090006082374, 37.9271025750828, 37.9451038444129,
37.9630049547664, 37.9808064261408, 37.9985087637145, 38.0161124549964,
38.0336179734073, 38.0510257756606, 38.0683363048293, 38.0855499870236,
38.1026672357657, 38.1196884486032, 38.1366140107796, 38.1534442910924,
38.1701796470854, 38.1868204204564, 38.2033669415581, 38.2198195249735,
38.2361784746205, 38.2524440791669, 38.2686166160704, 38.2846963481008,
38.3006835261952, 38.3165783890704, 38.3323811614011, 38.3480920564971,
38.3637112736246, 38.3792390009633, 38.3946754130837, 38.4100206728362,
38.4252749293159, 38.4404383204303, 38.4555109705401, 38.4704929925236,
38.4853844850299, 38.5001855362607, 38.5148962198147, 38.5295165982694,
38.5440467200941, 38.5584866218206, 38.5728363271117, 38.5870958472277,
38.6012651793252, 38.6153443093285, 38.629333208128, 38.6432318360453,
38.6570401376072, 38.670758046363, 38.684385481021, 38.6979223479721,
38.7113685398104, 38.7247239349367, 38.7379884000929, 38.7511617857575,
38.7642439311501, 38.7772346590262, 38.7901337808324, 38.8029410919209,
38.8156563751269, 38.8282793970572, 38.8408099121518, 38.8532476581625,
38.865592361234, 38.877843729249, 38.8900014587311, 38.9020652284304,
38.9140347046908, 38.9259095360921, 38.9376893586157, 38.9493737905985,
38.9609624369689, 38.9724548850766, 38.9838507088844, 38.9951494636204,
39.0063506910751, 39.0174539163475, 39.0284586462466, 39.0393643745615,
39.05017057558, 39.0608767095718, 39.0714822171156, 39.0819865251073,
39.0923890401102, 39.1026891543754, 39.1128862395446, 39.1229796535302,
39.1329687326205, 39.1428527984061, 39.1526311517042, 39.1623030775114,
39.1718678404131, 39.1813246883321, 39.1906728477217, 39.199911528907,
39.2090399205426, 39.2180571938361, 39.2269624992342, 39.2357549667289,
39.2444337083123, 39.2529978130782, 39.2614463525713, 39.2697783738833,
39.2779929070221, 39.28608895693, 39.2940655099318, 39.3019215280794,
39.3096559535962, 39.3172677037989, 39.3247556757764, 39.3321187408153,
39.3393557498253, 39.3464655268798, 39.3534468740051, 39.3602985675711,
39.3670193603561, 39.3736079784372, 39.3800631235048, 39.3863834698938,
39.3925676666143, 39.3986143351158, 39.4045220686833, 39.4102894343671,
39.4159149688177, 39.4213971814072, 39.4267345508319, 39.4319255263988,
39.4369685255292, 39.4418619360456, 39.4466041125389, 39.451193377326,
39.4556280194739, 39.4599062940958, 39.4640264210152, 39.4679865851237,
39.471784934444, 39.4754195799749, 39.4788885944803, 39.4821900115524,
39.4853218247947, 39.4882819872413, 39.4910684089741, 39.4936789576808,
39.4961114568045, 39.4983636822029, 39.5004333662267, 39.5023181900198,
39.5040157873157, 39.5055237408116, 39.5068395794376, 39.5079607785615,
39.5088847588695, 39.5096088825276, 39.5101304540473, 39.5104467142662,
39.5105548434037, 39.5104519552204, 39.510135096546, 39.5096012441735,
39.5088473033011, 39.5078701034415, 39.5066663979697, 39.5052328591409,
39.5035660760377, 39.5016625518232, 39.4995186993156, 39.4971308389636,
39.494495193108, 39.4916078852114, 39.4884649309263, 39.4850622390609
), lower = c(7.92852667773705, 8.66899576416754, 9.38578933079495,
10.0795278454174, 10.7508933957681, 11.4005797911291, 12.0292745352567,
12.6376513758492, 13.2263670369884, 13.7960598150793, 14.3473490783802,
14.8808352324417, 15.3970999358125, 15.8967064535504, 16.3802000867254,
16.8481086426048, 17.3009429247567, 17.7391972304919, 18.1633498477956,
18.5738635470064, 18.9711860641172, 19.3557505738318, 19.7279761512478,
20.088268221443, 20.4370189966073, 20.7746079007188, 21.1014019815875,
21.4177563104733, 21.7240143696337, 22.0205084276052, 22.3075599030311,
22.5854797167639, 22.8545686330312, 23.1151175896412, 23.3674080175496,
23.6117121503413, 23.8482933236656, 24.0774062649539, 24.2992973739542,
24.5142049939938, 24.7223596745136, 24.9239844251844, 25.119294961625,
25.3084999431199, 25.491801202752, 25.66939396993, 25.8414670856036,
26.0082032105896, 26.1697790269758, 26.3263654330763, 26.4781277319494,
26.6252258137474, 26.767814332068, 26.9060428747215, 27.040056128707,
27.1699940400104, 27.2959919678801, 27.4181808343625, 27.5366872690024,
27.6516337482958, 27.7631387312192, 27.8713167900999, 27.9762787368766,
28.0781317460617, 28.1769794726695, 28.2729221669899, 28.3660567858314,
28.4564770989883, 28.5442737938418, 28.6295345750816, 28.7123442620887,
28.792784883116, 28.8709357657768, 28.9468736250546, 29.0206726489125,
29.0924045797971, 29.16213879506, 29.2299423834597, 29.2958802200047,
29.3600150382321, 29.4224074996608, 29.4831162615243, 29.5421980424001,
29.5997076848059, 29.6556982170252, 29.7102209119393, 29.7633253443856,
29.8150594468069, 29.8654695624899, 29.9146004976819, 29.9624955720443,
30.0091966665558, 30.0547442713486, 30.0991775304623, 30.1425342863324,
30.1848511221186, 30.226163402945, 30.2665053157387, 30.3059099080167,
30.3444091246209, 30.3820338444454, 30.4188139149567, 30.454778185988,
30.4899545426987, 30.5243699365313, 30.5580504166818, 30.5910211588507,
30.623306494297, 30.6549299372498, 30.6859142119773, 30.7162812783359,
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31.818685512097, 31.8343676388765, 31.8499572576007, 31.8654571623394,
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32.6503719273791, 32.6628034562844, 32.6751919218421, 32.6875371964082,
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33.3155576550292, 33.3252222334887, 33.3348422803843, 33.344418112939,
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ggplot(df_partial_2, aes(log(log(v)))) + theme_bw() + xlab("v") + ylab(bquote(lnT[v])) + scale_x_continuous(labels = ~floor(exp(exp(.))), sec.axis=sec_axis(~., name = "ln ln v")) +
geom_line(aes(y=log(upper)), linetype="dashed") +
geom_line(aes(y=log(Tv_partial))) +
geom_line(aes(y=log(lower)), linetype="dashed")
library("grid")
grid.lines(x = unit(c(0, 0), "npc"), y = unit(c(0.05, 0.1), "npc")) # line
grid.lines(x = unit(c(1, 1), "npc"), y = unit(c(0.05, 0.1), "npc")) # line
grid.text("<- unit(c(0, 0)) is here", 0.01, .075, just=c("left", "bottom"))
grid.text("unit(c(1, 1)) is here ->", 0.84, .075, just=c("left", "bottom"))
grid.lines(x = unit(c(0.4, 0.4), "npc"), y = unit(c(0.05, 0.1), "npc")) # line
grid.text("What is the value of v at this tick?", .3, .11,just=c("left", "bottom"))
As shown in the plot, the function grid put the ticks at a location based on a scaled percentage of the entire plot panel (not the axis). In other words, unit(c(0.4, 0.4)) on x means the tick is at the 40%-60% separation of the entire plot panel, not of the axis. As a consequence, I don't know what is the actual value on the axis for the tick location.
Is there a way to figure out what is the axis value of the tick location?
Or, if I want a small tick to be add onto v = 18 in the plot, is there a way to do it?
Any help is appreciated. Thank you!
There's no consistent answer. Per the grid::unit() docs, "all drawing occurs relative to a viewport." Which means the location will change based on the viewport aspect ratio (and maybe other factors too). For instance, in your example, the tick is about 2/3 between 11 and 27. But if my viewport has a lower aspect ratio, the same code puts the tick about halfway between 11 and 27:
If you're trying to add an extra tick mark, specify breaks including the extra tick within scale_x_continuous():
ggplot(df_partial_2, aes(log(log(v)))) +
geom_line(aes(y=log(upper)), linetype="dashed") +
geom_line(aes(y=log(Tv_partial))) +
geom_line(aes(y=log(lower)), linetype="dashed") +
theme_bw() +
xlab("v") +
ylab(bquote(lnT[v])) +
scale_x_continuous(
labels = ~floor(exp(exp(.))),
breaks = c(.9, 1.1, 1.2, 1.5, 1.8),
sec.axis=sec_axis(~., breaks = c(.9, 1.1, 1.2, 1.5, 1.8), name = "ln ln v")
)
I have a dataframe with observations of a temporal event. I can easily plot the observations based on their Xand Y values, either in base R or ggplot2:
plot(df$Y ~ df$X)
ggplot(df, aes(x=X, y=Y)) +
geom_point()
What I'd like to do though is add in the temporal dimension by coloring the observations differently depending on the time they were made. This could be done by defining thresholds for different time steps and assigning discrete colors to each time step. But what I'm interested in is a continuous coloring where the flow of time can be directly read off the flow of colors or color hues or color transparencies. Any help is greatly appreciated.
Reproducible data (slightly shorter than data underlying shown graphs):
structure(list(X = c(171.000358830368, 171.453956550099, 171.075127685269,
171.140924277581, 171.271520544141, 171.582558980529, 171.23762532992,
171.70218914837, 171.318375693213, 170.939546828382, 171.70218914837,
171.779948757467, 171.809856299427, 172.066064242221, 171.603494259901,
171.718139837416, 171.947430992445, 171.930483385334, 172.002261486039,
172.153793031971, 122.654817251517, 171.710164492893, 172.012230666692,
171.395138384244, 171.750041215507, 171.631407965731, 171.927492631138,
172.059085815763, 171.816834725885, 170.787018364384, 170.328436054326,
170.083194210252, 170.405198745358, 170.505887469957, 170.429124778926,
171.187779426653, 171.00634033876, 170.984408141322, 170.731190952725,
170.924593057402, 170.570687144205, 170.751129314032, 170.539782684179,
170.561714881617, 170.461026157017, 170.631499146191, 170.686329639785,
170.863781055416, 170.782033774058, 170.655425179759, 170.645455999106,
170.612557702949, 170.658415933955, 170.514859732545, 170.382269629855,
170.167932245806, 170.187870607113, 169.841940038438, 175.365863038509,
190.973612269532, 206.626222813496, 214.924568789419, 214.509850874236,
211.538038121446, 209.610995501136, 207.007045514458, 204.585531533737,
202.489012842319, 200.693563406635, 199.331773329375, 198.61997383072,
198.494362154486, 202.238786407918, 205.8695620019, 206.616253632843,
207.53541208909, 208.81146721273, 209.850255836818, 210.903998231887,
211.630751501523, 211.825150524265, 211.487195300113, 210.759445112412,
209.407624215806, 207.816542983517, 205.843642132201, 203.585622714198,
201.110275157949, 198.862224920598, 196.914247020916, 195.676074783759,
195.283289066014, 196.015026925976, 197.60710507633, 200.479226022586,
204.110001616568, 207.405812740595, 210.878078362188, 214.015379513825,
216.768867210305, 218.423751198776, 219.404718575074, 219.467524413191,
218.760709504862, 217.317172146244, 215.572565531892, 213.46408382369,
211.338654508377, 209.181323814973, 207.720838849244, 206.537497105681,
205.904454134187, 205.898472625795, 205.953303119389, 206.365030280376,
206.977137972497, 208.319986606516, 209.067675155523, 209.547192744954,
210.106463779612, 210.356690214013, 210.602928976153, 210.692651602034,
210.849167738293, 210.88405987058, 210.998705448095, 211.037585252643,
210.902004395756, 210.895025969299, 210.958828725481, 210.92692734739,
210.975776332592, 211.201079815359, 211.164193846942, 211.304759294155,
210.646793371028, 198.816366689593, 179.579835700717, 164.568243472769,
159.956500502489, 159.636489803513, 159.535801078913, 159.997374143168,
160.238628314981, 160.281495791791, 160.576583539133, 160.637395541118,
156.724492134644, 153.810500629644, 153.846389679996, 154.022844177562,
154.29300897327, 154.442546683072, 154.536256981214, 154.665856329709,
154.665856329709, 154.833338564686, 156.847113056681, 176.676810294436,
177.112463488991, 176.71868085318, 176.042770404877, 175.822451512436,
175.75964567432, 176.817375741649, 176.028813551962, 176.347827332872,
176.622976718907, 182.215687065486, 118.910392998086, 174.380907989949,
171.889609744655, 168.855988071813, 164.924143222097, 160.275514283399,
156.671655477181, 154.165403460906, 107.676123319726, 107.769833617868,
108.581324923058, 109.676937876871, 109.244275436511, 110.393721965853,
161.248506315174, 163.97707106002, 165.507340290323, 166.298893234206,
168.008607716271, 169.06434394747, 170.018394536004, 170.41118025375,
170.202824378093, 170.201827460028, 121.025853132745, 117.483803246579,
120.870333914552, 166.984772863163, 166.489304584687, 168.118268703459,
181.382263562859, 196.653054487796, 135.095357788943, 135.297732156208,
202.44614536551, 203.460011037964, 204.440978414263, 205.227546767819,
205.43490572541, 204.935449774673, 203.891676560258, 202.264706277617,
199.827241607851, 176.081650209426, 194.729002621683, 194.670184455827,
191.186952735516, 190.463190220076, 190.508051533017, 191.482040482858,
186.606114225261, 171.208714706025, 158.889798172571, 149.82880987666,
152.986049389604, 156.597883540345, 159.647455902232, 161.754940692369,
162.893421122992, 114.542894953814, 162.976165322415, 114.268742485845,
160.762010299286, 159.259654774813, 157.995562667957, 156.561994489993,
155.638848361484, 154.469463470836, 154.00390273432, 154.431580584353,
154.255126086787, 155.244068807608, 157.058459686534, 159.101144802424,
161.906472238301, 165.29399982434, 120.406767014167, 172.028181355737,
175.03588315888, 177.740521870158, 179.910812498411, 181.483949205524,
181.988389746588, 181.854802725832, 180.508963337618, 178.901931416283,
176.58609075049, 173.537515306668, 170.679351213327, 167.374567826712,
164.487493109477, 162.203553821774, 160.569605112675, 159.562717866678,
159.828894990125, 159.632502131252, 160.2495944137, 161.450880682439,
162.705003608642, 164.622077048298, 166.212161362521, 167.468278124855,
168.602770883216, 169.155063491416, 169.462114255542, 169.404293007752,
169.003531945484, 168.422328713389, 167.728473739909, 166.825265972708,
165.984864043623, 169.386348482576, 183.504702123976, 200.99862033463,
214.553715269111, 218.552353629205, 217.590327696148, 217.000152201465,
216.115885877505, 215.405083296914, 214.675339273083, 214.063231580962,
213.56477254829, 212.972603217475, 212.488101037718, 212.097309156103,
211.685581995116, 211.786270719716, 211.46426618461, 210.97178866033,
210.657759469747, 210.36167480434, 210.032691842776, 209.635918452769,
209.435537921635, 209.197274504018, 209.046739876151, 208.712772324261,
208.585166811897, 208.3319496233, 203.956476234505, 189.73444311431,
179.21097601654, 176.815381905519, 177.826256823777, 175.90718954799,
175.461567172782, 177.582011897768, 177.488301599626, 177.463378647992,
177.577027307441, 177.676719113976, 177.633851637166, 177.843204430888,
177.995732894886, 177.92196095805, 176.699739409939, 176.824354168107,
176.859246300394, 176.68877331122, 175.325986315895, 176.695751737677,
174.103764767783, 176.520294158177, 178.304777495142, 176.684785638959,
176.697745573808, 177.861148956064, 176.614004456319, 176.121526932039,
176.364774939983, 173.25239673998, 176.064702602315, 174.207444246579,
174.133672309744, 173.831606135945, 174.066878799366, 174.03597433934,
175.830426856959, 174.100774013587, 174.019026732229, 173.965193156701,
173.955223976047, 174.028995912883, 173.886436629538, 174.420784712563,
179.872929611928, 198.741597834692, 208.031877285631, 208.418681494985,
208.232257816765, 247.112062365176, 207.772678588642, 207.722832685375,
207.639091567886, 207.613171698187, 207.569307303312, 207.722832685375,
207.850438197739, 208.002966661736, 208.157488961865, 208.43463218403,
208.722741504914, 209.112536468464, 209.628940026312, 210.13038981318,
211.046557515231, 211.660659043483, 212.448224315105, 213.349438246175,
212.024534137333, 215.36321273817, 216.563502088844, 217.81264042472,
217.271313915238, 218.686937568026, 220.266055783531, 221.81426953901,
223.14814591044, 224.246749618449, 225.106092990776, 225.724182191289,
226.127934007753, 226.088057285139, 225.885682917874, 225.557696874376,
225.048271742986, 257.697338382997, 223.992535511786, 223.464168937154,
223.130201385264, 222.831125965661), Y = c(150.561649721083,
150.067708443465, 150.155166858818, 149.178216605502, 149.407794945803,
148.660423032789, 148.913853668186, 148.276798619991, 148.487493893341,
147.692417390134, 148.3284785927, 147.692417390134, 147.963737246853,
147.216365333839, 147.264069924031, 145.992941364529, 145.626212327424,
144.316323788391, 144.345145311632, 143.45465962804, 118.779460351005,
143.071035215242, 143.299619709914, 142.858352250634, 142.574112400738,
141.615051368744, 141.139993158078, 140.643070343573, 140.190870582374,
140.33597204421, 140.341935117984, 139.946384557638, 140.207765958067,
139.045960417756, 139.269575684283, 138.122677828407, 138.177339338002,
137.268964433088, 137.874216421154, 137.406115129891, 138.076960929472,
137.840425669768, 138.343311558047, 137.691348825417, 138.413874597706,
137.837444132881, 138.70109598449, 138.061059399408, 138.395985376384,
137.616810403241, 138.267779290242, 137.52736429663, 138.054102480005,
137.291822882555, 137.941797923927, 137.242130601105, 137.811604146527,
137.343502855264, 137.326607479571, 135.242513195539, 137.238155218589,
138.312502343547, 139.236778778526, 138.86110513076, 139.273551066799,
138.584816045896, 138.903840492808, 137.509475075308, 137.144733729462,
135.697694493625, 135.567500716225, 134.488184363121, 135.142134787009,
134.959267191271, 135.420411563131, 134.819134957581, 135.649989903432,
135.13120248509, 136.041565081262, 135.646014520916, 136.444072561011,
135.969014350344, 136.521592520073, 135.799066747784, 136.416244883398,
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133.129597388266, 133.61658174648, 133.007354375898, 133.341286507245,
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You could do:
library(ggplot2)
ggplot(df, aes(x = X, y = Y, color = starttime_ms)) +
geom_point() +
scale_color_gradientn(colors = c("red", "gold", "forestgreen"), name = "time")
An alternative that might help keep track of the motion better would be to use geom_segment:
df$X2 <- dplyr::lag(df$X)
df$Y2 <- dplyr::lag(df$Y)
ggplot(df, aes(x = X, y = Y, color = starttime_ms)) +
geom_segment(aes(xend = X2, yend = Y2), size = 1) +
scale_color_gradientn(colors = c("red", "gold", "forestgreen"), name = "time")
I am trying to create a stratigraphic plot of geochemical element data which should be possible using package tidypaleo.
I want multiple plots of the different element data with Depth (cm) downcore set as the y axis. The data look as follows.
Image of data
I am using this code:
ggplot(wapITRAX, aes(x =BrTi , y = wapITRAX$Depth))+
labs(y = "Depth (cm)")+
geom_lineh()+
theme_classic()+
scale_y_reverse()
However, this only plots one element and I am trying to achieve a plot like this Image of plot
> dput(head(wapITRAX))
structure(list(Depth = 0:5, IncCoh = c(6.049230907, 5.975282432,
5.736199822, 5.658584418, 5.659008377, 5.597103404), BrTi =
c(50.50197628,
22.09236453, 23.48370927, 18.62638581, 14.36924414, 17.48777896
), AlIncCOh = c(16.69633736, 8.200449193, 23.70907643, 20.32310407,
28.62692352, 26.44224866), BrCl = c(8.04090623, 4.306048968,
3.417836951, 3.156895904, 2.787628518, 2.059316731), FeTi =
c(332.715415,
235.9371921, 372.726817, 390.7871397, 396.986099, 495.2624867
), CaTi = c(4.071146245, 3.27955665, 4.395989975, 3.677383592,
3.028670721, 4.523910733), ZrRb = structure(c(363L, 447L, 407L,
395L, 450L, 410L), .Label = c("#DIV/0!", "0.447638604",
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1",
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"1.740819711",
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"1.91858679",
"1.929152149", "1.944140197", "1.946996466", "1.986547085",
"2.007683864",
"2.070983811", "2.099778271", "2.156359393", "2.159613059",
"2.163963964", "2.25951087", "2.261603376", "2.329896907",
"2.402555911", "2.414500684",
"2.444075305", "2.450268817", "2.484520124", "2.51119403",
"2.515064562",
"2.526086957", "2.554", "2.609715243", "2.61965812", "2.643854749",
"2.704166667", "2.883275261", "3.013186813", "3.02739726",
"3.206896552",
"3.320930233", "3.411627907", "3.688931298", "3.709677419",
"3.748267898",
"3.878865979", "3.936440678", "3.994230769", "33.15909091",
"4.095854922",
"4.29330254", "4.390957447", "4.514634146", "4.6367713",
"4.847665848",
"5.284023669", "5.387755102", "6.171339564", "6.183908046",
"6.36121673",
"6.847826087", "7.003496503", "7.193220339", "8.160550459",
"8.751879699"
), class = "factor"), MnFe = c(0.012176723, 0.010329834,
0.009460859,
0.004488071, 0.0033725, 0.003435313), MnIncCoh = c(169.4430276,
331.1977339, 490.5686845, 279.5752228, 272.3091921, 286.0408118
), CuRb = c(0.392971246, 1.484304933, 0.735426009, 0.491651206,
1.142857143, 0.4345898)), row.names = c(NA, 6L), class =
"data.frame")
Using your posted data. This should approximate the desired design.
First step, Transform the data from a wide format to a long format using the pivot_longer function from tidyr.
Then plot the data using "depth" as the independent variable and the parameters' values as the dependent variables.
Then use facet_wrap() to separate the plots. coord_flip() will make the independent variable (Depth) appear on the y-axis.
#fixed 1 column of data.
originaldata$ZrRb <- as.numeric(as.character(originaldata$ZrRb))
library(tidyr)
#Make wide
wapITRAX<-pivot_longer(originaldata, -1, names_to="parameter", values_to = "value")
library(ggplot2)
ggplot(wapITRAX, aes(x = Depth , y = value))+
labs(x = "Depth (cm)")+
geom_line() +
theme_classic() +
coord_flip() +
scale_x_reverse() +
facet_wrap(vars(parameter), nrow=1, scales = "free_x")
It is my data:
> dput(data)
structure(list(foldchange = c(-0.17853057272962, 3.60013440830337,
0.648944710423407, 1.38528656859267, 2.38882890772698, 1.91371568283765,
1.77591931363495, -1.51447851175922, 3.1416903855924, 1.51711016957237,
3.14707703341916, -1.44751697381751, 1.23658565660726, -0.512829478520189,
1.68928069854351, 2.07214007434345, 1.24799276690488, 6.25149659558487,
6.35918877435554, 5.86088034655694, 6.38890659730165, 5.05510489389194,
4.62060389613534, 3.75508710774868, 4.18575763169519, 5.31627264153051,
5.87091236649665, 6.71464565321037, 5.24000610137973, 4.25821377851955,
7.32277714374523, 3.1963295806222, 7.26249808789293, 4.44427454088613,
6.21495395454133, 8.74469985969472, 7.49982946564144, 4.45020943795387,
5.66199031471621, 5.29959827685333, 8.65819317196484, 5.86664903755707,
4.5740575604176, 8.24504501687473, 5.7916074097308, 4.18199181353134,
6.73956641707995, 4.60357435173805, 5.9205153184753, 3.65014593638562,
3.25607795403669, 5.56919529940933, 5.76811109641351, 6.10600807588152,
5.69234974521511, 5.5102283323841, 4.71232921328194, 6.55727667796477,
6.19995053763513, 4.64209842048131, 2.29238227264409, 6.79465189260383,
7.51968952300944, 7.81695579226993, 6.29926703626301, 4.64687557749141,
-2.44220257171186, 5.33199370895397, 5.18820654974805, 5.03498241997507,
6.29395095024283, 6.27602377186869, 6.78363927671209, 2.93759015053983,
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5.825851099141, 5.22439201628482, 7.72829018644622, 5.24910611944979,
4.01783420322782, 6.3888069709767, 5.26066649741256, 4.81678726754752,
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3.21738153172066, 6.23015085020594, 5.50091556711613, 3.99948543388746,
5.85816098688073, 4.33775608630599, 5.91715214825299, 5.45674826103132,
7.66790792082782, 6.63325838131012, 3.89631178894691, 2.38526575667126,
1.58661549426288, 4.76626341270591, 6.73426272316295, 5.54006035262931,
4.07996836453406, 7.12087390022358, 6.96007461543701, 5.68202490906633,
6.58504044389069, 5.41036820315057, 6.61076809589319, 1.23772469006557,
4.1661166499875, 2.94059625298825, 8.38336956160413, 4.84906289871508,
4.93787691221829, 6.82379835301371, 5.82520798412864, 4.87582657907206,
5.36621724700676, 8.91922991774938, 3.49025109999629, 5.1232073414505,
4.27193651596412, 5.07417945071012, 3.61930149745523, 2.7469092502892,
6.67162003616042, 4.86698118654996, 7.53876919017093, 4.58878989189686,
5.78956520376246, 3.98567045767003, 8.14934433289609, 6.88879716040936,
7.00251456012974, 5.05095662412332, 6.39777439550296, 7.96268799093557,
4.82826575143863, 8.31032763539508, 4.74493707321909, 6.8929416113222,
6.84202549278968, 8.20121430968127, 2.91031632522241, 4.86190488550545,
5.5516465446887, 7.74996457744065, 2.25505738807845, 5.71069872298306,
1.97493599527532, 5.60445326341706, 6.39297603198736, 7.16298115056911,
4.52688105225386, 6.46061751569601, 4.78104064111529, 2.84526825975018,
6.5537923066898, 6.98258253798747, 5.0967396817644, 6.64593966293456,
4.8990397150507, 4.59878411928317, 5.55158425631398, 2.1065660739172,
2.40396884881286, 6.45421536580342, 5.98567305090568, 6.48593538806214,
7.41313242816247, 5.99024340460149, 5.63812101302136, -1.43793573368627
), all_pvalue = c(0.818887590433193, 0.00892139546812015, 0.434133425685163,
0.0536266013313456, 0.0450933986128537, 0.0367856407800243, 0.0941222253709068,
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0.000694779973318456, 0.0120079549431507, 0.0196183531679123,
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0.023898721968545, 0.00665918028588502, 0.06907634259105, 0.00518730999717143,
0.0109717740506543, 0.394662670743417, 0.0165847750353483, 0.0593829446004973,
0.000113216713641592, 0.0222583368635018, 0.0694462386106761,
0.00437955933335859, 0.0631677226779205, 0.00649674049335009,
1.10699021652115e-07, 0.00543997929535101, 0.00292890932795308,
0.021574456097881, 0.17997075681454, 0.279770535484078, 0.050945514039484,
0.0102923410906512, 0.0103389721465925, 0.112227938286441, 0.00398090342551613,
0.0428676019413789, 0.00337313863923396, 0.0092822848687081,
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0.0801294647165026, 0.0797698230881222, 3.72112644308374e-05,
0.00728653989704988, 0.0320006421510141, 0.000420503611946363,
0.0207086037412542, 0.0448889114898146, 6.94555482668648e-07,
0.000135994029220134, 0.0982385638169219, 0.0130399195487442,
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0.008734949388329, 0.0138918131322944, 0.00507817315892406, 0.000173786133243839,
0.00225184544628237, 0.0181059516295825, 0.541544494598043),
probename = c("Mark_1", "Mark_2", "Mark_3", "Mark_4", "Mark_5",
"Mark_6", "Mark_7", "Mark_8", "Mark_9", "Mark_10", "Mark_11",
"Mark_12", "Mark_13", "Mark_14", "Mark_15", "Mark_16", "Mark_17",
"Mark_18", "Mark_19", "Mark_20", "Mark_21", "Mark_22", "Mark_23",
"Mark_24", "Mark_25", "Mark_26", "Mark_27", "Mark_28", "Mark_29",
"Mark_30", "Mark_31", "Mark_32", "Mark_33", "Mark_34", "Mark_35",
"Mark_36", "Mark_37", "Mark_38", "Mark_39", "Mark_40", "Mark_41",
"Mark_42", "Mark_43", "Mark_44", "Mark_45", "Mark_46", "Mark_47",
"Mark_48", "Mark_49", "Mark_50", "Mark_51", "Mark_52", "Mark_53",
"Mark_54", "Mark_55", "Mark_56", "Mark_57", "Mark_58", "Mark_59",
"Mark_60", "Mark_61", "Mark_62", "Mark_63", "Mark_64", "Mark_65",
"Mark_66", "Mark_67", "Mark_68", "Mark_69", "Mark_70", "Mark_71",
"Mark_72", "Mark_73", "Mark_74", "Mark_75", "Mark_76", "Mark_77",
"Mark_78", "Mark_79", "Mark_80", "Mark_81", "Mark_82", "Mark_83",
"Mark_84", "Mark_85", "Mark_86", "Mark_87", "Mark_88", "Mark_89",
"Mark_90", "Mark_91", "Mark_92", "Mark_93", "Mark_94", "Mark_95",
"Mark_96", "Mark_97", "Mark_98", "Mark_99", "Mark_100", "Mark_101",
"Mark_102", "Mark_103", "Mark_104", "Mark_105", "Mark_106",
"Mark_107", "Mark_108", "Mark_109", "Mark_110", "Mark_111",
"Mark_112", "Mark_113", "Mark_114", "Mark_115", "Mark_116",
"Mark_117", "Mark_118", "Mark_119", "Mark_120", "Mark_121",
"Mark_122", "Mark_123", "Mark_124", "Mark_125", "Mark_126",
"Mark_127", "Mark_128", "Mark_129", "Mark_130", "Mark_131",
"Mark_132", "Mark_133", "Mark_134", "Mark_135", "Mark_136",
"Mark_137", "Mark_138", "Mark_139", "Mark_140", "Mark_141",
"Mark_142", "Mark_143", "Mark_144", "Mark_145", "Mark_146",
"Mark_147", "Mark_148", "Mark_149", "Mark_150", "Mark_151",
"Mark_152", "Mark_153", "Mark_154", "Mark_155", "Mark_156",
"Mark_157", "Mark_158", "Mark_159", "Mark_160", "Mark_161",
"Mark_162", "Mark_163", "Mark_164", "Mark_165", "Mark_166",
"Mark_167", "Mark_168", "Mark_169", "Mark_170", "Mark_171",
"Mark_172", "Mark_173", "Mark_174", "Mark_175", "Mark_176",
"Mark_177", "Mark_178", "Mark_179", "Mark_180", "Mark_181",
"Mark_182", "Mark_183", "Mark_184", "Mark_185", "Mark_186",
"Mark_187", "Mark_188", "Mark_189", "Mark_190", "Mark_191",
"Mark_192", "Mark_193", "Mark_194", "Mark_195", "Mark_196",
"Mark_197", "Mark_198", "Mark_199", "Mark_200", "Mark_201",
"Mark_202", "Mark_203", "Mark_204", "Mark_205", "Mark_206",
"Mark_207", "Mark_208", "Mark_209", "Mark_210", "Mark_211",
"Mark_212", "Mark_213", "Mark_214", "Mark_215", "Mark_216",
"Mark_217", "Mark_218", "Mark_219", "Mark_220", "Mark_221",
"Mark_222", "Mark_223", "Mark_224", "Mark_225", "Mark_226",
"Mark_227", "Mark_228", "Mark_229", "Mark_230", "Mark_231",
"Mark_232", "Mark_233", "Mark_234", "Mark_235", "Mark_236",
"Mark_237", "Mark_238", "Mark_239", "Mark_240", "Mark_241",
"Mark_242")), row.names = c("Mark_1", "Mark_2", "Mark_3",
"Mark_4", "Mark_5", "Mark_6", "Mark_7", "Mark_8", "Mark_9", "Mark_10",
"Mark_11", "Mark_12", "Mark_13", "Mark_14", "Mark_15", "Mark_16",
"Mark_17", "Mark_18", "Mark_19", "Mark_20", "Mark_21", "Mark_22",
"Mark_23", "Mark_24", "Mark_25", "Mark_26", "Mark_27", "Mark_28",
"Mark_29", "Mark_30", "Mark_31", "Mark_32", "Mark_33", "Mark_34",
"Mark_35", "Mark_36", "Mark_37", "Mark_38", "Mark_39", "Mark_40",
"Mark_41", "Mark_42", "Mark_43", "Mark_44", "Mark_45", "Mark_46",
"Mark_47", "Mark_48", "Mark_49", "Mark_50", "Mark_51", "Mark_52",
"Mark_53", "Mark_54", "Mark_55", "Mark_56", "Mark_57", "Mark_58",
"Mark_59", "Mark_60", "Mark_61", "Mark_62", "Mark_63", "Mark_64",
"Mark_65", "Mark_66", "Mark_67", "Mark_68", "Mark_69", "Mark_70",
"Mark_71", "Mark_72", "Mark_73", "Mark_74", "Mark_75", "Mark_76",
"Mark_77", "Mark_78", "Mark_79", "Mark_80", "Mark_81", "Mark_82",
"Mark_83", "Mark_84", "Mark_85", "Mark_86", "Mark_87", "Mark_88",
"Mark_89", "Mark_90", "Mark_91", "Mark_92", "Mark_93", "Mark_94",
"Mark_95", "Mark_96", "Mark_97", "Mark_98", "Mark_99", "Mark_100",
"Mark_101", "Mark_102", "Mark_103", "Mark_104", "Mark_105", "Mark_106",
"Mark_107", "Mark_108", "Mark_109", "Mark_110", "Mark_111", "Mark_112",
"Mark_113", "Mark_114", "Mark_115", "Mark_116", "Mark_117", "Mark_118",
"Mark_119", "Mark_120", "Mark_121", "Mark_122", "Mark_123", "Mark_124",
"Mark_125", "Mark_126", "Mark_127", "Mark_128", "Mark_129", "Mark_130",
"Mark_131", "Mark_132", "Mark_133", "Mark_134", "Mark_135", "Mark_136",
"Mark_137", "Mark_138", "Mark_139", "Mark_140", "Mark_141", "Mark_142",
"Mark_143", "Mark_144", "Mark_145", "Mark_146", "Mark_147", "Mark_148",
"Mark_149", "Mark_150", "Mark_151", "Mark_152", "Mark_153", "Mark_154",
"Mark_155", "Mark_156", "Mark_157", "Mark_158", "Mark_159", "Mark_160",
"Mark_161", "Mark_162", "Mark_163", "Mark_164", "Mark_165", "Mark_166",
"Mark_167", "Mark_168", "Mark_169", "Mark_170", "Mark_171", "Mark_172",
"Mark_173", "Mark_174", "Mark_175", "Mark_176", "Mark_177", "Mark_178",
"Mark_179", "Mark_180", "Mark_181", "Mark_182", "Mark_183", "Mark_184",
"Mark_185", "Mark_186", "Mark_187", "Mark_188", "Mark_189", "Mark_190",
"Mark_191", "Mark_192", "Mark_193", "Mark_194", "Mark_195", "Mark_196",
"Mark_197", "Mark_198", "Mark_199", "Mark_200", "Mark_201", "Mark_202",
"Mark_203", "Mark_204", "Mark_205", "Mark_206", "Mark_207", "Mark_208",
"Mark_209", "Mark_210", "Mark_211", "Mark_212", "Mark_213", "Mark_214",
"Mark_215", "Mark_216", "Mark_217", "Mark_218", "Mark_219", "Mark_220",
"Mark_221", "Mark_222", "Mark_223", "Mark_224", "Mark_225", "Mark_226",
"Mark_227", "Mark_228", "Mark_229", "Mark_230", "Mark_231", "Mark_232",
"Mark_233", "Mark_234", "Mark_235", "Mark_236", "Mark_237", "Mark_238",
"Mark_239", "Mark_240", "Mark_241", "Mark_242"), class = "data.frame")
I would like to create a nice graph (publication wise) to represent a data stored in this data frame. In general I would like to create a scatterplot or volcano plot with colors/shapes indicating what is important in my data.
I would like to achieve something like that:
Or:
As a filter cutoff we can start with: foldchange > 4 & all_pvalue < 0.05. I would like to also have a possibility to highlight (different color/shape and with a label) only couple of rows. Lets say as a starting point I would like to highlight Mark_23 and Mark_65.
Is it doable in R ? I have already tried something with volcano plot:
volcano = ggplot(data = data, aes(x = foldchange, y = -1*log10(all_pvalue)))
volcano + geom_point()
Can someone help me with going further ?
Here is an attempt to show what's possible
data$zones := interaction(abs(data$foldchange)>4,data$all_pvalue<0.05)
library(ggplot2)
library(ggrepel)
ggplot(data = data, aes(x = foldchange, y = -1*log10(all_pvalue),color = zones))+
geom_point()+
theme_light()+
geom_label_repel(aes(label=ifelse(probename %in% c("Mark_23","Mark_65"),as.character(probename),"")),
box.padding = 0.35,
point.padding = 0.5,
segment.color = 'grey50',show.legend = FALSE) +
geom_hline(yintercept = -1*log10(0.05),linetype = "dashed")+
geom_vline(xintercept = 4,linetype = "dashed")+
scale_color_manual(labels = c("bad", "also bad","good","not sure"), values = c("gray50","green","blue", "red"))+
labs(x = "fold change",
y = expression(log[10](p)),
color = "meaning")
there are many things here. geom_label_repel from library(ggrepel) allow to link your few points you want to show with a label. The easiest way of having the different colours is to create a variable that says in what zone you are. That is what I did with the zones variable, that you use in colour to have a changing color. You can manualy change it with the scale_color_manual function.
In the labs function I used the expression function that allows you to do superscripts. You can of course change the theme including, margins, axis, text size etc.
You can for example add theme(legend.position="top") to your plot to have the legend on top.
Instead of adding legends outside the plot, I want to add names such as "Quantile 1", "Quantile 10" etc. inside the plot as labels.
ggplot() +
geom_line(data=df.quants, aes(x=xvars, y=q01), color="black", size =0.5) +
geom_line(data=df.quants, aes(x=xvars, y=q10), color="black", size =0.7) +
geom_line(data=df.quants, aes(x=xvars, y=q25), color="black", size =1) +
geom_line(data=df.quants, aes(x=xvars, y=q50), color="black", size =1.2) +
geom_line(data=df.quants, aes(x=xvars, y=q75), color="black", size =1) +
geom_line(data=df.quants, aes(x=xvars, y=q90), color="black", size =0.7) +
geom_line(data=df.quants, aes(x=xvars, y=q99), color="black", size =0.5) +
geom_ribbon(data=df.quants,aes(x=xvars,ymin=q25,ymax=q75),alpha=0.8)+
geom_ribbon(data=df.quants,aes(x=xvars,ymin=q10,ymax=q25),alpha=0.5)+
geom_ribbon(data=df.quants,aes(x=xvars,ymin=q75,ymax=q90),alpha=0.5)+
geom_ribbon(data=df.quants,aes(x=xvars,ymin=q01,ymax=q10),alpha=0.2)+
geom_ribbon(data=df.quants,aes(x=xvars,ymin=q90,ymax=q99),alpha=0.2)+
theme_bw()+
ggtitle("Q")+
ggsave("save.png")
How can I add labels on the plot in either or both of these cases:
At the end of the lines (e.g. https://stackoverflow.com/a/37696769/3942806)
Hovering over the lines towards the left hand side (https://stackoverflow.com/a/37672486/3942806)
dput(df.quants)
structure(list(xvars = c(21.1084, 40.4038, 42.4758, 44.0298,
44.8068, 53.0948, 53.3538, 54.3898, 56.4617, 62.9367, 67.3397,
68.8937, 68.8937, 74.3327, 78.7356, 80.2896, 87.8006, 95.0526,
98.6785, 105.6715, 114.4775, 116.5495, 121.7294, 127.4274, 133.6434,
146.3343, 153.0683, 158.2483, 163.6872, 169.9032, 180.7812, 186.4791,
186.9971, 194.5081, 196.3211, 203.8321, 209.789, 215.746, 218.336,
222.998, 230.7679, 237.5019, 241.1279, 242.12505, 250.9698, 254.0778,
264.1788, 274.5387, 284.8987, 292.6687, 303.0286, 310.7986, 326.3385,
336.6985, 344.4684, 362.5983, 378.1383, 389.275200000003, 393.6782,
409.2181, 427.348, 450.6579, 450.6579, 450.6579, 453.2479, 463.6079,
476.5578, 489.5078, 499.8677, 510.2277, 523.1776, 533.5376, 543.8975,
567.2074, 611.2372, 613.8272, 621.5971, 637.1371, 652.677, 660.447,
668.2169, 678.5769, 696.447800000002, 714.8367, 744.880600000001,
764.0465, 766.6365, 779.5864, 784.7664, 810.6663, 815.8463, 839.1561,
852.1061, 872.826, 896.1359, 903.9059, 916.8558, 937.5757, 966.0656,
984.1955), q01 = c(0.07287449, 0.0573897264, 0.0557969357, 0.0537193707,
0.0518303892, 0.0518080158, 0.0514479006, 0.0517025388, 0.0516258276,
0.0459982978, 0.0471084591, 0.0402322638, 0.0406957203, 0.0373694866919881,
0.0375932247971234, 0.0378606448, 0.0374813557445557, 0.036479866,
0.0368506252, 0.0362731762, 0.0367099924, 0.0329852952, 0.0280992996,
0.0278553199, 0.0277327966, 0.0279245722, 0.0279458806, 0.0277967218,
0.0279831703, 0.0237609194, 0.0207585756691242, 0.0207543139705945,
0.0196036650330279, 0.0188940975085873, 0.0186277436, 0.0167249092,
0.0167046666, 0.0166865548, 0.0161687604, 0.0161591718, 0.0161879376,
0.011199656, 0.0111985905, 0.01105689088, 0.0110845916, 0.0106222032239633,
0.0109610059070531, 0.0109652675220967, 0.0109769869296186, 0.01043682232,
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0.00955359025, 0.00895376068, 0.00836565071, 0.00829852949, 0.00825058604,
0.00660771382, 0.00658320918, 0.00658320918, 0.00647347103215001,
0.00720008536, 0.00722565544, 0.00697102063, 0.00688152578, 0.00688898372,
0.00692733882, 0.00618580850401875, 0.0061218835, 0.0061090985,
0.00609311725, 0.00584274444, 0.00583954821, 0.00575325, 0.00575325,
0.0050873645, 0.00522693399, 0.00516087826, 0.00496803746, 0.00490198142,
0.00490198142, 0.00490198142, 0.0057798848, 0.00555082036, 0.00518857905,
0.00508949534, 0.0050127851, 0.0049701683, 0.0049275515, 0.00487428075,
0.00479011332, 0.00476347782, 0.0047783937, 0.00476880492, 0.00487747698,
0.00485510337, 0.0048582996, 0.00479330958), q10 = c(0.492542083954826,
0.45454932, 0.43124864, 0.41944381, 0.37937352, 0.38026848, 0.37053055,
0.37472832, 0.35278072, 0.34281907, 0.34762414, 0.28118472, 0.28004471,
0.272746634508843, 0.24855102, 0.25194972, 0.242531451945451,
0.2256552, 0.206232684634562, 0.19673984, 0.20522054, 0.18095038,
0.170956713240997, 0.16841043, 0.163157896833582, 0.16456426,
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0.1429789, 0.14078417, 0.13547836, 0.13492432, 0.13260178, 0.12952273,
0.1337311, 0.1273386, 0.123471123238866, 0.12135096, 0.10445342,
0.10836355, 0.10458128, 0.10262094, 0.10075645, 0.10061794, 0.099659066,
0.099925431, 0.0973364588484978, 0.0949499261725975, 0.0949499261725975,
0.1001705, 0.09823141, 0.091689753, 0.0820796952618794, 0.080683995,
0.079256336, 0.078052418, 0.0678883475337737, 0.067302367, 0.0675474110377157,
0.065970594, 0.068889834, 0.069379928, 0.06499041, 0.0639143363015129,
0.0628169628570211, 0.061410608, 0.0606541642970382, 0.0605369686562966,
0.06094183, 0.0605476229844449, 0.0566162367773279, 0.056371194,
0.054080544, 0.0546025993937779, 0.051779245, 0.052375877, 0.051907098,
0.050639252, 0.050308969, 0.050308969, 0.050308969, 0.053643725,
0.053505218, 0.0507671, 0.049691026, 0.04884935, 0.04810356,
0.04757085, 0.04687833, 0.045727678, 0.045503944, 0.04687833,
0.046729174, 0.051971022, 0.050308975, 0.0498615, 0.048039636
), q25 = c(0.6404219, 0.6244939, 0.605822475, 0.602040281120818,
0.5927978, 0.588349675, 0.579639875, 0.5777754, 0.5689325, 0.55953015,
0.5641647, 0.53696995, 0.53358725, 0.518511625, 0.509855075,
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0.27794055, 0.28041765, 0.2627317, 0.252370517653953, 0.248348618836565,
0.2258683, 0.2306094, 0.22400385, 0.2216066, 0.21785105, 0.214521628563819,
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0.206317924738973, 0.200431525, 0.189537609205199, 0.187220325,
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0.15347325, 0.150916225, 0.14910505, 0.14990415, 0.1474537, 0.1441509,
0.142712575, 0.138690575, 0.14098125, 0.135813975, 0.137385475,
0.14217985, 0.139969074168975, 0.139516275, 0.139516275, 0.139516275,
0.143751322267206, 0.1424995, 0.140688225, 0.1389303, 0.136639675,
0.134801865933305, 0.137785025, 0.135813975, 0.132537822288515,
0.128356075, 0.129900875, 0.1293416, 0.14106115, 0.137598575,
0.1421266, 0.1387705), q50 = c(0.7691242, 0.7631579, 0.75559345,
0.751917760334541, 0.7506925, 0.746484148060942, 0.7420094, 0.7371617,
0.7325804, 0.72565525, 0.72682715, 0.7165992, 0.7147347, 0.702002962412103,
0.69640955, 0.6950778, 0.6869806, 0.6838909, 0.6740358, 0.6714255,
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0.613253782228852, 0.603665, 0.593756671084594, 0.579267, 0.5622203,
0.5610484, 0.5582783, 0.5308971, 0.5144897, 0.5100149, 0.49355425,
0.4915832, 0.4779459, 0.4607394, 0.4513105, 0.424462, 0.42510125,
0.4174302, 0.4121031, 0.40336673736416, 0.3968677, 0.3919668,
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0.3834434, 0.37646495, 0.3681014, 0.3637332, 0.3615491, 0.3576603,
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0.33187725, 0.33059875, 0.3258044, 0.3180268, 0.3064138, 0.3049222,
0.3091839, 0.3065736, 0.2999148, 0.29900915, 0.2925634, 0.3009802,
0.2956531, 0.29698485, 0.3044961, 0.30412315, 0.3014596, 0.3014596,
0.3014596, 0.3147773, 0.3135521, 0.3128596, 0.30998295, 0.3091306,
0.3039633, 0.30907735, 0.303856783177072, 0.2949073, 0.28595785,
0.285371829778393, 0.2846793, 0.2958662, 0.29607925, 0.3035372,
0.30359045), q75 = c(0.8668229, 0.8637865, 0.86104305, 0.858752425,
0.8584061, 0.8549169, 0.852066925, 0.8492436, 0.8462604, 0.843783275,
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0.519017675, 0.517899, 0.50905605, 0.495258875, 0.5004794, 0.50298315,
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0.86893244, 0.863030027896868, 0.86177288, 0.8616024, 0.859290453515875,
0.8365012, 0.82799918, 0.824568514587684, 0.819273379833795,
0.81630088, 0.81448968, 0.79439591, 0.78960152, 0.783315567773279,
0.776464946030258, 0.776731300370765, 0.76594926, 0.75919456,
0.75371832, 0.75075644, 0.74735775, 0.74310678, 0.72495204, 0.7112508,
0.713807792386533, 0.7141487, 0.71468144, 0.713530774319199,
0.71050504, 0.707809474097592, 0.70632856, 0.70217348, 0.69276586,
0.68746007, 0.68621354, 0.68354994, 0.67928834, 0.66894312, 0.66838907,
0.66891114, 0.66275304248029, 0.65147025, 0.655188582416365,
0.65889626, 0.64831662, 0.640571045322821, 0.64626035, 0.64103984,
0.637385467717878, 0.63600045, 0.639899844314937, 0.638908996019603,
0.64134882, 0.64137014, 0.64137014, 0.64137014, 0.6497443, 0.64977628,
0.64734715, 0.64238229, 0.6446303, 0.634775211037716, 0.635307911037716,
0.631685502855317, 0.62823354, 0.62139354, 0.61645005, 0.61583208,
0.61267846, 0.61427655, 0.6135734, 0.61338161), q99 = c(0.9813552,
0.983496688, 0.982289538, 0.981875103, 0.98133816, 0.981210342,
0.980869382, 0.98074156, 0.980605188, 0.980628629, 0.980474118,
0.97956530234349, 0.979405495101854, 0.979192435, 0.979102933,
0.97900704, 0.978866424, 0.97889414, 0.978801398, 0.978465764,
0.978167456, 0.97708924, 0.977054095, 0.977258668, 0.975373952,
0.972782846, 0.972770058, 0.972859574, 0.972306655, 0.97231411,
0.972591068, 0.97259746, 0.972355645, 0.962840406286384, 0.963136582842531,
0.943974016, 0.944772016962071, 0.944242504, 0.944018764, 0.935328143137652,
0.935241848623481, 0.934724015665886, 0.926759001178564, 0.926816535265289,
0.926234804, 0.917745605, 0.91511187081824, 0.915103346793096,
0.913937796999999, 0.90959943, 0.903311344, 0.894027274664394,
0.895148090432559, 0.897357759215854, 0.897743441, 0.894050713829107,
0.893945237587897, 0.889042197096101, 0.889281912489239, 0.888979338,
0.886543834, 0.886235893490944, 0.886239091206478, 0.886258277499681,
0.868235644, 0.868526506, 0.870900274999999, 0.871323255148946,
0.869995737948434, 0.867188371, 0.864700617419987, 0.864726187301939,
0.856755777, 0.844385296, 0.855691437, 0.83904428249137, 0.832750945,
0.837923525, 0.856581078, 0.855506063483912, 0.855462386340294,
0.838475343, 0.838475343, 0.838475343, 0.855438949824206, 0.855484757560196,
0.855492214633497, 0.855447472193693, 0.855524173519071, 0.85631259,
0.859764525, 0.861629, 0.865305772, 0.861820776, 0.861149560000001,
0.861581055999999, 0.861485167999999, 0.858912205, 0.86234816,
0.860478344)), .Names = c("xvars", "q01", "q10", "q25", "q50",
"q75", "q90", "q99"), row.names = c(NA, -100L), class = "data.frame")
You should try the directlabels package. Here's an example:
library(tidyverse)
library(directlabels)
df.quants %>%
gather(var,val,-1) %>%
ggplot(aes(xvars,val,fill=var)) +
geom_area(position="identity", alpha = .5) +
geom_line() +
scale_fill_grey(guide="none") +
geom_dl(aes(label=var), method="last.points")
Make sure to browse through its documentation as there are many more options.
You can extend that approach to also use custom labels, linewidths, fillings etc. One way could be:
labs <- setNames(c("G", "F", "E", "D", "C", "B", "A"), c("q99", "q90", "q75", "q50", "q25", "q10", "q01"))
df.quants %>%
rev %>%
gather(var,val,-xvars,factor_key=TRUE) %>%
ggplot(aes(xvars,val,fill=var)) +
geom_area(position="identity") +
geom_line(aes(size=var)) +
scale_fill_manual(values = c(grey.colors(3,.9,.3), grey.colors(4)), guide="none") +
scale_size_manual(values = c(1:3,4:1), guide="none") +
geom_dl(aes(label=labs[var]), method="last.points")