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Commit cb45b332 authored by mahendra-mariadassou's avatar mahendra-mariadassou
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Merge branch 'master' of gitlab-ssh.irstea.fr:cedric.midoux/easy16S

parents 7dc5e253 73aa8517
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.gitignore
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.Rhistory
.RData
*.Rproj
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.Rproj.user
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demo/biorare.tsv 0 → 100644
View file @ cb45b332
Nom Reacteur Compartiment Date
170517_4A 4 anode 17/05/2017
170517_4C 4 cathode 17/05/2017
170517_5A 5 anode 17/05/2017
170517_5C 5 cathode 17/05/2017
170517_6A 6 anode 17/05/2017
170517_6C 6 cathode 17/05/2017
170517_7A 7 anode 17/05/2017
170517_7C 7 cathode 17/05/2017
170517_8A 8 anode 17/05/2017
170517_8C 8 cathode 17/05/2017
170517_9A 9 anode 17/05/2017
170517_9C 9 cathode 17/05/2017
170517_10A 10 anode 17/05/2017
170517_10C 10 cathode 17/05/2017
170517_11A 11 anode 17/05/2017
170517_11C 11 cathode 17/05/2017
170517_12A 12 anode 17/05/2017
170517_12C 12 cathode 17/05/2017
demo/cellulose.biom 0 → 100644
View file @ cb45b332
This diff is collapsed.
demo/cellulose.tsv 0 → 100644
View file @ cb45b332
Sample_name Substrate Incubation_name Sampling_timepoint Incubation_days Substrate_D0 Substrate_D0_phase Acetate Propionate DIC DOC pH Alpha_app CH4_cum CO2_cum Biogaz_cum QPCR_bact QPCR_GH48 QPCR_hydA Sequencing_Run
C1-0 Cotton C1 T0 0 D0 D0 0 0 1480.353333 21.62766667 8.46 NA 0 0 0 1669972.571 83.07776765 1162333.742 1
C1-1 Cotton C1 T1 12 Cotton Cotton_Phase1 44.49579661 0 1519.31 94.302 8.23 1.071584086 3.792787147 23.91424224 33.8705172 18936399.31 304983.356 35099629.71 1
C1-2 Cotton C1 T2 18 Cotton Cotton_Phase1 282.4814237 16.92 1401.096667 327.639 N/A 1.065926511 71.84801024 138.7166245 230.0597396 52182556.74 943269.1878 97980564.06 1
C1-3 Cotton C1 T3 25 Cotton Cotton_Phase1 433.7218983 23.21827397 1394.38 575.2153333 7.25 1.070000183 133.7760619 241.598022 399.3824074 46231090.45 547236.9934 53610983.19 1
C1-4 Cotton C1 T4 32 Cotton Cotton_Phase2 623.5667797 38.91180822 1308.675333 568.3643333 7.3 1.072372065 138.0545943 304.2138227 488.4263082 40921577.33 908486.2198 36445156.38 1
C1-5 Cotton C1 T5 40 Cotton Cotton_Phase2 490.2366102 31.17156164 1238.016 559.767 7.37 1.065320856 169.374826 326.0854961 557.6144352 48875235.67 324880.4355 41303618.4 1
C1-6 Cotton C1 T6 50 Cotton Cotton_Phase2 295.3852881 25.07350685 1454.83 400.8506667 7.26 1.058478367 267.7138729 338.6028806 678.2287435 28442384.48 421833.528 33073811.73 1
C2-0 Cotton C2 T0 0 D0 D0 0 0 1590.506667 23.777 8.47 NA 0 0 0 1909156.172 108.3186006 1411501.101 1
C2-1 Cotton C2 T1 12 Cotton Cotton_Phase1 72.08359322 0 1220.284 111.228 8 1.072531448 8.617383915 36.90466352 57.76774973 48542049.1 444090.4744 86490915.02 1
C2-2 Cotton C2 T2 18 Cotton Cotton_Phase1 356.7024407 17.028 1326.138667 452.166 NA 1.063758522 106.366342 221.0557349 347.3204703 46979807.68 740987.6353 43352872.8 1
C2-3 Cotton C2 T3 25 Cotton Cotton_Phase1 563.7528814 35.61189041 1194.626333 544.9903333 7.34 1.065527847 142.601703 274.6242604 442.0752072 77219827.66 1750821.053 50341658.39 1
C2-4 Cotton C2 T4 32 Cotton Cotton_Phase2 568.0706441 44.04846575 1066.606667 476.2116667 7.33 1.066945145 160.2967801 342.6850257 576.2745812 47135839.41 766970.4687 37366422.6 1
C2-5 Cotton C2 T5 40 Cotton Cotton_Phase2 471.8682712 37.08419178 1326.138667 561.782 7.35 1.063867953 209.8813846 363.3965433 661.7243732 62996094.43 219427.2225 64238168.05 1
C2-6 Cotton C2 T6 50 Cotton Cotton_Phase2 72.26 0 1618.716667 142.7963333 7.34 1.041098691 431.6374822 391.8251247 918.7865618 38368976.15 98850.72594 45188582.67 1
C3-0 Cotton C3 T0 0 D0 D0 0 0 1468.263333 42.04633333 8.48 NA 0 0 0 2786381.62 123.4290902 2175718.307 2
C3-1 Cotton C3 T1 12 Cotton Cotton_Phase1 18.20542373 0 1461.546667 74.01766667 8.36 1.085491011 4.346320858 16.07479901 20.02779198 6830749.602 53311.27793 9332745.606 2
C3-2 Cotton C3 T2 18 Cotton Cotton_Phase1 207.3730169 0 1364.826667 231.5906667 N/A 1.063440797 54.23647325 106.9262672 178.9593378 72119938.24 740987.6353 152385172.8 2
C3-3 Cotton C3 T3 25 Cotton Cotton_Phase1 416.3204746 21.22323288 1244.195333 463.9873333 7.33 1.073161308 116.6346013 202.2110238 337.7466124 52273043.06 2636814.232 86785060.45 2
C3-4 Cotton C3 T4 32 Cotton Cotton_Phase2 601.5461695 36.97939726 1222.702 557.349 7.3 1.076361686 134.0180938 263.0764968 400.775302 87715296.7 3779998.816 105685681.1 2
C3-5 Cotton C3 T5 40 Cotton Cotton_Phase2 485.7183051 28.94547945 1249.703 570.9166667 7.31 1.072318611 168.5704801 300.2433373 490.8531781 78885828.71 3231948.409 93995932.06 2
C3-6 Cotton C3 T6 50 Cotton Cotton_Phase2 111.1649492 29.21769863 1594.536667 212.2466667 7.34 1.047261446 396.1301754 312.8519259 726.4555106 55772369.87 867007.6585 65940914.36 2
C4-0 Cotton C4 T0 0 D0 D0 0 0 NA NA 8.49 NA 0 0 0 1607046.557 98.83985942 967404.0188 2
C4-1 Cotton C4 T1 12 Cotton Cotton_Phase1 20.28101695 0 NA NA 8.36 1.086226314 5.685682409 16.01338107 22.11791839 8088439.916 147183.4446 13447494.23 2
C4-2 Cotton C4 T2 18 Cotton Cotton_Phase1 254.5037288 0 NA NA NA 1.062407126 60.90768726 123.8379233 203.8343752 87885595.61 89996.90961 163243992 2
C4-3 Cotton C4 T3 25 Cotton Cotton_Phase1 522.2698983 34.61523288 NA NA 7.31 1.06883299 131.82389 233.5815379 386.1754188 56338303.22 140157.2569 104580794.7 2
C4-4 Cotton C4 T4 32 Cotton Cotton_Phase2 547.399322 42.82224658 NA NA 7.33 1.070917559 157.3149285 301.7155673 495.3882402 42728421.34 1353404.467 43614030.77 2
C4-5 Cotton C4 T5 40 Cotton Cotton_Phase2 510.2011525 40.48372603 NA NA 7.35 1.066886873 210.1926977 334.9709302 596.9705068 52158223.96 1240762.865 36944956.77 2
C4-6 Cotton C4 T6 50 Cotton Cotton_Phase2 69.11 0 1614.686667 148.5726667 7.38 1.045037054 435.4545182 369.3795043 870.8412241 43607661.4 104623.2296 12824266.1 2
Inoc-a Inoculum Inoculum Inoculum 0 D0 D0 NA NA NA NA NA NA NA NA NA NA NA NA 1
Inoc-b Inoculum Inoculum Inoculum 0 D0 D0 NA NA NA NA NA NA NA NA NA NA NA NA 2
K1-0 Tissue K1 T0 0 D0 D0 0 0 1519.31 6.716666667 8.38 NA 0 0 0 2059792.145 147.8544573 1463813.46 1
K1-1 Tissue K1 T1 12 Tissue Tissue_Phase1 608.3347119 69.54041096 1258.703333 740.1766667 7.2 1.056386714 45.89384843 199.1529436 244.8513597 120152628.6 16146.16045 9203483.054 1
K1-2 Tissue K1 T2 18 Tissue Tissue_Phase1 690.5587119 93.12879452 1411.843333 859.7333333 7.82 1.059538659 70.35255594 261.198124 335.5609165 61009811.54 28399.85548 10095058.57 1
K1-3 Tissue K1 T3 25 Tissue Tissue_Phase1 503.7189153 90.19479452 1484.383333 690.4733333 7.39 1.054760073 150.6847342 285.6059126 445.4628078 48783883.88 19375.73185 12101490.52 1
K1-4 Tissue K1 T4 32 Tissue Tissue_Phase2 91.10542373 43.86452055 1668.42 225.68 7.4 1.039305968 362.9778685 312.2878125 686.4082301 60882674.87 29989.20967 12332202.27 1
K1-5 Tissue K1 T5 40 Tissue Tissue_Phase2 0 0 1723.496667 63.13666667 7.49 1.037070195 479.3033963 351.0273365 850.0633136 40645246.8 34822.48536 11884528.67 1
K1-6 Tissue K1 T6 50 Tissue Tissue_Phase2 0 0 1716.78 45.67333333 7.51 1.037739754 484.0909778 360.2723661 874.6090871 56884549.86 41758.72972 17735756.58 1
K2-0 Tissue K2 T0 0 D0 D0 0 0 1456.173333 26.195 8.44 NA 0 0 0 1299270.862 67.33630131 1134238.848 1
K2-1 Tissue K2 T1 12 Tissue Tissue_Phase1 725.3070508 81.18936986 1191.268 745.0126667 7.21 1.056117764 39.62155259 214.3853729 255.5079505 87177266.28 81370.06965 10916067.83 1
K2-2 Tissue K2 T2 18 Tissue Tissue_Phase1 689.1038644 92.04608219 1176.76 705.3843333 NA 1.060501886 59.40781571 267.1776799 335.8048148 144590960.8 20281.01652 16731347.11 1
K2-3 Tissue K2 T3 25 Tissue Tissue_Phase1 517.6342373 101.186137 1409.156667 648.427 7.43 1.054236017 154.930776 289.6452602 458.7573284 49844641.16 24256.42042 8395040.513 1
K2-4 Tissue K2 T4 32 Tissue Tissue_Phase2 49.23925424 51.59342466 1294.167333 157.4386667 7.39 1.036654913 377.7292898 322.1408517 723.4694829 39057883.99 36211.06216 7884695.515 1
K2-5 Tissue K2 T5 40 Tissue Tissue_Phase2 0 0 1633.493333 68.77866667 7.5 1.036828062 498.1125395 362.7822625 892.9754443 41198728.6 42170.7713 11431571.69 1
K2-6 Tissue K2 T6 50 Tissue Tissue_Phase2 0 0 1693.943333 48.36 7.55 1.037224544 502.2747811 372.9365977 917.4126325 46041521.11 64639.7369 14537671.19 1
K3-0 Tissue K3 T0 0 D0 D0 0 0 1397.066667 24.71733333 8.46 NA 0 0 0 2225069.211 155.5849088 1554473.131 2
K3-1 Tissue K3 T1 12 Tissue Tissue_Phase1 608.8887458 70.47246575 1303.570667 745.8186667 7.19 1.057433452 60.96685726 212.1000205 272.7599345 104952071.2 10955.24637 26495662.97 2
K3-2 Tissue K3 T2 18 Tissue Tissue_Phase1 609.0728136 87.34290411 1372.886667 794.9846667 7.78 1.061330009 83.39490101 270.1007265 362.1370976 124047898 20281.01652 17667940.27 2
K3-3 Tissue K3 T3 25 Tissue Tissue_Phase1 427.1597288 90.5949863 1454.83 593.0816667 7.53 1.053223524 204.9547826 286.7754125 495.5274659 44200224.24 6917.151896 11261607.79 2
K3-4 Tissue K3 T4 32 Tissue Tissue_Phase2 84.36305085 43.55284932 1481.696667 176.2453333 7.44 1.039383589 392.9638995 325.4245847 738.4461544 53840600.72 9088.034925 14189704.42 2
K3-5 Tissue K3 T5 40 Tissue Tissue_Phase2 0 0 1221.09 58.032 7.6 1.03830415 497.1059894 357.0740401 884.5765992 44291052.55 4732.228267 12779520.16 2
K3-6 Tissue K3 T6 50 Tissue Tissue_Phase2 0 0 1696.63 49.70333333 7.56 1.039240543 501.4694958 368.7505691 905.7274353 38607044.58 7965.83019 10630506.52 2
K4-0 Tissue K4 T0 0 D0 D0 0 0 NA NA 8.47 NA 0 0 0 1599102.998 107.8265007 1170726.199 2
K4-1 Tissue K4 T1 12 Tissue Tissue_Phase1 556.6171525 48.39164384 NA NA 7.3 1.057918994 57.64468616 203.6911848 262.3668797 65151504.37 122938.552 10101852.8 2
K4-2 Tissue K4 T2 18 Tissue Tissue_Phase1 551.0936949 57.73832877 NA NA 7.87 1.058119283 83.97092311 261.2312061 352.0664658 43485462.6 48680.32123 5384416.806 2
K4-3 Tissue K4 T3 25 Tissue Tissue_Phase1 328.324678 73.61210959 NA NA 7.42 1.05053357 223.4286722 278.2892386 498.2155377 51636620.74 30181.00872 13881985.79 2
K4-4 Tissue K4 T4 32 Tissue Tissue_Phase2 41.75857627 80.50068493 NA NA 7.47 1.036289299 373.8491447 313.9960977 700.0368216 33503534.93 51926.3741 6745872.746 2
K4-5 Tissue K4 T5 40 Tissue Tissue_Phase2 0 0 NA NA 7.55 1.035528593 472.5382457 354.6098942 851.4410033 64364978.72 105535.2126 19802321.51 2
K4-6 Tissue K4 T6 50 Tissue Tissue_Phase2 0 0 1628.12 40.3 7.54 1.037883064 490.9695748 359.7677868 881.6095109 42693250.93 98352.83251 20295581.11 2
P1-0 Whatman P1 T0 0 D0 D0 0 0 1652.3 9.403333333 8.49 NA 0 0 0 1628751.87 NA 1152114.143 1
P1-1 Whatman P1 T1 12 Whatman Whatman_Phase1 527.8930169 40.42528767 1422.59 634.0533333 7.13 1.061578699 34.91841819 163.1319142 197.5861458 146707463.2 143.2689677 27172842.19 1
P1-2 Whatman P1 T2 18 Whatman Whatman_Phase1 671.7473898 63.66846575 1101.533333 631.3666667 7.78 1.067447787 65.19019179 246.5794142 316.56792 51779639.23 238701.1912 20682379.34 1
P1-3 Whatman P1 T3 25 Whatman Whatman_Phase1 629.2824407 69.52610959 1296.316667 769.73 7.29 1.070183093 90.68138342 290.0735899 390.3199369 68412001.58 315707.5695 28899552.22 1
P1-4 Whatman P1 T4 32 Whatman Whatman_Phase2 597.7913898 78.73890411 1433.336667 668.98 7.22 1.063712848 164.3510647 320.034336 509.4056795 37947298.09 517211.0956 8773720.924 1
P1-5 Whatman P1 T5 40 Whatman Whatman_Phase2 48.23755932 23.36942466 1668.42 132.99 7.33 1.042535743 412.5280978 356.2777831 799.6521625 55724363.6 40255.07821 14378025.01 1
P1-6 Whatman P1 T6 50 Whatman Whatman_Phase2 0 0 1677.823333 45.67333333 7.48 1.041464427 492.624472 382.9043099 915.5728815 28000194.86 183625.4336 8718071.405 1
P2-0 Whatman P2 T0 0 D0 D0 0 0 1532.743333 23.374 8.54 NA 0 0 0 2444234.416 164.7664536 1687249.721 1
P2-1 Whatman P2 T1 12 Whatman Whatman_Phase1 442.0598644 25.19482192 1283.152 507.9143333 7.28 1.061624674 33.71470941 141.9639337 178.7602106 119470185.5 874455.3436 79286750.73 1
P2-2 Whatman P2 T2 18 Whatman Whatman_Phase1 650.6654237 50.82410959 1172.595667 642.5163333 7.8 1.064840497 78.94870949 243.5411823 328.9113701 51465545.18 112635.6512 34801317.47 1
P2-3 Whatman P2 T3 25 Whatman Whatman_Phase1 631.2772881 56.02783562 1228.344 694.5033333 7.34 1.068945493 94.37414854 281.7905364 387.9777966 56852059.57 242894.3463 34542069.16 1
P2-4 Whatman P2 T4 32 Whatman Whatman_Phase2 585.7704407 49.4440274 1157.013 595.0966667 7.23 1.067821831 120.9862875 307.233822 455.4847144 45373680.01 126205.5484 17790483.87 1
P2-5 Whatman P2 T5 40 Whatman Whatman_Phase2 363.5452881 35.676 1386.32 441.0163333 7.27 1.055127324 258.6109839 333.5661505 637.2750918 47912936.36 208579.9357 21259978.87 1
P2-6 Whatman P2 T6 50 Whatman Whatman_Phase2 8.26 0 1683.196667 70.10856667 7.5 1.037650444 480.3205514 370.4179974 899.4719484 35511777.45 83654.46007 19143682.71 1
P3-0 Whatman P3 T0 0 D0 D0 0 0 1466.92 21.89633333 8.52 NA 0 0 0 540445.0421 62.32027747 552300.5737 2
P3-1 Whatman P3 T1 12 Whatman Whatman_Phase1 218.3029831 13.86 1438.71 235.8893333 7.66 1.064933464 26.78501012 61.49634693 90.87357838 81897034.21 382417.8129 5788012.535 2
P3-2 Whatman P3 T2 18 Whatman Whatman_Phase1 487.5124068 37.41361644 1338.766 445.315 7.88 1.06540782 55.56847083 151.4005484 215.6639221 57507347.75 112635.6512 18702620.36 2
P3-3 Whatman P3 T3 25 Whatman Whatman_Phase1 559.891322 49.55079452 1256.688333 598.7236667 7.3 1.066836368 109.5744614 245.3980808 357.2515273 108500695.4 367527.8555 28054529.28 2
P3-4 Whatman P3 T4 32 Whatman Whatman_Phase2 556.4747797 57.906 1218.269 560.4386667 7.24 1.068952814 132.6926414 290.2597811 437.0150985 75972103.39 268441.6667 27829638.12 2
P3-5 Whatman P3 T5 40 Whatman Whatman_Phase2 460.076339 62.70953425 1283.286333 523.2283333 7.26 1.062483762 194.4949147 317.258307 544.5647129 115532970.6 203795.1007 62744959.63 2
P3-6 Whatman P3 T6 50 Whatman Whatman_Phase2 48.18305085 13.30052055 1289.331333 84.3076 7.45 1.04284106 422.7539337 350.8222838 811.0568653 66095094.11 327317.6367 33335735.32 2
P4-0 Whatman P4 T0 0 D0 D0 0 0 NA NA 8.53 NA 0 0 0 5470687.755 108.0124416 1452596.252 2
P4-1 Whatman P4 T1 12 Whatman Whatman_Phase1 421.7017627 21.83375342 NA NA 7.29 1.061680413 36.22483741 142.6930831 179.8973567 148997245.1 1003438.123 112454084.2 2
P4-2 Whatman P4 T2 18 Whatman Whatman_Phase1 492.8808814 35.00309589 NA NA 7.84 1.066727809 94.85611324 240.8776302 331.1023481 44905922.05 118475.7533 23560088.16 2
P4-3 Whatman P4 T3 25 Whatman Whatman_Phase1 614.9871864 46.7119726 NA NA 7.33 1.069818298 98.65239398 283.338421 391.5762658 44837761.33 119310.7303 16607557.89 2
P4-4 Whatman P4 T4 32 Whatman Whatman_Phase2 592.9714576 44.62643836 NA NA 7.27 1.068911468 118.5920965 305.9593268 448.8427159 51468850.31 575688.9598 27310530.47 2
P4-5 Whatman P4 T5 40 Whatman Whatman_Phase2 455.7903051 54.12723288 NA NA 7.29 1.057704538 217.5518534 335.9347734 601.0146334 43040441.16 189857.7726 15849199.93 2
P4-6 Whatman P4 T6 50 Whatman Whatman_Phase2 12.69 0 1646.926667 64.97703333 7.47 1.042227202 450.9993681 367.5599891 861.3732365 42933461.77 173399.3966 16529197.26 2
server.R
View file @ cb45b332
......@@ -27,7 +27,7 @@ shinyServer
options = list(
dom = "lBtip",
pageLength = 10,
lengthMenu = list(c(10, 25, 50, 100,-1), list('10', '25', '50', '100', 'All')),
lengthMenu = list(c(10, 25, 50, 100, -1), list('10', '25', '50', '100', 'All')),
buttons = list(
'colvis',
list(
......@@ -114,14 +114,51 @@ shinyServer
return(d)
} else if (input$dataset == "rdata")
{
if (is.null(input$fileRData))
{
return()
}
load(input$fileRData$datapath)
return(data)
if (exists("data"))
{
return(data)
} else {
return()
}
} else {
load("demo/demo.RData")
return(get(input$dataset))
}
})
data <- reactiveValues()
{
observe({
if (!is.null(data16S()))
isolate(data <<- data16S())
})
}
output$downloadData <- {
downloadHandler(
filename = function() {
paste("Easy16S-data", Sys.Date(), "RData", sep = ".")
},
content = function(file) {
save(data, file = file)
}
)
}
output$downloadUI <- renderUI({
validate(need(data16S(), ""))
tags$div(
style = "text-align:center",
title = "Download as RData",
downloadButton("downloadData", "Download", style = "color: black; background-color: gray90")
)
})
output$rarefactionMin <- renderText({
validate(need(input$fileBiom, ""),
need(input$dataset == "input", ""))
......
ui.R
View file @ cb45b332
......@@ -67,7 +67,7 @@ shinyUI(dashboardPage(
fileInput("fileTree",
label = "Phylogenetic tree : ",
placeholder = "data.nwk")
)#,
),
# tags$div(
# title = "Representative FASTA sequences of OTU",
# fileInput(
......@@ -75,7 +75,8 @@ shinyUI(dashboardPage(
# label = "FASTA sequences : "),
# placeholder = "data.fasta"
# )
# )
# ),
uiOutput("downloadUI")
),
dashboardBody(
tabsetPanel(
......
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