Help with a code!

Patrizia · March 27, 2024, 9:23am

Hello, I'm very new to R and I'm trying to plot some data I have, but I cannot find the way. I'm sure it's a dumb question, but I'm not able to figure it out. Here is the question:

I have two excel tables, representing Species abundance (in rows) and treatment in columns. In one table treatments are NGS1, NGS2, NGS3 and so on, up to NGS49. In the other treatments are Taxonomy1, Taxonomy2, Taxonomy 3 and so on, up to Taxonomy 49. So, what I want is to plot all the samples of the first table, against those of the second.
The first thing I did (which maybe was not the right move), was to join both tables in one, with the "data.frame" code. Now, when I try to plot NGS columns, against Taxonomy columns, it just picks the first columns of both, so I get a plot representing just the two samples.
Is there maybe a way to split the treatment into two groups (NGS and Taxonomy), so that I can compare the 49 NGS samples to the 49 Taxonomy samples at the same time? Or any other way I can do this?

Thank you in advance and sorry in case the question is very dumb!

jrkrideau · March 27, 2024, 3:24pm

Welcome to the forum.

That is not a dumb question at all. R can be complicated and quirky.

What we probably need is to see your code and some sample data. Just copy your code and paste it here between
```

```

A handy way to supply some sample data is the dput() function. In the case of a large dataset something like dput(head(mydata, 100)) should supply the data we need. Just do dput(mydata) where mydata is your data. Copy the output and paste it here between
```

```

For general information see FAQ Asking Questions

Patrizia · April 1, 2024, 6:46am

Thank you so much for your help. I run the dput(mydata)code, using 40 instead of 100 cause there is a limited number of characters I can use in here, and this is the output:

structure(list(X = 1:20, Taxa = c("Ulnaria_ulna", "Achnanthidium_minutissimum",
"Nitzschia_palea", "Navicula_veneta", "Nitzschia_paleacea", "Melosira_varians",
"Fistulifera_saprophila", "Planothidium_lanceolatum", "Mayamaea_permitis",
"Cyclotella_meneghiniana", "Amphora_copulata", "Craticula_buderi",
"Nitzschia_inconspicua", "Nitzschia_capitellata", "Nitzschia_fonticola",
"Rhoicosphenia_abbreviata", "Achnanthidium_pyrenaicum", "Navicula_tripunctata",
"Nitzschia_frustulum", "Achnanthidium_eutrophilum"), NGS1 = c(6.75756458793289,
48.001501355042, 8.3306767145682, 10.3849857752652, 7.51387027290675,
0.0825314625126759, 14.5331481902685, 2.50713122347551, 6.15930432264964,
0.400839878207915, 0.00717923149693301, 0.640848605239318, 0.456304854406408,
0.0686260208429785, 0.0770565555143074, 0.0195811939250948, 0.055983831151006,
0.0121455015504516, 0.0244157009475025, 0), NGS2 = c(0.038795273236234,
0.178641131291838, 1.28059147873554, 3.00503979128826, 3.62342159306193,
0.601892399707542, 52.1268271605447, 0, 12.6842233044189, 1.48178656334284,
0.00324594737319074, 0.0510723493464696, 0.538484073830391, 1.99205251501901,
7.63170996220914, 0.0594087972866456, 0.0433487371963869, 3.45906327681437,
0.29845829928569, 0), NGS3 = c(22.6722980359667, 1.86400699048099,
0, 1.66738837369278, 6.41331274085265, 0.41022645328324, 27.9499987475793,
0.495243355464875, 55.7675249754809, 1.49308524225046, 0, 0.107375109458671,
1.03858045961821, 0.00300535660422078, 0.419814469756588, 0,
0.0746906005150969, 0.43937420716304, 0, 0), NGS4 = c(1.98817738959961,
31.1455339059451, 6.42519426128803, 2.21958063376199, 30.1598330522632,
0.331734375729987, 3.2766681157527, 0, 2.60804216179849, 0.00681150359517639,
0, 0.0294051872966077, 0.0197212942792069, 0, 13.5523522332935,
0.00153701299028779, 0.0399936075982398, 0.00589345607230487,
0, 4.77922705812871), NGS5 = c(66.3418400875589, 70.6528737139084,
4.07697490512422, 0.127644498015147, 0.243491396956423, 0.0125753884666739,
0, 0, 7.01912208175821, 0, 0, 1.99767051257378, 0.306455120740074,
0, 0, 0, 0.234517996979732, 0.0305267285646451, 0.271889348987913,
0), NGS6 = c(0.0770861376314104, 3.4960077452707, 1.72387386500296,
4.79128284290855, 0.819814684060119, 0.0891336806089489, 10.5830954881967,
0.0219361090645771, 32.8896075526215, 6.62841224236684, 0.00211836429654436,
0.0243965005589301, 7.2156853777225, 0.14263800858223, 5.20757392457809,
0.0531124248068363, 0.0276093947709671, 1.24276514768251, 0.0159432093963653,
2.7554603418784), NGS7 = c(0.0235330507711375, 0, 0.109760790344592,
0.413302708324854, 0.0784875760499812, 0.0479659875022809, 24.5095347853423,
0, 33.5719444119724, 0.0277365049097493, 4.80827210068893e-05,
0.0198981834257057, 15.3325158799713, 0.0176287508284037, 0.0471431814135667,
0.0036402822859042, 0.0188932171249289, 0.317713871733895, 0.0202095855308715,
0.433126639468088), NGS8 = c(0.699990008484979, 0.0879217015073157,
4.8357587932647, 26.2363831669907, 4.71818995897286, 0.0649749426898937,
10.8201530764522, 0, 12.2688381660485, 17.9125394808746, 0, 0.0471811437112339,
12.8484438152835, 0, 1.03234450999463, 0, 0.0435874765450315,
0.68031779119738, 0, 0), NGS9 = c(1.98817738959961, 31.1455339059451,
6.42519426128803, 2.21958063376199, 30.1598330522632, 0.331734375729987,
3.2766681157527, 0, 2.60804216179849, 0.00681150359517639, 0,
0.0294051872966077, 0.0197212942792069, 0, 13.5523522332935,
0.00153701299028779, 0.0399936075982398, 0.00589345607230487,
0, 4.77922705812871), NGS10 = c(0.212895109077827, 1.41760332681894,
1.54433252563773, 2.08551391290243, 0.662741636621971, 1.0431151243743,
38.6956648316489, 0.480680321226273, 28.8891304636822, 0.135350589465012,
0, 4.45754331244848, 2.44987910627988, 0.26536049581679, 0, 0,
0.104767994679205, 0, 0.127304876428737, 0), NGS11 = c(2.67369439990577,
0, 0, 33.1419931649068, 0, 0.87247757745402, 0, 0, 0.363024635900267,
0.0243527035470181, 0, 0.160913812703452, 64.5943214104103, 0.0733830332703782,
0, 0, 0.137590699782888, 0.0351174515755595, 0, 0), NGS12 = c(0.00970324070126635,
0.05815388803551, 0.300004336016836, 3.04575231546984, 0, 0.117135488221385,
18.0120917855259, 0.0300368844824414, 13.551661271095, 0.132065921283674,
0, 0.406145085053839, 3.63140635972473, 0.0692589226600411, 0,
0, 0.0263457675153483, 0.00879326855153554, 10.5796305607206,
0), NGS13 = c(0.89129232573996, 63.8052325950042, 6.05427281191083,
1.69861734038755, 0.114272546796966, 0.0122571383074336, 0.108779492752137,
0.031305855621518, 2.77702047859779, 2.45710860217695, 0.00119696763807262,
0.0703783045236121, 0.0694749655829953, 0, 5.93292352592199,
0, 0.0432191758307795, 0, 0, 0), NGS14 = c(43.2466503678865,
19.092085674355, 11.4600445856731, 2.01093095889098, 23.3564857254299,
0.0349593106793192, 22.2178314802238, 2.12148785075818, 12.6487848095367,
1.30141905121475, 0, 1.77324188913567, 0, 0.927777003826284,
0, 0, 0.261825891294896, 0.359136715614307, 0, 0), NGS15 = c(0.0118609048039743,
0, 0.0500623495416463, 0.863628550044531, 0.65096228603167, 0.0622759509602226,
22.9058435836596, 0, 39.4271113156173, 0.0978917976039213, 0.00210044191420881,
0.100194236115897, 7.71469779771595, 0.0409051038507131, 0.70536182360338,
0.0608895775668088, 0.0254458755581918, 0.869260414119914, 0.44474464467547,
0.396873445687882), NGS16 = c(0.0633616755292545, 1.67971605052316,
0.0133596284604961, 1.76252869190939, 0.950518506186873, 0.0558024612300993,
8.59721913394335, 0.610819672663073, 71.1870865912346, 0.0711272112283994,
0.00511521273160857, 0.0312391178864928, 1.14041089105528, 0,
0.230161918275085, 0.269721828652593, 0.0407635898768825, 0.670017387178846,
0.530668538497962, 0.886535605866803), NGS17 = c(0.116065761947912,
0.0411558201657061, 1.4425441836918, 2.39739934612035, 4.90953529368773,
0.0056653589061287, 40.6257216474984, 0.0109642735914728, 9.59140575976374,
0.274894761574383, 0, 37.7191796977375, 1.00635521375811, 0.043623272618896,
0.0902116289168572, 0, 0.0267054367131122, 0.00655597640399995,
0.151714771837674, 0), NGS18 = c(0.0155568640378596, 0.200041966111998,
0.705147116811079, 3.93288959011783, 0.731318157798135, 0.0718207595302126,
32.5662717879409, 0.11070041812053, 25.0445532710654, 0.328549267405352,
0, 0.0439443325030369, 0.44582467089248, 0.1453976121149, 13.1991203202991,
0, 0.0602806982982041, 0.213057402869678, 0.362988908755808,
0), NGS19 = c(0.0102010191988962, 0, 0, 0.0285188564380729, 0,
0.0528335487206541, 0, 0, 77.3351924686194, 0, 0, 0.0492980041366107,
0, 0, 0, 2.16591054502635, 0.0333788112913038, 0, 0, 0), NGS20 = c(1.37171041694148,
1.05938159548026, 2.22469549203164, 6.93915670988272, 1.5107360339536,
1.32828949274285, 2.30536317734806, 0.0250364083736036, 4.47867665059335,
0.844646866908582, 0.003867984046573, 0.290820696159609, 58.9067077834377,
0.0325594974199782, 0.229522513940953, 0.222533694938119, 0.0894771481673056,
7.62882271622015, 0.199461780848306, 0), NGS21 = c(0.095405389105136,
0.122970737464592, 3.90603309087424, 2.6749250515277, 1.39850291888671,
1.6962807549052, 18.4624448697781, 0, 48.6772899732811, 4.38236314112619,
0.00508447263700371, 0.0667974300977575, 2.27193111337114, 0.18725082877951,
4.82443076052411, 0, 0.0644951451248493, 1.43239054436544, 0,
0), NGS22 = c(0.00587620820770449, 0.052608349272676, 0.0266330294174837,
0.023564809624273, 0, 0.239052706429299, 9.08069934266108, 0.033655229348185,
75.7131258861879, 0.846747507787196, 0, 0.0319608252756607, 2.19076061957665,
0, 1.30021204517531, 0.0178565476294567, 0.0289595623175037,
8.59303727449197, 0.519209724882013, 0), NGS23 = c(12.117037778003,
53.7453108218954, 1.63833882763018, 0.337667578589081, 2.2077654845525,
1.11286265352503, 5.1877316904526, 2.90468633398779, 2.38315836802453,
0.268437954302248, 0, 18.3532701714575, 0.181560501348137, 0.100134389614811,
0.16005916290385, 0, 0.166729294667256, 2.47673290605602, 0,
0), NGS24 = c(0.453312302479855, 20.6772368176635, 1.19401735091211,
2.05470973763835, 3.72519493437489, 0.430472936988045, 22.6684802482249,
5.18883281377227, 24.5062608615091, 0.0203907690047059, 0.00196689348197841,
0.0959985374701597, 0.410781560407799, 0, 0, 0, 0.0603561407425555,
0.785207085110148, 0.258180395049816, 0), NGS25 = c(0.215959040413695,
9.45817871966076, 0.263842950490453, 0.295741866847134, 0, 0.996061117679763,
15.4760267279724, 0, 35.2852263810116, 0, 0, 1.97560130837423,
0.139845144583154, 0, 0, 0, 0.0621394631875393, 18.5884256427741,
0, 0), NGS26 = c(0.106717715627339, 48.5995453662778, 5.02718274261967,
4.60666116758564, 0.202825890854143, 0.600968881267653, 4.83031441519942,
0.0852547036274241, 19.2603379124576, 0.101281777399355, 0, 5.82334512351938,
1.08874761817846, 2.45613484109394, 0, 0, 0.121434491623436,
0.118551597699814, 0, 0), NGS27 = c(1.38405004586779, 0.281982057966211,
1.17554426537326, 11.2722886791376, 0.553905517643514, 1.17988737951704,
1.02057799163474, 0.617839945413178, 12.0292550437032, 0.874965472277289,
0, 62.8755930202999, 0.423049746950747, 4.86475306108754, 0.12426663871192,
0, 0.0711323215179966, 0, 0.894947727436878, 0), NGS28 = c(0.0191640663142572,
0.332941309314527, 1.12573235287691, 5.33563198550724, 23.8598850211779,
0.00471436990068833, 0.420552716498557, 0.0191560901333315, 66.4983757817094,
0.0426600288567991, 0, 0.839759073928477, 0.0615860292688866,
0.219538992906787, 0.0191044959623414, 0, 0.0253010222439906,
0.016789792512543, 0.0486401526375178, 0.0205342231806092), NGS29 = c(2.58381091575222,
0, 10.4509861518145, 12.0221291023134, 24.3640290330514, 0.0378567088953281,
0.980312821690078, 0, 15.6413976153468, 0.0133925931120002, 0.00619925786723509,
0.07154784481367, 16.9683942423556, 3.24529412079043, 0, 0, 0.044983516470162,
0.028886701375902, 4.14013471320046, 5.22204430888329), NGS30 = c(0.0249192413241342,
0, 7.04781993167599, 1.72961774864539, 0.0903114593837887, 0.000629808966477128,
9.56884792721437, 0, 80.0550030242479, 0, 0, 0.0147374586352985,
0.00767404455840156, 0, 0.122032121116964, 0, 0.00835220355849928,
0.00175535768246551, 0.00328684834736466, 0), NGS31 = c(0.247524385649142,
0.0291941742303935, 1.40630658594772, 31.5886819015501, 2.11706824756424,
0.104013267796908, 8.14973683376881, 0.157820174102885, 38.5486842572878,
0.13999896434821, 0, 1.69947153449797, 4.69667232175603, 0.36072918175886,
0, 0, 0.0191098645180767, 0, 0, 0), NGS32 = c(0.0136418812930442,
0.0539663689905043, 0.251791521691668, 0.431881173178304, 0.626756336433486,
0.0893970673862854, 16.1797870228652, 0.186311054994927, 47.9551958140764,
0, 0.00146993543256943, 0.0111320548757885, 0.357576355504187,
0.0565428750671224, 1.11064090963957, 0, 0.0151643669981176,
0.267364211731787, 0, 0.0230917139394665), NGS33 = c(3.57968280619678,
0.38119745163622, 1.57318592995171, 3.3837657436895, 0.860648849119932,
0.207940166788424, 11.1294700427591, 0.0200436245230077, 25.9310997928775,
18.9168673852773, 0.0169081013411048, 0.0735627806621822, 7.42036824260661,
0, 7.1479876974325, 0.343095329909432, 0.0582411760452999, 6.97613060833301,
0, 0.82205807694753), NGS34 = c(51.8256348486766, 21.6743973716663,
5.70647562459785, 0.125064449249115, 11.5545483923808, 0.182125508123183,
3.01774782668866, 3.67313534889541, 32.5421010940533, 1.59190758242991,
0, 0.167021314137343, 5.40566167813367, 0, 0, 0, 0.186153269594592,
0, 0, 10.8862792115102), NGS35 = c(0.0379174151217574, 6.88949979827231,
0, 17.7700720356958, 0.185649623714352, 0.00660751904181822,
11.5019870015044, 0, 0.931633752548541, 0, 0, 0.237861922360634,
0.615216023619618, 0.0956104491431537, 0, 0.984342571851699,
0.240939088591682, 0.0486660242203091, 0, 60.2056839476113),
NGS36 = c(0.153543723674718, 0.0113849023240514, 0, 2.96541275098069,
0.0147126086676334, 0.00866592183283487, 1.69941358907703,
0, 3.02060902090392, 0.00344090148247645, 0, 0.02182677716208,
9.51161644066397, 0, 0, 0, 0.0211561648730562, 0.00421761539989854,
3.30503816491175, 0), NGS37 = c(2.60104583451819, 9.56196604835829,
0, 0.475890169289509, 22.0119594319306, 0.112058225900441,
18.5883977874014, 0, 12.5943214362925, 1.11696061782757,
0, 1.91250433303342, 11.1264476181189, 0, 0, 0, 0.0284823182202242,
0, 0.661560379141532, 1.3566166145361), NGS38 = c(4.07945297808818,
22.61723378543, 0.064940282721813, 0.148475809064216, 18.9319364474526,
0.0371942939348831, 17.861848454438, 0.209951077977353, 9.00649404905959,
0.0214789973423628, 0, 2.07468333596762, 8.66793510722633,
0, 0, 0, 1.81195213921089, 0, 0.451147172851238, 0), NGS39 = c(0.0706604498023882,
0, 7.26531295210697, 26.4219240001236, 22.4085663512891,
0.00165311516893303, 5.73895549168155, 0.18739818170712,
4.51096028189232, 3.10955763829639, 0.00102670310983547,
1.50608672343921, 4.82967745052514, 0, 0, 0.00206988847486799,
0.0292668921856204, 0.010317697990696, 13.6739197692217,
0), NGS40 = c(0.112821033258729, 0.85410542028602, 1.34193798248575,
3.31197893387122, 0.0264262132194336, 0.00796556532024077,
28.5580691088651, 0.012827413899182, 46.0875347185858, 0.15430199370529,
0, 8.16651981277506, 1.83077776355542, 0.337793998293254,
0.0253298729109259, 0, 0.0184171892314341, 0.00447120679268883,
0.0102552900209923, 0), NGS41 = c(0.0133008743459121, 48.6773410850511,
1.3556896461801, 5.51281277318208, 0.129259627734828, 0.00143876103833793,
2.82238457369471, 0, 3.07104499014821, 0.0485765044782552,
0, 36.0761340141425, 0.614499627318652, 0.0913422676789195,
0, 0.00136039493697304, 0.0182150660355393, 0.0103534449778949,
0.00808298456621801, 0), NGS42 = c(0.00833564556055011, 0.0572938262507176,
0.943125790806968, 11.8118252123699, 0.0244660698072901,
0.00130114661365017, 0.861095763108183, 0.0054203056785881,
0.191846196978028, 1.23401223126569, 0, 63.1102184492069,
0.391040702219935, 13.7913418203266, 0, 0, 0.0266821746860153,
0.00602979890494902, 6.33948689784295, 0), NGS43 = c(1.85840966734622,
0.353610069968206, 13.181616997741, 9.10266081276299, 0.562382732976902,
0.225910535399374, 5.8851121278011, 0.830513445343487, 14.9498856759981,
6.83452662330844, 0, 29.6310890716873, 8.36434215687838,
0.593165034193873, 0.698037013942465, 0, 0.0296214919862156,
0.146568658639062, 0.0293772620212207, 0.374520362270232),
NGS44 = c(8.98357766336455, 0.589318063929205, 0.561058789856876,
6.26961311341626, 0.514784226319922, 0.046999556166536, 0.328513475771223,
0, 61.0746683872156, 0.330067912326817, 0.00287856725561097,
14.5717153784831, 1.85571576986379, 1.17765452253105, 0.152312796725635,
0, 0.0899808521638762, 0.289230095503815, 1.7740213493065,
0.213706162886409), NGS45 = c(0.00628075967437536, 0, 0,
1.46198077035109, 0, 0.0167400761510954, 21.7812870990465,
0, 52.5240752549622, 0, 0, 0.0159884851452056, 0.564837244497352,
0, 0, 0, 0.0308269626567839, 0.374807830958602, 0, 0.0578890858616403
), NGS46 = c(7.76086880356853, 0.14534983778136, 0.346542099683442,
3.69773967872993, 0, 0.0465164490894812, 0.583143119204788,
0, 65.6370271479614, 0.193627680309858, 0.00353838527659947,
12.584056074471, 2.39483006636567, 0.79813108049551, 0, 0,
0.0773077697032965, 0.0825342088535844, 1.95439048298546,
0), NGS47 = c(0.789438602727383, 44.5981995002164, 2.6949855169119,
4.97115908383563, 37.8108060507954, 0.103522196389958, 2.04295949705074,
1.12244459968807, 0.174087842241501, 0.2350316425656, 0,
0.0398888568016094, 0.0419399897826563, 0, 5.74158766569327,
0, 0.024183222326248, 0, 0, 0), NGS48 = c(15.3597635277663,
62.0666163108133, 0.191264922880888, 1.07297041022047, 0.184062955782019,
0.0340051078988955, 1.7935310171756, 0.0223205914836636,
2.66784410905841, 0.0596624635854359, 0.000950953086560778,
0.163080593024591, 0.135021670372934, 0, 3.12674045074837,
0.0113326188961648, 0.181219223293187, 18.1252004899456,
0, 0), NGS49 = c(16.8191116279315, 47.6631722592845, 3.23927443486789,
1.63679045126097, 0.0873853764447723, 0.0276415711824677,
3.4717915406365, 0, 5.79383032055487, 0.17439740838611, 0.000524209929433917,
2.25447389864684, 1.84097821491911, 0, 0.790064717350159,
0.0102224796503141, 2.4778163938617, 0.181051116354679, 0,
0.0670936287726436), Taxa.1 = c("Ulnaria_ulna", "Achnanthidium_minutissimum",
"Nitzschia_palea", "Navicula_veneta", "Nitzschia_paleacea",
"Melosira_varians", "Fistulifera_saprophila", "Planothidium_lanceolatum",
"Mayamaea_permitis", "Cyclotella_meneghiniana", "Amphora_copulata",
"Craticula_buderi", "Nitzschia_inconspicua", "Nitzschia_capitellata",
"Nitzschia_fonticola", "Rhoicosphenia_abbreviata", "Achnanthidium_pyrenaicum",
"Navicula_tripunctata", "Nitzschia_frustulum", "Achnanthidium_eutrophilum"
), Taxonomy1 = c(0, 86.6141732283464, 0, 0.78740157480315,
0.26246719160105, 0, 0, 0.26246719160105, 2.88713910761155,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0.26246719160105, 0), Taxonomy2 = c(1.06100795755968,
1.3262599469496, 0, 0.795755968169761, 0.795755968169761,
0, 0, 0.26525198938992, 39.5225464190981, 0, 0, 0, 0.530503978779841,
0, 0, 0, 0, 0, 0, 0), Taxonomy3 = c(0L, 100L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L
), Taxonomy4 = c(0, 30.9090909090909, 0.727272727272727,
2.54545454545454, 46.5454545454545, 0.363636363636364, 0,
0, 1.45454545454545, 0.363636363636364, 0, 0, 0.363636363636364,
0, 0, 0, 0, 0, 0, 0), Taxonomy5 = c(0, 9.88700564971751,
0.282485875706215, 22.316384180791, 0, 0, 0.564971751412429,
0, 7.34463276836158, 2.25988700564972, 0, 0, 16.1016949152542,
0, 5.64971751412429, 0, 0, 0.282485875706215, 0, 0), Taxonomy6 = c(0,
0, 0, 14.6529562982005, 8.48329048843188, 0, 0.51413881748072,
0, 16.452442159383, 7.7120822622108, 0, 0, 26.9922879177378,
0, 0, 0, 0, 0, 0, 0), Taxonomy7 = c(0, 0, 0, 0, 0, 0, 0,
0, 7.45501285347044, 0.25706940874036, 0, 0, 25.9640102827763,
0, 0, 0, 0, 4.11311053984576, 0, 0.25706940874036), Taxonomy8 = c(0,
0, 0, 2.3121387283237, 13.5838150289017, 0.578034682080925,
9.53757225433526, 0, 7.22543352601156, 0, 0, 0, 0, 2.60115606936416,
1.44508670520231, 0.289017341040462, 0, 0.578034682080925,
0, 0), Taxonomy9 = c(1.98817738959961, 31.1455339059451,
6.42519426128803, 2.21958063376199, 30.1598330522632, 0.331734375729987,
3.2766681157527, 0, 2.60804216179849, 0.00681150359517639,
0, 0.0294051872966077, 0.0197212942792069, 0, 13.5523522332935,
0.00153701299028779, 0.0399936075982398, 0.00589345607230487,
0, 4.77922705812871), Taxonomy10 = c(0, 0, 0, 0.263157894736842,
0, 0, 10.2631578947368, 0, 30.7894736842105, 0, 0, 0, 0.789473684210526,
0, 0, 0, 0, 0, 0, 0), Taxonomy11 = c(0.337837837837838, 2.7027027027027,
0, 0, 7.43243243243243, 0.337837837837838, 0, 0, 0, 0.675675675675676,
0, 0, 23.9864864864865, 0, 4.39189189189189, 0, 0, 0, 0,
0), Taxonomy12 = c(0, 0, 0, 1.44927536231884, 0, 0, 0, 0,
0, 0, 0, 0, 1.93236714975845, 0, 0, 0, 0, 0, 0, 0), Taxonomy13 = c(0,
95.8448753462604, 1.10803324099723, 0.554016620498615, 0,
0, 0, 0, 0.554016620498615, 0, 0, 0, 0.277008310249307, 0,
0, 0, 0, 0, 0, 0), Taxonomy14 = c(2.18579234972678, 5.46448087431694,
1.09289617486339, 1.63934426229508, 2.18579234972678, 1.09289617486339,
1.09289617486339, 0, 0.546448087431694, 0, 0, 0, 2.73224043715847,
0.546448087431694, 0, 0, 0, 0, 0, 0), Taxonomy15 = c(0, 0,
0, 0.510204081632653, 0.510204081632653, 0, 0, 0, 56.1224489795919,
0.255102040816327, 0, 0, 13.265306122449, 0, 0, 4.59183673469388,
0, 0.255102040816327, 0, 0), Taxonomy16 = c(0, 0, 0, 1.57728706624606,
0.315457413249211, 0, 0, 0, 14.8264984227129, 0, 0.315457413249211,
0, 18.2965299684543, 0, 0, 0, 0, 0.315457413249211, 0, 0),
Taxonomy17 = c(0.557103064066852, 0.835654596100279, 0, 11.6991643454039,
4.17827298050139, 0, 11.4206128133705, 0, 23.3983286908078,
0.557103064066852, 0, 10.8635097493036, 10.3064066852368,
0, 0, 0, 0, 0, 0, 0), Taxonomy18 = c(0, 0, 0, 1.69971671388102,
0, 0, 1.69971671388102, 0, 6.23229461756374, 1.13314447592068,
0, 0, 0, 0, 10.1983002832861, 0, 0, 0, 0.28328611898017,
0), Taxonomy19 = c(0, 1.26582278481013, 0, 1.26582278481013,
0.253164556962025, 0, 0.759493670886076, 0, 0.759493670886076,
2.0253164556962, 0, 0, 0, 0, 0.759493670886076, 0, 0, 0,
3.54430379746835, 0), Taxonomy20 = c(0, 0, 0, 2.96495956873315,
0, 0, 0, 0, 2.69541778975741, 0.269541778975741, 0, 0, 56.3342318059299,
0, 0, 0, 0, 4.31266846361186, 0, 0), Taxonomy21 = c(0, 0,
0, 3.1413612565445, 3.92670157068063, 0, 1.30890052356021,
0, 17.2774869109948, 0.261780104712042, 0, 0, 2.61780104712042,
0, 0, 0, 0, 0, 0, 0), Taxonomy22 = c(0, 1.50753768844221,
0, 8.29145728643216, 0.50251256281407, 0, 0, 0, 3.51758793969849,
0, 0, 0, 26.6331658291457, 0, 2.51256281407035, 0, 0, 2.01005025125628,
0, 0), Taxonomy23 = c(1.52671755725191, 55.3435114503817,
0.381679389312977, 0, 0, 0.381679389312977, 0, 1.90839694656488,
0, 0.381679389312977, 0, 1.52671755725191, 0, 0, 0, 0, 0,
0.381679389312977, 0, 0), Taxonomy24 = c(0, 20.1058201058201,
1.58730158730159, 2.64550264550265, 0.529100529100529, 0,
16.1375661375661, 0, 18.7830687830688, 0.264550264550265,
0, 0, 3.17460317460317, 0, 0, 0, 0, 0, 0, 0), Taxonomy25 = c(0,
9.67741935483871, 0, 1.34408602150538, 0, 1.0752688172043,
4.3010752688172, 0, 29.3010752688172, 0, 0, 0, 0.806451612903226,
0, 0, 0, 0, 7.79569892473118, 0, 0), Taxonomy26 = c(0, 4.52674897119342,
0, 1.23456790123457, 0, 0, 0, 0, 0, 0, 0, 1.23456790123457,
0.823045267489712, 0, 0, 0, 0, 0, 0, 0), Taxonomy27 = c(0.377358490566038,
0, 0.377358490566038, 17.3584905660377, 0.377358490566038,
10.5660377358491, 0, 0, 12.8301886792453, 0, 0, 7.16981132075472,
0.754716981132076, 2.64150943396226, 0, 0, 0, 0, 0, 0), Taxonomy28 = c(0,
0, 0, 6.79611650485437, 50.4854368932039, 0, 0, 0, 23.7864077669903,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Taxonomy29 = c(1.31926121372032,
0.527704485488127, 0.527704485488127, 25.065963060686, 3.16622691292876,
0, 0, 0, 5.54089709762533, 0, 0, 0, 25.8575197889182, 1.84696569920844,
0, 0, 0.527704485488127, 0, 0, 0), Taxonomy30 = c(0, 0.522193211488251,
0, 1.82767624020888, 0, 0, 0, 0, 95.3002610966058, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0), Taxonomy31 = c(0, 0, 0, 18.0156657963446,
0, 0, 0.522193211488251, 0, 53.2637075718016, 0, 0, 0, 5.48302872062663,
0, 0, 0, 0, 0, 0, 0), Taxonomy32 = c(0, 0, 0, 0, 0, 0, 1.98511166253102,
0, 27.2952853598015, 0, 0, 0, 1.98511166253102, 0, 0.248138957816377,
0, 0, 0, 0, 0), Taxonomy33 = c(0, 2.81329923273657, 0, 1.0230179028133,
0, 0, 0, 0, 3.32480818414322, 0.51150895140665, 0, 0, 23.2736572890026,
0, 1.79028132992327, 0.255754475703325, 0, 0.255754475703325,
0, 0), Taxonomy34 = c(0.31055900621118, 30.1242236024845,
0.62111801242236, 7.7639751552795, 3.72670807453416, 0, 0,
0.31055900621118, 4.6583850931677, 0, 0, 0, 7.14285714285714,
0, 0, 0, 0, 0, 0, 4.03726708074534), Taxonomy35 = c(0, 43.0517711171662,
0, 3.81471389645776, 1.63487738419618, 0, 0, 0, 4.63215258855586,
0, 0.272479564032697, 0, 1.63487738419618, 0, 0, 1.90735694822888,
0, 0, 0, 0.272479564032697), Taxonomy36 = c(0, 1.01351351351351,
0, 0.675675675675676, 0, 0, 1.01351351351351, 0, 5.74324324324324,
1.01351351351351, 0, 0, 9.7972972972973, 0, 0, 0, 0, 0, 1.01351351351351,
0), Taxonomy37 = c(0.255102040816327, 28.5714285714286, 0,
3.8265306122449, 47.1938775510204, 0, 1.02040816326531, 0,
0.76530612244898, 0, 0, 0.255102040816327, 0.76530612244898,
0, 0, 0, 0, 0, 0, 0), Taxonomy38 = c(0, 58.974358974359,
0, 0, 0, 0, 0, 0, 0, 0, 2.56410256410256, 0, 0, 0, 0, 0,
0, 0, 0, 0), Taxonomy39 = c(0, 0, 0, 7.52688172043011, 15.3225806451613,
0, 0.537634408602151, 0, 21.2365591397849, 0.537634408602151,
0, 0, 3.76344086021505, 0, 0, 0, 0, 0, 0, 0), Taxonomy40 = c(0,
0.584795321637427, 0, 4.3859649122807, 0, 0, 2.92397660818713,
0, 58.187134502924, 2.33918128654971, 0, 0.87719298245614,
0, 0.584795321637427, 0, 0, 0, 0, 0, 0), Taxonomy41 = c(0,
59.6825396825397, 4.44444444444444, 10.7936507936508, 0,
0, 0, 0, 0, 0, 0, 9.20634920634921, 2.85714285714286, 0,
0, 0, 0, 0, 0, 0), Taxonomy42 = c(0, 0, 0, 21.256038647343,
0, 0, 0, 0, 0, 0.241545893719807, 0, 1.69082125603865, 3.3816425120773,
16.4251207729469, 0, 0, 0, 0, 38.6473429951691, 0), Taxonomy43 = c(0,
0, 0.26525198938992, 9.81432360742705, 0, 0, 0, 0, 6.36604774535809,
15.6498673740053, 0, 2.38726790450928, 30.5039787798408,
0.26525198938992, 0, 0, 0, 0, 0, 0), Taxonomy44 = c(0, 0,
0, 0.251256281407035, 0, 0, 0, 0, 6.28140703517588, 0, 0,
0, 2.26130653266332, 0, 0, 0, 0, 0, 0, 0), Taxonomy45 = c(0,
0, 0, 1.02040816326531, 0.255102040816327, 0, 0, 0, 4.59183673469388,
0, 0, 0, 9.69387755102041, 0, 0, 0, 0, 0, 0, 0), Taxonomy46 = c(0,
0, 0.2710027100271, 1.3550135501355, 5.14905149051491, 1.3550135501355,
0, 0, 0.2710027100271, 0, 0, 0, 0.813008130081301, 0, 1.0840108401084,
1.8970189701897, 0, 1.3550135501355, 1.6260162601626, 1.3550135501355
), Taxonomy47 = c(0.302114803625378, 57.0996978851964, 0,
5.13595166163142, 24.4712990936556, 0.302114803625378, 0,
0, 3.62537764350453, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Taxonomy48 = c(0.520833333333333,
82.8125, 0.520833333333333, 1.04166666666667, 1.5625, 0,
0, 0, 0, 0.520833333333333, 0, 0.520833333333333, 0.520833333333333,
0, 2.08333333333333, 0, 0, 0, 0.520833333333333, 0), Taxonomy49 = c(0,
98.7616099071207, 0.309597523219814, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0)), row.names = c(NA, 20L), class = "data.frame")

Basically it's two dataframes with the same number of samples, 49, but two different tratments, and what I want to do is compare data of each couple of samples (e.g. Sample 1_NGS against Sample_1 Taxonomy) and plot results in different ways.

Thank you again for your help!

jrkrideau · April 1, 2024, 2:03pm

Great, the data came through with no problem. I have saved it is a file called raw.data.csv.

I am not sure I have a good grasp of what you want but here is a first try at a plot.

Depending on how your machine is set up you may have to install one or two packages {data.table} and {tidyverse}

Does this give you anything usefull?. You have a lot of overlapping data so I have added a bit of jittering to the plot.

suppressMessages(library(data.table)); 
suppressMessages(library(tidyverse))

dat1 <- read.csv("raw.data.csv")  # read in data
DT  <- as.data.table(dat1)  # Convert to data.table focmat. 

DT <- DT[, !c("X", "Taxa.1")]   # Drop unneeded variables. 


T1 <- DT[, .(Taxa, NGS1, Taxonomy1 )] # subset the first sample

## Convert from 'wide' to 'long' format to plot.
 F1 <- melt(T1,
            id.vars       = "Taxa",
            variable.name = "Sample",
            value.name    = "Value")

p1 <-  ggplot(F1, aes(Taxa, Value, colour = Sample, shape = Sample)) +
     geom_point() +
      coord_flip() + 
       theme(legend.position = "top") + ggtitle("Jitter") +
           geom_jitter() 
p1

nsg1

Patrizia · April 1, 2024, 2:44pm

Oh that's great, thank you so so much! I'll adapt your script using the entire data set and see what comes out.
Indeed, this has been really helpful!!

dromano · April 1, 2024, 3:02pm

Hi Patrizia,

Would you mind editing the post where you shared your data, as follows?

In the line before the structure() commands starts, place this code:

[details = "data (click to open)"]
``` r

In the line after the complete structure() command, place this code (i.e., just three backticks):

```

(Just in case: Backticks are made with the key to the left of 1/! on your keyboard.)

That would make it easier for folks to both read your post and copy your data.

jrkrideau · April 1, 2024, 4:50pm

This assumes a QUERTY keyboard layout. On one French keyboard layout that I have installed it seems to be "ALT+7".

dromano · April 1, 2024, 4:53pm

Oops — thanks for pointing that out!

Patrizia · April 2, 2024, 7:44am

Hi Dromano,
thanks for the advice!!

[details = "data (click to open)"]

structure(list(X = 1:20, Taxa = c("Ulnaria_ulna", "Achnanthidium_minutissimum",
"Nitzschia_palea", "Navicula_veneta", "Nitzschia_paleacea", "Melosira_varians",
"Fistulifera_saprophila", "Planothidium_lanceolatum", "Mayamaea_permitis",
"Cyclotella_meneghiniana", "Amphora_copulata", "Craticula_buderi",
"Nitzschia_inconspicua", "Nitzschia_capitellata", "Nitzschia_fonticola",
"Rhoicosphenia_abbreviata", "Achnanthidium_pyrenaicum", "Navicula_tripunctata",
"Nitzschia_frustulum", "Achnanthidium_eutrophilum"), NGS1 = c(6.75756458793289,
48.001501355042, 8.3306767145682, 10.3849857752652, 7.51387027290675,
0.0825314625126759, 14.5331481902685, 2.50713122347551, 6.15930432264964,
0.400839878207915, 0.00717923149693301, 0.640848605239318, 0.456304854406408,
0.0686260208429785, 0.0770565555143074, 0.0195811939250948, 0.055983831151006,
0.0121455015504516, 0.0244157009475025, 0), NGS2 = c(0.038795273236234,
0.178641131291838, 1.28059147873554, 3.00503979128826, 3.62342159306193,
0.601892399707542, 52.1268271605447, 0, 12.6842233044189, 1.48178656334284,
0.00324594737319074, 0.0510723493464696, 0.538484073830391, 1.99205251501901,
7.63170996220914, 0.0594087972866456, 0.0433487371963869, 3.45906327681437,
0.29845829928569, 0), NGS3 = c(22.6722980359667, 1.86400699048099,
0, 1.66738837369278, 6.41331274085265, 0.41022645328324, 27.9499987475793,
0.495243355464875, 55.7675249754809, 1.49308524225046, 0, 0.107375109458671,
1.03858045961821, 0.00300535660422078, 0.419814469756588, 0,
0.0746906005150969, 0.43937420716304, 0, 0), NGS4 = c(1.98817738959961,
31.1455339059451, 6.42519426128803, 2.21958063376199, 30.1598330522632,
0.331734375729987, 3.2766681157527, 0, 2.60804216179849, 0.00681150359517639,
0, 0.0294051872966077, 0.0197212942792069, 0, 13.5523522332935,
0.00153701299028779, 0.0399936075982398, 0.00589345607230487,
0, 4.77922705812871), NGS5 = c(66.3418400875589, 70.6528737139084,
4.07697490512422, 0.127644498015147, 0.243491396956423, 0.0125753884666739,
0, 0, 7.01912208175821, 0, 0, 1.99767051257378, 0.306455120740074,
0, 0, 0, 0.234517996979732, 0.0305267285646451, 0.271889348987913,
0), NGS6 = c(0.0770861376314104, 3.4960077452707, 1.72387386500296,
4.79128284290855, 0.819814684060119, 0.0891336806089489, 10.5830954881967,
0.0219361090645771, 32.8896075526215, 6.62841224236684, 0.00211836429654436,
0.0243965005589301, 7.2156853777225, 0.14263800858223, 5.20757392457809,
0.0531124248068363, 0.0276093947709671, 1.24276514768251, 0.0159432093963653,
2.7554603418784), NGS7 = c(0.0235330507711375, 0, 0.109760790344592,
0.413302708324854, 0.0784875760499812, 0.0479659875022809, 24.5095347853423,
0, 33.5719444119724, 0.0277365049097493, 4.80827210068893e-05,
0.0198981834257057, 15.3325158799713, 0.0176287508284037, 0.0471431814135667,
0.0036402822859042, 0.0188932171249289, 0.317713871733895, 0.0202095855308715,
0.433126639468088), NGS8 = c(0.699990008484979, 0.0879217015073157,
4.8357587932647, 26.2363831669907, 4.71818995897286, 0.0649749426898937,
10.8201530764522, 0, 12.2688381660485, 17.9125394808746, 0, 0.0471811437112339,
12.8484438152835, 0, 1.03234450999463, 0, 0.0435874765450315,
0.68031779119738, 0, 0), NGS9 = c(1.98817738959961, 31.1455339059451,
6.42519426128803, 2.21958063376199, 30.1598330522632, 0.331734375729987,
3.2766681157527, 0, 2.60804216179849, 0.00681150359517639, 0,
0.0294051872966077, 0.0197212942792069, 0, 13.5523522332935,
0.00153701299028779, 0.0399936075982398, 0.00589345607230487,
0, 4.77922705812871), NGS10 = c(0.212895109077827, 1.41760332681894,
1.54433252563773, 2.08551391290243, 0.662741636621971, 1.0431151243743,
38.6956648316489, 0.480680321226273, 28.8891304636822, 0.135350589465012,
0, 4.45754331244848, 2.44987910627988, 0.26536049581679, 0, 0,
0.104767994679205, 0, 0.127304876428737, 0), NGS11 = c(2.67369439990577,
0, 0, 33.1419931649068, 0, 0.87247757745402, 0, 0, 0.363024635900267,
0.0243527035470181, 0, 0.160913812703452, 64.5943214104103, 0.0733830332703782,
0, 0, 0.137590699782888, 0.0351174515755595, 0, 0), NGS12 = c(0.00970324070126635,
0.05815388803551, 0.300004336016836, 3.04575231546984, 0, 0.117135488221385,
18.0120917855259, 0.0300368844824414, 13.551661271095, 0.132065921283674,
0, 0.406145085053839, 3.63140635972473, 0.0692589226600411, 0,
0, 0.0263457675153483, 0.00879326855153554, 10.5796305607206,
0), NGS13 = c(0.89129232573996, 63.8052325950042, 6.05427281191083,
1.69861734038755, 0.114272546796966, 0.0122571383074336, 0.108779492752137,
0.031305855621518, 2.77702047859779, 2.45710860217695, 0.00119696763807262,
0.0703783045236121, 0.0694749655829953, 0, 5.93292352592199,
0, 0.0432191758307795, 0, 0, 0), NGS14 = c(43.2466503678865,
19.092085674355, 11.4600445856731, 2.01093095889098, 23.3564857254299,
0.0349593106793192, 22.2178314802238, 2.12148785075818, 12.6487848095367,
1.30141905121475, 0, 1.77324188913567, 0, 0.927777003826284,
0, 0, 0.261825891294896, 0.359136715614307, 0, 0), NGS15 = c(0.0118609048039743,
0, 0.0500623495416463, 0.863628550044531, 0.65096228603167, 0.0622759509602226,
22.9058435836596, 0, 39.4271113156173, 0.0978917976039213, 0.00210044191420881,
0.100194236115897, 7.71469779771595, 0.0409051038507131, 0.70536182360338,
0.0608895775668088, 0.0254458755581918, 0.869260414119914, 0.44474464467547,
0.396873445687882), NGS16 = c(0.0633616755292545, 1.67971605052316,
0.0133596284604961, 1.76252869190939, 0.950518506186873, 0.0558024612300993,
8.59721913394335, 0.610819672663073, 71.1870865912346, 0.0711272112283994,
0.00511521273160857, 0.0312391178864928, 1.14041089105528, 0,
0.230161918275085, 0.269721828652593, 0.0407635898768825, 0.670017387178846,
0.530668538497962, 0.886535605866803), NGS17 = c(0.116065761947912,
0.0411558201657061, 1.4425441836918, 2.39739934612035, 4.90953529368773,
0.0056653589061287, 40.6257216474984, 0.0109642735914728, 9.59140575976374,
0.274894761574383, 0, 37.7191796977375, 1.00635521375811, 0.043623272618896,
0.0902116289168572, 0, 0.0267054367131122, 0.00655597640399995,
0.151714771837674, 0), NGS18 = c(0.0155568640378596, 0.200041966111998,
0.705147116811079, 3.93288959011783, 0.731318157798135, 0.0718207595302126,
32.5662717879409, 0.11070041812053, 25.0445532710654, 0.328549267405352,
0, 0.0439443325030369, 0.44582467089248, 0.1453976121149, 13.1991203202991,
0, 0.0602806982982041, 0.213057402869678, 0.362988908755808,
0), NGS19 = c(0.0102010191988962, 0, 0, 0.0285188564380729, 0,
0.0528335487206541, 0, 0, 77.3351924686194, 0, 0, 0.0492980041366107,
0, 0, 0, 2.16591054502635, 0.0333788112913038, 0, 0, 0), NGS20 = c(1.37171041694148,
1.05938159548026, 2.22469549203164, 6.93915670988272, 1.5107360339536,
1.32828949274285, 2.30536317734806, 0.0250364083736036, 4.47867665059335,
0.844646866908582, 0.003867984046573, 0.290820696159609, 58.9067077834377,
0.0325594974199782, 0.229522513940953, 0.222533694938119, 0.0894771481673056,
7.62882271622015, 0.199461780848306, 0), NGS21 = c(0.095405389105136,
0.122970737464592, 3.90603309087424, 2.6749250515277, 1.39850291888671,
1.6962807549052, 18.4624448697781, 0, 48.6772899732811, 4.38236314112619,
0.00508447263700371, 0.0667974300977575, 2.27193111337114, 0.18725082877951,
4.82443076052411, 0, 0.0644951451248493, 1.43239054436544, 0,
0), NGS22 = c(0.00587620820770449, 0.052608349272676, 0.0266330294174837,
0.023564809624273, 0, 0.239052706429299, 9.08069934266108, 0.033655229348185,
75.7131258861879, 0.846747507787196, 0, 0.0319608252756607, 2.19076061957665,
0, 1.30021204517531, 0.0178565476294567, 0.0289595623175037,
8.59303727449197, 0.519209724882013, 0), NGS23 = c(12.117037778003,
53.7453108218954, 1.63833882763018, 0.337667578589081, 2.2077654845525,
1.11286265352503, 5.1877316904526, 2.90468633398779, 2.38315836802453,
0.268437954302248, 0, 18.3532701714575, 0.181560501348137, 0.100134389614811,
0.16005916290385, 0, 0.166729294667256, 2.47673290605602, 0,
0), NGS24 = c(0.453312302479855, 20.6772368176635, 1.19401735091211,
2.05470973763835, 3.72519493437489, 0.430472936988045, 22.6684802482249,
5.18883281377227, 24.5062608615091, 0.0203907690047059, 0.00196689348197841,
0.0959985374701597, 0.410781560407799, 0, 0, 0, 0.0603561407425555,
0.785207085110148, 0.258180395049816, 0), NGS25 = c(0.215959040413695,
9.45817871966076, 0.263842950490453, 0.295741866847134, 0, 0.996061117679763,
15.4760267279724, 0, 35.2852263810116, 0, 0, 1.97560130837423,
0.139845144583154, 0, 0, 0, 0.0621394631875393, 18.5884256427741,
0, 0), NGS26 = c(0.106717715627339, 48.5995453662778, 5.02718274261967,
4.60666116758564, 0.202825890854143, 0.600968881267653, 4.83031441519942,
0.0852547036274241, 19.2603379124576, 0.101281777399355, 0, 5.82334512351938,
1.08874761817846, 2.45613484109394, 0, 0, 0.121434491623436,
0.118551597699814, 0, 0), NGS27 = c(1.38405004586779, 0.281982057966211,
1.17554426537326, 11.2722886791376, 0.553905517643514, 1.17988737951704,
1.02057799163474, 0.617839945413178, 12.0292550437032, 0.874965472277289,
0, 62.8755930202999, 0.423049746950747, 4.86475306108754, 0.12426663871192,
0, 0.0711323215179966, 0, 0.894947727436878, 0), NGS28 = c(0.0191640663142572,
0.332941309314527, 1.12573235287691, 5.33563198550724, 23.8598850211779,
0.00471436990068833, 0.420552716498557, 0.0191560901333315, 66.4983757817094,
0.0426600288567991, 0, 0.839759073928477, 0.0615860292688866,
0.219538992906787, 0.0191044959623414, 0, 0.0253010222439906,
0.016789792512543, 0.0486401526375178, 0.0205342231806092), NGS29 = c(2.58381091575222,
0, 10.4509861518145, 12.0221291023134, 24.3640290330514, 0.0378567088953281,
0.980312821690078, 0, 15.6413976153468, 0.0133925931120002, 0.00619925786723509,
0.07154784481367, 16.9683942423556, 3.24529412079043, 0, 0, 0.044983516470162,
0.028886701375902, 4.14013471320046, 5.22204430888329), NGS30 = c(0.0249192413241342,
0, 7.04781993167599, 1.72961774864539, 0.0903114593837887, 0.000629808966477128,
9.56884792721437, 0, 80.0550030242479, 0, 0, 0.0147374586352985,
0.00767404455840156, 0, 0.122032121116964, 0, 0.00835220355849928,
0.00175535768246551, 0.00328684834736466, 0), NGS31 = c(0.247524385649142,
0.0291941742303935, 1.40630658594772, 31.5886819015501, 2.11706824756424,
0.104013267796908, 8.14973683376881, 0.157820174102885, 38.5486842572878,
0.13999896434821, 0, 1.69947153449797, 4.69667232175603, 0.36072918175886,
0, 0, 0.0191098645180767, 0, 0, 0), NGS32 = c(0.0136418812930442,
0.0539663689905043, 0.251791521691668, 0.431881173178304, 0.626756336433486,
0.0893970673862854, 16.1797870228652, 0.186311054994927, 47.9551958140764,
0, 0.00146993543256943, 0.0111320548757885, 0.357576355504187,
0.0565428750671224, 1.11064090963957, 0, 0.0151643669981176,
0.267364211731787, 0, 0.0230917139394665), NGS33 = c(3.57968280619678,
0.38119745163622, 1.57318592995171, 3.3837657436895, 0.860648849119932,
0.207940166788424, 11.1294700427591, 0.0200436245230077, 25.9310997928775,
18.9168673852773, 0.0169081013411048, 0.0735627806621822, 7.42036824260661,
0, 7.1479876974325, 0.343095329909432, 0.0582411760452999, 6.97613060833301,
0, 0.82205807694753), NGS34 = c(51.8256348486766, 21.6743973716663,
5.70647562459785, 0.125064449249115, 11.5545483923808, 0.182125508123183,
3.01774782668866, 3.67313534889541, 32.5421010940533, 1.59190758242991,
0, 0.167021314137343, 5.40566167813367, 0, 0, 0, 0.186153269594592,
0, 0, 10.8862792115102), NGS35 = c(0.0379174151217574, 6.88949979827231,
0, 17.7700720356958, 0.185649623714352, 0.00660751904181822,
11.5019870015044, 0, 0.931633752548541, 0, 0, 0.237861922360634,
0.615216023619618, 0.0956104491431537, 0, 0.984342571851699,
0.240939088591682, 0.0486660242203091, 0, 60.2056839476113),
NGS36 = c(0.153543723674718, 0.0113849023240514, 0, 2.96541275098069,
0.0147126086676334, 0.00866592183283487, 1.69941358907703,
0, 3.02060902090392, 0.00344090148247645, 0, 0.02182677716208,
9.51161644066397, 0, 0, 0, 0.0211561648730562, 0.00421761539989854,
3.30503816491175, 0), NGS37 = c(2.60104583451819, 9.56196604835829,
0, 0.475890169289509, 22.0119594319306, 0.112058225900441,
18.5883977874014, 0, 12.5943214362925, 1.11696061782757,
0, 1.91250433303342, 11.1264476181189, 0, 0, 0, 0.0284823182202242,
0, 0.661560379141532, 1.3566166145361), NGS38 = c(4.07945297808818,
22.61723378543, 0.064940282721813, 0.148475809064216, 18.9319364474526,
0.0371942939348831, 17.861848454438, 0.209951077977353, 9.00649404905959,
0.0214789973423628, 0, 2.07468333596762, 8.66793510722633,
0, 0, 0, 1.81195213921089, 0, 0.451147172851238, 0), NGS39 = c(0.0706604498023882,
0, 7.26531295210697, 26.4219240001236, 22.4085663512891,
0.00165311516893303, 5.73895549168155, 0.18739818170712,
4.51096028189232, 3.10955763829639, 0.00102670310983547,
1.50608672343921, 4.82967745052514, 0, 0, 0.00206988847486799,
0.0292668921856204, 0.010317697990696, 13.6739197692217,
0), NGS40 = c(0.112821033258729, 0.85410542028602, 1.34193798248575,
3.31197893387122, 0.0264262132194336, 0.00796556532024077,
28.5580691088651, 0.012827413899182, 46.0875347185858, 0.15430199370529,
0, 8.16651981277506, 1.83077776355542, 0.337793998293254,
0.0253298729109259, 0, 0.0184171892314341, 0.00447120679268883,
0.0102552900209923, 0), NGS41 = c(0.0133008743459121, 48.6773410850511,
1.3556896461801, 5.51281277318208, 0.129259627734828, 0.00143876103833793,
2.82238457369471, 0, 3.07104499014821, 0.0485765044782552,
0, 36.0761340141425, 0.614499627318652, 0.0913422676789195,
0, 0.00136039493697304, 0.0182150660355393, 0.0103534449778949,
0.00808298456621801, 0), NGS42 = c(0.00833564556055011, 0.0572938262507176,
0.943125790806968, 11.8118252123699, 0.0244660698072901,
0.00130114661365017, 0.861095763108183, 0.0054203056785881,
0.191846196978028, 1.23401223126569, 0, 63.1102184492069,
0.391040702219935, 13.7913418203266, 0, 0, 0.0266821746860153,
0.00602979890494902, 6.33948689784295, 0), NGS43 = c(1.85840966734622,
0.353610069968206, 13.181616997741, 9.10266081276299, 0.562382732976902,
0.225910535399374, 5.8851121278011, 0.830513445343487, 14.9498856759981,
6.83452662330844, 0, 29.6310890716873, 8.36434215687838,
0.593165034193873, 0.698037013942465, 0, 0.0296214919862156,
0.146568658639062, 0.0293772620212207, 0.374520362270232),
NGS44 = c(8.98357766336455, 0.589318063929205, 0.561058789856876,
6.26961311341626, 0.514784226319922, 0.046999556166536, 0.328513475771223,
0, 61.0746683872156, 0.330067912326817, 0.00287856725561097,
14.5717153784831, 1.85571576986379, 1.17765452253105, 0.152312796725635,
0, 0.0899808521638762, 0.289230095503815, 1.7740213493065,
0.213706162886409), NGS45 = c(0.00628075967437536, 0, 0,
1.46198077035109, 0, 0.0167400761510954, 21.7812870990465,
0, 52.5240752549622, 0, 0, 0.0159884851452056, 0.564837244497352,
0, 0, 0, 0.0308269626567839, 0.374807830958602, 0, 0.0578890858616403
), NGS46 = c(7.76086880356853, 0.14534983778136, 0.346542099683442,
3.69773967872993, 0, 0.0465164490894812, 0.583143119204788,
0, 65.6370271479614, 0.193627680309858, 0.00353838527659947,
12.584056074471, 2.39483006636567, 0.79813108049551, 0, 0,
0.0773077697032965, 0.0825342088535844, 1.95439048298546,
0), NGS47 = c(0.789438602727383, 44.5981995002164, 2.6949855169119,
4.97115908383563, 37.8108060507954, 0.103522196389958, 2.04295949705074,
1.12244459968807, 0.174087842241501, 0.2350316425656, 0,
0.0398888568016094, 0.0419399897826563, 0, 5.74158766569327,
0, 0.024183222326248, 0, 0, 0), NGS48 = c(15.3597635277663,
62.0666163108133, 0.191264922880888, 1.07297041022047, 0.184062955782019,
0.0340051078988955, 1.7935310171756, 0.0223205914836636,
2.66784410905841, 0.0596624635854359, 0.000950953086560778,
0.163080593024591, 0.135021670372934, 0, 3.12674045074837,
0.0113326188961648, 0.181219223293187, 18.1252004899456,
0, 0), NGS49 = c(16.8191116279315, 47.6631722592845, 3.23927443486789,
1.63679045126097, 0.0873853764447723, 0.0276415711824677,
3.4717915406365, 0, 5.79383032055487, 0.17439740838611, 0.000524209929433917,
2.25447389864684, 1.84097821491911, 0, 0.790064717350159,
0.0102224796503141, 2.4778163938617, 0.181051116354679, 0,
0.0670936287726436), Taxa.1 = c("Ulnaria_ulna", "Achnanthidium_minutissimum",
"Nitzschia_palea", "Navicula_veneta", "Nitzschia_paleacea",
"Melosira_varians", "Fistulifera_saprophila", "Planothidium_lanceolatum",
"Mayamaea_permitis", "Cyclotella_meneghiniana", "Amphora_copulata",
"Craticula_buderi", "Nitzschia_inconspicua", "Nitzschia_capitellata",
"Nitzschia_fonticola", "Rhoicosphenia_abbreviata", "Achnanthidium_pyrenaicum",
"Navicula_tripunctata", "Nitzschia_frustulum", "Achnanthidium_eutrophilum"
), Taxonomy1 = c(0, 86.6141732283464, 0, 0.78740157480315,
0.26246719160105, 0, 0, 0.26246719160105, 2.88713910761155,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0.26246719160105, 0), Taxonomy2 = c(1.06100795755968,
1.3262599469496, 0, 0.795755968169761, 0.795755968169761,
0, 0, 0.26525198938992, 39.5225464190981, 0, 0, 0, 0.530503978779841,
0, 0, 0, 0, 0, 0, 0), Taxonomy3 = c(0L, 100L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L
), Taxonomy4 = c(0, 30.9090909090909, 0.727272727272727,
2.54545454545454, 46.5454545454545, 0.363636363636364, 0,
0, 1.45454545454545, 0.363636363636364, 0, 0, 0.363636363636364,
0, 0, 0, 0, 0, 0, 0), Taxonomy5 = c(0, 9.88700564971751,
0.282485875706215, 22.316384180791, 0, 0, 0.564971751412429,
0, 7.34463276836158, 2.25988700564972, 0, 0, 16.1016949152542,
0, 5.64971751412429, 0, 0, 0.282485875706215, 0, 0), Taxonomy6 = c(0,
0, 0, 14.6529562982005, 8.48329048843188, 0, 0.51413881748072,
0, 16.452442159383, 7.7120822622108, 0, 0, 26.9922879177378,
0, 0, 0, 0, 0, 0, 0), Taxonomy7 = c(0, 0, 0, 0, 0, 0, 0,
0, 7.45501285347044, 0.25706940874036, 0, 0, 25.9640102827763,
0, 0, 0, 0, 4.11311053984576, 0, 0.25706940874036), Taxonomy8 = c(0,
0, 0, 2.3121387283237, 13.5838150289017, 0.578034682080925,
9.53757225433526, 0, 7.22543352601156, 0, 0, 0, 0, 2.60115606936416,
1.44508670520231, 0.289017341040462, 0, 0.578034682080925,
0, 0), Taxonomy9 = c(1.98817738959961, 31.1455339059451,
6.42519426128803, 2.21958063376199, 30.1598330522632, 0.331734375729987,
3.2766681157527, 0, 2.60804216179849, 0.00681150359517639,
0, 0.0294051872966077, 0.0197212942792069, 0, 13.5523522332935,
0.00153701299028779, 0.0399936075982398, 0.00589345607230487,
0, 4.77922705812871), Taxonomy10 = c(0, 0, 0, 0.263157894736842,
0, 0, 10.2631578947368, 0, 30.7894736842105, 0, 0, 0, 0.789473684210526,
0, 0, 0, 0, 0, 0, 0), Taxonomy11 = c(0.337837837837838, 2.7027027027027,
0, 0, 7.43243243243243, 0.337837837837838, 0, 0, 0, 0.675675675675676,
0, 0, 23.9864864864865, 0, 4.39189189189189, 0, 0, 0, 0,
0), Taxonomy12 = c(0, 0, 0, 1.44927536231884, 0, 0, 0, 0,
0, 0, 0, 0, 1.93236714975845, 0, 0, 0, 0, 0, 0, 0), Taxonomy13 = c(0,
95.8448753462604, 1.10803324099723, 0.554016620498615, 0,
0, 0, 0, 0.554016620498615, 0, 0, 0, 0.277008310249307, 0,
0, 0, 0, 0, 0, 0), Taxonomy14 = c(2.18579234972678, 5.46448087431694,
1.09289617486339, 1.63934426229508, 2.18579234972678, 1.09289617486339,
1.09289617486339, 0, 0.546448087431694, 0, 0, 0, 2.73224043715847,
0.546448087431694, 0, 0, 0, 0, 0, 0), Taxonomy15 = c(0, 0,
0, 0.510204081632653, 0.510204081632653, 0, 0, 0, 56.1224489795919,
0.255102040816327, 0, 0, 13.265306122449, 0, 0, 4.59183673469388,
0, 0.255102040816327, 0, 0), Taxonomy16 = c(0, 0, 0, 1.57728706624606,
0.315457413249211, 0, 0, 0, 14.8264984227129, 0, 0.315457413249211,
0, 18.2965299684543, 0, 0, 0, 0, 0.315457413249211, 0, 0),
Taxonomy17 = c(0.557103064066852, 0.835654596100279, 0, 11.6991643454039,
4.17827298050139, 0, 11.4206128133705, 0, 23.3983286908078,
0.557103064066852, 0, 10.8635097493036, 10.3064066852368,
0, 0, 0, 0, 0, 0, 0), Taxonomy18 = c(0, 0, 0, 1.69971671388102,
0, 0, 1.69971671388102, 0, 6.23229461756374, 1.13314447592068,
0, 0, 0, 0, 10.1983002832861, 0, 0, 0, 0.28328611898017,
0), Taxonomy19 = c(0, 1.26582278481013, 0, 1.26582278481013,
0.253164556962025, 0, 0.759493670886076, 0, 0.759493670886076,
2.0253164556962, 0, 0, 0, 0, 0.759493670886076, 0, 0, 0,
3.54430379746835, 0), Taxonomy20 = c(0, 0, 0, 2.96495956873315,
0, 0, 0, 0, 2.69541778975741, 0.269541778975741, 0, 0, 56.3342318059299,
0, 0, 0, 0, 4.31266846361186, 0, 0), Taxonomy21 = c(0, 0,
0, 3.1413612565445, 3.92670157068063, 0, 1.30890052356021,
0, 17.2774869109948, 0.261780104712042, 0, 0, 2.61780104712042,
0, 0, 0, 0, 0, 0, 0), Taxonomy22 = c(0, 1.50753768844221,
0, 8.29145728643216, 0.50251256281407, 0, 0, 0, 3.51758793969849,
0, 0, 0, 26.6331658291457, 0, 2.51256281407035, 0, 0, 2.01005025125628,
0, 0), Taxonomy23 = c(1.52671755725191, 55.3435114503817,
0.381679389312977, 0, 0, 0.381679389312977, 0, 1.90839694656488,
0, 0.381679389312977, 0, 1.52671755725191, 0, 0, 0, 0, 0,
0.381679389312977, 0, 0), Taxonomy24 = c(0, 20.1058201058201,
1.58730158730159, 2.64550264550265, 0.529100529100529, 0,
16.1375661375661, 0, 18.7830687830688, 0.264550264550265,
0, 0, 3.17460317460317, 0, 0, 0, 0, 0, 0, 0), Taxonomy25 = c(0,
9.67741935483871, 0, 1.34408602150538, 0, 1.0752688172043,
4.3010752688172, 0, 29.3010752688172, 0, 0, 0, 0.806451612903226,
0, 0, 0, 0, 7.79569892473118, 0, 0), Taxonomy26 = c(0, 4.52674897119342,
0, 1.23456790123457, 0, 0, 0, 0, 0, 0, 0, 1.23456790123457,
0.823045267489712, 0, 0, 0, 0, 0, 0, 0), Taxonomy27 = c(0.377358490566038,
0, 0.377358490566038, 17.3584905660377, 0.377358490566038,
10.5660377358491, 0, 0, 12.8301886792453, 0, 0, 7.16981132075472,
0.754716981132076, 2.64150943396226, 0, 0, 0, 0, 0, 0), Taxonomy28 = c(0,
0, 0, 6.79611650485437, 50.4854368932039, 0, 0, 0, 23.7864077669903,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Taxonomy29 = c(1.31926121372032,
0.527704485488127, 0.527704485488127, 25.065963060686, 3.16622691292876,
0, 0, 0, 5.54089709762533, 0, 0, 0, 25.8575197889182, 1.84696569920844,
0, 0, 0.527704485488127, 0, 0, 0), Taxonomy30 = c(0, 0.522193211488251,
0, 1.82767624020888, 0, 0, 0, 0, 95.3002610966058, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0), Taxonomy31 = c(0, 0, 0, 18.0156657963446,
0, 0, 0.522193211488251, 0, 53.2637075718016, 0, 0, 0, 5.48302872062663,
0, 0, 0, 0, 0, 0, 0), Taxonomy32 = c(0, 0, 0, 0, 0, 0, 1.98511166253102,
0, 27.2952853598015, 0, 0, 0, 1.98511166253102, 0, 0.248138957816377,
0, 0, 0, 0, 0), Taxonomy33 = c(0, 2.81329923273657, 0, 1.0230179028133,
0, 0, 0, 0, 3.32480818414322, 0.51150895140665, 0, 0, 23.2736572890026,
0, 1.79028132992327, 0.255754475703325, 0, 0.255754475703325,
0, 0), Taxonomy34 = c(0.31055900621118, 30.1242236024845,
0.62111801242236, 7.7639751552795, 3.72670807453416, 0, 0,
0.31055900621118, 4.6583850931677, 0, 0, 0, 7.14285714285714,
0, 0, 0, 0, 0, 0, 4.03726708074534), Taxonomy35 = c(0, 43.0517711171662,
0, 3.81471389645776, 1.63487738419618, 0, 0, 0, 4.63215258855586,
0, 0.272479564032697, 0, 1.63487738419618, 0, 0, 1.90735694822888,
0, 0, 0, 0.272479564032697), Taxonomy36 = c(0, 1.01351351351351,
0, 0.675675675675676, 0, 0, 1.01351351351351, 0, 5.74324324324324,
1.01351351351351, 0, 0, 9.7972972972973, 0, 0, 0, 0, 0, 1.01351351351351,
0), Taxonomy37 = c(0.255102040816327, 28.5714285714286, 0,
3.8265306122449, 47.1938775510204, 0, 1.02040816326531, 0,
0.76530612244898, 0, 0, 0.255102040816327, 0.76530612244898,
0, 0, 0, 0, 0, 0, 0), Taxonomy38 = c(0, 58.974358974359,
0, 0, 0, 0, 0, 0, 0, 0, 2.56410256410256, 0, 0, 0, 0, 0,
0, 0, 0, 0), Taxonomy39 = c(0, 0, 0, 7.52688172043011, 15.3225806451613,
0, 0.537634408602151, 0, 21.2365591397849, 0.537634408602151,
0, 0, 3.76344086021505, 0, 0, 0, 0, 0, 0, 0), Taxonomy40 = c(0,
0.584795321637427, 0, 4.3859649122807, 0, 0, 2.92397660818713,
0, 58.187134502924, 2.33918128654971, 0, 0.87719298245614,
0, 0.584795321637427, 0, 0, 0, 0, 0, 0), Taxonomy41 = c(0,
59.6825396825397, 4.44444444444444, 10.7936507936508, 0,
0, 0, 0, 0, 0, 0, 9.20634920634921, 2.85714285714286, 0,
0, 0, 0, 0, 0, 0), Taxonomy42 = c(0, 0, 0, 21.256038647343,
0, 0, 0, 0, 0, 0.241545893719807, 0, 1.69082125603865, 3.3816425120773,
16.4251207729469, 0, 0, 0, 0, 38.6473429951691, 0), Taxonomy43 = c(0,
0, 0.26525198938992, 9.81432360742705, 0, 0, 0, 0, 6.36604774535809,
15.6498673740053, 0, 2.38726790450928, 30.5039787798408,
0.26525198938992, 0, 0, 0, 0, 0, 0), Taxonomy44 = c(0, 0,
0, 0.251256281407035, 0, 0, 0, 0, 6.28140703517588, 0, 0,
0, 2.26130653266332, 0, 0, 0, 0, 0, 0, 0), Taxonomy45 = c(0,
0, 0, 1.02040816326531, 0.255102040816327, 0, 0, 0, 4.59183673469388,
0, 0, 0, 9.69387755102041, 0, 0, 0, 0, 0, 0, 0), Taxonomy46 = c(0,
0, 0.2710027100271, 1.3550135501355, 5.14905149051491, 1.3550135501355,
0, 0, 0.2710027100271, 0, 0, 0, 0.813008130081301, 0, 1.0840108401084,
1.8970189701897, 0, 1.3550135501355, 1.6260162601626, 1.3550135501355
), Taxonomy47 = c(0.302114803625378, 57.0996978851964, 0,
5.13595166163142, 24.4712990936556, 0.302114803625378, 0,
0, 3.62537764350453, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Taxonomy48 = c(0.520833333333333,
82.8125, 0.520833333333333, 1.04166666666667, 1.5625, 0,
0, 0, 0, 0.520833333333333, 0, 0.520833333333333, 0.520833333333333,
0, 2.08333333333333, 0, 0, 0, 0.520833333333333, 0), Taxonomy49 = c(0,
98.7616099071207, 0.309597523219814, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0)), row.names = c(NA, 20L), class = "data.frame")

dromano · April 2, 2024, 12:01pm

Thanks, Patrizia! And I forgot to say: the last thing to add is

[/details]

at the end — or you can remove the [details =...] line at the beginning).

dromano · April 2, 2024, 1:21pm

I would recommend creating a master table in long format, so that it's easier to make plots (as @jrkrideau illustrated). For example, you could:

Save the data from each excel table in its own data frame, say, NGS and Taxonomy
For each of the two resulting data frames, create long format versions (I'm not familiar with the data.table, so I use tidyverse tools):

NGS |> 
  pivot_longer(contains('NGS'), names_to = 'Treatment') -> NGS_long

Taxonomy |> 
  pivot_longer(contains('Taxo'), names_to = 'Treatment') -> Taxonomy_long

Combine the two long-format tables "vertically":

NGS |> 
  bind_rows(Taxonomy) -> NGS_Taxonomy_Treatment

Split the Treatment column to separate the treatment type (NGS or Taxonomy) from the treatment number:

NGS_Taxonomy_Treatment  |>
  separate_wider_regex(
    cols = Treatment, 
    patterns = c("Type" = '[:alpha:]+', "Number" = '[:digit:]+'),
    cols_remove = F
  ) -> NGS_Taxonomy_Treatment_Type

NGS_Taxonomy_Treatment_Type
#> # A tibble: 1,960 × 7
#>        X Taxa         Taxa.1       Type  Number Treatment   value
#>    <int> <chr>        <chr>        <chr> <chr>  <chr>       <dbl>
#>  1     1 Ulnaria_ulna Ulnaria_ulna NGS   1      NGS1       6.76  
#>  2     1 Ulnaria_ulna Ulnaria_ulna NGS   2      NGS2       0.0388
#>  3     1 Ulnaria_ulna Ulnaria_ulna NGS   3      NGS3      22.7   
#>  4     1 Ulnaria_ulna Ulnaria_ulna NGS   4      NGS4       1.99  
#>  5     1 Ulnaria_ulna Ulnaria_ulna NGS   5      NGS5      66.3   
#>  6     1 Ulnaria_ulna Ulnaria_ulna NGS   6      NGS6       0.0771
#>  7     1 Ulnaria_ulna Ulnaria_ulna NGS   7      NGS7       0.0235
#>  8     1 Ulnaria_ulna Ulnaria_ulna NGS   8      NGS8       0.700 
#>  9     1 Ulnaria_ulna Ulnaria_ulna NGS   9      NGS9       1.99  
#> 10     1 Ulnaria_ulna Ulnaria_ulna NGS   10     NGS10      0.213 
#> # ℹ 1,950 more rows

Remove any columns you decide you don't need:

NGS_Taxonomy_Treatment_Type |>
  select(!c(X, Taxa.1))
#> # A tibble: 1,960 × 5
#>    Taxa         Type  Number Treatment   value
#>    <chr>        <chr> <chr>  <chr>       <dbl>
#>  1 Ulnaria_ulna NGS   1      NGS1       6.76  
#>  2 Ulnaria_ulna NGS   2      NGS2       0.0388
#>  3 Ulnaria_ulna NGS   3      NGS3      22.7   
#>  4 Ulnaria_ulna NGS   4      NGS4       1.99  
#>  5 Ulnaria_ulna NGS   5      NGS5      66.3   
#>  6 Ulnaria_ulna NGS   6      NGS6       0.0771
#>  7 Ulnaria_ulna NGS   7      NGS7       0.0235
#>  8 Ulnaria_ulna NGS   8      NGS8       0.700 
#>  9 Ulnaria_ulna NGS   9      NGS9       1.99  
#> 10 Ulnaria_ulna NGS   10     NGS10      0.213 
#> # ℹ 1,950 more rows

^{Created on 2024-04-02 with reprex v2.0.2}
Using this table, you can, for example, pool all the results by type to create boxplots.

Patrizia · April 2, 2024, 1:21pm

Is it ok like this?

data (click to open)

structure(list(X = 1:20, Taxa = c("Ulnaria_ulna", "Achnanthidium_minutissimum",
"Nitzschia_palea", "Navicula_veneta", "Nitzschia_paleacea", "Melosira_varians",
"Fistulifera_saprophila", "Planothidium_lanceolatum", "Mayamaea_permitis",
"Cyclotella_meneghiniana", "Amphora_copulata", "Craticula_buderi",
"Nitzschia_inconspicua", "Nitzschia_capitellata", "Nitzschia_fonticola",
"Rhoicosphenia_abbreviata", "Achnanthidium_pyrenaicum", "Navicula_tripunctata",
"Nitzschia_frustulum", "Achnanthidium_eutrophilum"), NGS1 = c(6.75756458793289,
48.001501355042, 8.3306767145682, 10.3849857752652, 7.51387027290675,
0.0825314625126759, 14.5331481902685, 2.50713122347551, 6.15930432264964,
0.400839878207915, 0.00717923149693301, 0.640848605239318, 0.456304854406408,
0.0686260208429785, 0.0770565555143074, 0.0195811939250948, 0.055983831151006,
0.0121455015504516, 0.0244157009475025, 0), NGS2 = c(0.038795273236234,
0.178641131291838, 1.28059147873554, 3.00503979128826, 3.62342159306193,
0.601892399707542, 52.1268271605447, 0, 12.6842233044189, 1.48178656334284,
0.00324594737319074, 0.0510723493464696, 0.538484073830391, 1.99205251501901,
7.63170996220914, 0.0594087972866456, 0.0433487371963869, 3.45906327681437,
0.29845829928569, 0), NGS3 = c(22.6722980359667, 1.86400699048099,
0, 1.66738837369278, 6.41331274085265, 0.41022645328324, 27.9499987475793,
0.495243355464875, 55.7675249754809, 1.49308524225046, 0, 0.107375109458671,
1.03858045961821, 0.00300535660422078, 0.419814469756588, 0,
0.0746906005150969, 0.43937420716304, 0, 0), NGS4 = c(1.98817738959961,
31.1455339059451, 6.42519426128803, 2.21958063376199, 30.1598330522632,
0.331734375729987, 3.2766681157527, 0, 2.60804216179849, 0.00681150359517639,
0, 0.0294051872966077, 0.0197212942792069, 0, 13.5523522332935,
0.00153701299028779, 0.0399936075982398, 0.00589345607230487,
0, 4.77922705812871), NGS5 = c(66.3418400875589, 70.6528737139084,
4.07697490512422, 0.127644498015147, 0.243491396956423, 0.0125753884666739,
0, 0, 7.01912208175821, 0, 0, 1.99767051257378, 0.306455120740074,
0, 0, 0, 0.234517996979732, 0.0305267285646451, 0.271889348987913,
0), NGS6 = c(0.0770861376314104, 3.4960077452707, 1.72387386500296,
4.79128284290855, 0.819814684060119, 0.0891336806089489, 10.5830954881967,
0.0219361090645771, 32.8896075526215, 6.62841224236684, 0.00211836429654436,
0.0243965005589301, 7.2156853777225, 0.14263800858223, 5.20757392457809,
0.0531124248068363, 0.0276093947709671, 1.24276514768251, 0.0159432093963653,
2.7554603418784), NGS7 = c(0.0235330507711375, 0, 0.109760790344592,
0.413302708324854, 0.0784875760499812, 0.0479659875022809, 24.5095347853423,
0, 33.5719444119724, 0.0277365049097493, 4.80827210068893e-05,
0.0198981834257057, 15.3325158799713, 0.0176287508284037, 0.0471431814135667,
0.0036402822859042, 0.0188932171249289, 0.317713871733895, 0.0202095855308715,
0.433126639468088), NGS8 = c(0.699990008484979, 0.0879217015073157,
4.8357587932647, 26.2363831669907, 4.71818995897286, 0.0649749426898937,
10.8201530764522, 0, 12.2688381660485, 17.9125394808746, 0, 0.0471811437112339,
12.8484438152835, 0, 1.03234450999463, 0, 0.0435874765450315,
0.68031779119738, 0, 0), NGS9 = c(1.98817738959961, 31.1455339059451,
6.42519426128803, 2.21958063376199, 30.1598330522632, 0.331734375729987,
3.2766681157527, 0, 2.60804216179849, 0.00681150359517639, 0,
0.0294051872966077, 0.0197212942792069, 0, 13.5523522332935,
0.00153701299028779, 0.0399936075982398, 0.00589345607230487,
0, 4.77922705812871), NGS10 = c(0.212895109077827, 1.41760332681894,
1.54433252563773, 2.08551391290243, 0.662741636621971, 1.0431151243743,
38.6956648316489, 0.480680321226273, 28.8891304636822, 0.135350589465012,
0, 4.45754331244848, 2.44987910627988, 0.26536049581679, 0, 0,
0.104767994679205, 0, 0.127304876428737, 0), NGS11 = c(2.67369439990577,
0, 0, 33.1419931649068, 0, 0.87247757745402, 0, 0, 0.363024635900267,
0.0243527035470181, 0, 0.160913812703452, 64.5943214104103, 0.0733830332703782,
0, 0, 0.137590699782888, 0.0351174515755595, 0, 0), NGS12 = c(0.00970324070126635,
0.05815388803551, 0.300004336016836, 3.04575231546984, 0, 0.117135488221385,
18.0120917855259, 0.0300368844824414, 13.551661271095, 0.132065921283674,
0, 0.406145085053839, 3.63140635972473, 0.0692589226600411, 0,
0, 0.0263457675153483, 0.00879326855153554, 10.5796305607206,
0), NGS13 = c(0.89129232573996, 63.8052325950042, 6.05427281191083,
1.69861734038755, 0.114272546796966, 0.0122571383074336, 0.108779492752137,
0.031305855621518, 2.77702047859779, 2.45710860217695, 0.00119696763807262,
0.0703783045236121, 0.0694749655829953, 0, 5.93292352592199,
0, 0.0432191758307795, 0, 0, 0), NGS14 = c(43.2466503678865,
19.092085674355, 11.4600445856731, 2.01093095889098, 23.3564857254299,
0.0349593106793192, 22.2178314802238, 2.12148785075818, 12.6487848095367,
1.30141905121475, 0, 1.77324188913567, 0, 0.927777003826284,
0, 0, 0.261825891294896, 0.359136715614307, 0, 0), NGS15 = c(0.0118609048039743,
0, 0.0500623495416463, 0.863628550044531, 0.65096228603167, 0.0622759509602226,
22.9058435836596, 0, 39.4271113156173, 0.0978917976039213, 0.00210044191420881,
0.100194236115897, 7.71469779771595, 0.0409051038507131, 0.70536182360338,
0.0608895775668088, 0.0254458755581918, 0.869260414119914, 0.44474464467547,
0.396873445687882), NGS16 = c(0.0633616755292545, 1.67971605052316,
0.0133596284604961, 1.76252869190939, 0.950518506186873, 0.0558024612300993,
8.59721913394335, 0.610819672663073, 71.1870865912346, 0.0711272112283994,
0.00511521273160857, 0.0312391178864928, 1.14041089105528, 0,
0.230161918275085, 0.269721828652593, 0.0407635898768825, 0.670017387178846,
0.530668538497962, 0.886535605866803), NGS17 = c(0.116065761947912,
0.0411558201657061, 1.4425441836918, 2.39739934612035, 4.90953529368773,
0.0056653589061287, 40.6257216474984, 0.0109642735914728, 9.59140575976374,
0.274894761574383, 0, 37.7191796977375, 1.00635521375811, 0.043623272618896,
0.0902116289168572, 0, 0.0267054367131122, 0.00655597640399995,
0.151714771837674, 0), NGS18 = c(0.0155568640378596, 0.200041966111998,
0.705147116811079, 3.93288959011783, 0.731318157798135, 0.0718207595302126,
32.5662717879409, 0.11070041812053, 25.0445532710654, 0.328549267405352,
0, 0.0439443325030369, 0.44582467089248, 0.1453976121149, 13.1991203202991,
0, 0.0602806982982041, 0.213057402869678, 0.362988908755808,
0), NGS19 = c(0.0102010191988962, 0, 0, 0.0285188564380729, 0,
0.0528335487206541, 0, 0, 77.3351924686194, 0, 0, 0.0492980041366107,
0, 0, 0, 2.16591054502635, 0.0333788112913038, 0, 0, 0), NGS20 = c(1.37171041694148,
1.05938159548026, 2.22469549203164, 6.93915670988272, 1.5107360339536,
1.32828949274285, 2.30536317734806, 0.0250364083736036, 4.47867665059335,
0.844646866908582, 0.003867984046573, 0.290820696159609, 58.9067077834377,
0.0325594974199782, 0.229522513940953, 0.222533694938119, 0.0894771481673056,
7.62882271622015, 0.199461780848306, 0), NGS21 = c(0.095405389105136,
0.122970737464592, 3.90603309087424, 2.6749250515277, 1.39850291888671,
1.6962807549052, 18.4624448697781, 0, 48.6772899732811, 4.38236314112619,
0.00508447263700371, 0.0667974300977575, 2.27193111337114, 0.18725082877951,
4.82443076052411, 0, 0.0644951451248493, 1.43239054436544, 0,
0), NGS22 = c(0.00587620820770449, 0.052608349272676, 0.0266330294174837,
0.023564809624273, 0, 0.239052706429299, 9.08069934266108, 0.033655229348185,
75.7131258861879, 0.846747507787196, 0, 0.0319608252756607, 2.19076061957665,
0, 1.30021204517531, 0.0178565476294567, 0.0289595623175037,
8.59303727449197, 0.519209724882013, 0), NGS23 = c(12.117037778003,
53.7453108218954, 1.63833882763018, 0.337667578589081, 2.2077654845525,
1.11286265352503, 5.1877316904526, 2.90468633398779, 2.38315836802453,
0.268437954302248, 0, 18.3532701714575, 0.181560501348137, 0.100134389614811,
0.16005916290385, 0, 0.166729294667256, 2.47673290605602, 0,
0), NGS24 = c(0.453312302479855, 20.6772368176635, 1.19401735091211,
2.05470973763835, 3.72519493437489, 0.430472936988045, 22.6684802482249,
5.18883281377227, 24.5062608615091, 0.0203907690047059, 0.00196689348197841,
0.0959985374701597, 0.410781560407799, 0, 0, 0, 0.0603561407425555,
0.785207085110148, 0.258180395049816, 0), NGS25 = c(0.215959040413695,
9.45817871966076, 0.263842950490453, 0.295741866847134, 0, 0.996061117679763,
15.4760267279724, 0, 35.2852263810116, 0, 0, 1.97560130837423,
0.139845144583154, 0, 0, 0, 0.0621394631875393, 18.5884256427741,
0, 0), NGS26 = c(0.106717715627339, 48.5995453662778, 5.02718274261967,
4.60666116758564, 0.202825890854143, 0.600968881267653, 4.83031441519942,
0.0852547036274241, 19.2603379124576, 0.101281777399355, 0, 5.82334512351938,
1.08874761817846, 2.45613484109394, 0, 0, 0.121434491623436,
0.118551597699814, 0, 0), NGS27 = c(1.38405004586779, 0.281982057966211,
1.17554426537326, 11.2722886791376, 0.553905517643514, 1.17988737951704,
1.02057799163474, 0.617839945413178, 12.0292550437032, 0.874965472277289,
0, 62.8755930202999, 0.423049746950747, 4.86475306108754, 0.12426663871192,
0, 0.0711323215179966, 0, 0.894947727436878, 0), NGS28 = c(0.0191640663142572,
0.332941309314527, 1.12573235287691, 5.33563198550724, 23.8598850211779,
0.00471436990068833, 0.420552716498557, 0.0191560901333315, 66.4983757817094,
0.0426600288567991, 0, 0.839759073928477, 0.0615860292688866,
0.219538992906787, 0.0191044959623414, 0, 0.0253010222439906,
0.016789792512543, 0.0486401526375178, 0.0205342231806092), NGS29 = c(2.58381091575222,
0, 10.4509861518145, 12.0221291023134, 24.3640290330514, 0.0378567088953281,
0.980312821690078, 0, 15.6413976153468, 0.0133925931120002, 0.00619925786723509,
0.07154784481367, 16.9683942423556, 3.24529412079043, 0, 0, 0.044983516470162,
0.028886701375902, 4.14013471320046, 5.22204430888329), NGS30 = c(0.0249192413241342,
0, 7.04781993167599, 1.72961774864539, 0.0903114593837887, 0.000629808966477128,
9.56884792721437, 0, 80.0550030242479, 0, 0, 0.0147374586352985,
0.00767404455840156, 0, 0.122032121116964, 0, 0.00835220355849928,
0.00175535768246551, 0.00328684834736466, 0), NGS31 = c(0.247524385649142,
0.0291941742303935, 1.40630658594772, 31.5886819015501, 2.11706824756424,
0.104013267796908, 8.14973683376881, 0.157820174102885, 38.5486842572878,
0.13999896434821, 0, 1.69947153449797, 4.69667232175603, 0.36072918175886,
0, 0, 0.0191098645180767, 0, 0, 0), NGS32 = c(0.0136418812930442,
0.0539663689905043, 0.251791521691668, 0.431881173178304, 0.626756336433486,
0.0893970673862854, 16.1797870228652, 0.186311054994927, 47.9551958140764,
0, 0.00146993543256943, 0.0111320548757885, 0.357576355504187,
0.0565428750671224, 1.11064090963957, 0, 0.0151643669981176,
0.267364211731787, 0, 0.0230917139394665), NGS33 = c(3.57968280619678,
0.38119745163622, 1.57318592995171, 3.3837657436895, 0.860648849119932,
0.207940166788424, 11.1294700427591, 0.0200436245230077, 25.9310997928775,
18.9168673852773, 0.0169081013411048, 0.0735627806621822, 7.42036824260661,
0, 7.1479876974325, 0.343095329909432, 0.0582411760452999, 6.97613060833301,
0, 0.82205807694753), NGS34 = c(51.8256348486766, 21.6743973716663,
5.70647562459785, 0.125064449249115, 11.5545483923808, 0.182125508123183,
3.01774782668866, 3.67313534889541, 32.5421010940533, 1.59190758242991,
0, 0.167021314137343, 5.40566167813367, 0, 0, 0, 0.186153269594592,
0, 0, 10.8862792115102), NGS35 = c(0.0379174151217574, 6.88949979827231,
0, 17.7700720356958, 0.185649623714352, 0.00660751904181822,
11.5019870015044, 0, 0.931633752548541, 0, 0, 0.237861922360634,
0.615216023619618, 0.0956104491431537, 0, 0.984342571851699,
0.240939088591682, 0.0486660242203091, 0, 60.2056839476113),
NGS36 = c(0.153543723674718, 0.0113849023240514, 0, 2.96541275098069,
0.0147126086676334, 0.00866592183283487, 1.69941358907703,
0, 3.02060902090392, 0.00344090148247645, 0, 0.02182677716208,
9.51161644066397, 0, 0, 0, 0.0211561648730562, 0.00421761539989854,
3.30503816491175, 0), NGS37 = c(2.60104583451819, 9.56196604835829,
0, 0.475890169289509, 22.0119594319306, 0.112058225900441,
18.5883977874014, 0, 12.5943214362925, 1.11696061782757,
0, 1.91250433303342, 11.1264476181189, 0, 0, 0, 0.0284823182202242,
0, 0.661560379141532, 1.3566166145361), NGS38 = c(4.07945297808818,
22.61723378543, 0.064940282721813, 0.148475809064216, 18.9319364474526,
0.0371942939348831, 17.861848454438, 0.209951077977353, 9.00649404905959,
0.0214789973423628, 0, 2.07468333596762, 8.66793510722633,
0, 0, 0, 1.81195213921089, 0, 0.451147172851238, 0), NGS39 = c(0.0706604498023882,
0, 7.26531295210697, 26.4219240001236, 22.4085663512891,
0.00165311516893303, 5.73895549168155, 0.18739818170712,
4.51096028189232, 3.10955763829639, 0.00102670310983547,
1.50608672343921, 4.82967745052514, 0, 0, 0.00206988847486799,
0.0292668921856204, 0.010317697990696, 13.6739197692217,
0), NGS40 = c(0.112821033258729, 0.85410542028602, 1.34193798248575,
3.31197893387122, 0.0264262132194336, 0.00796556532024077,
28.5580691088651, 0.012827413899182, 46.0875347185858, 0.15430199370529,
0, 8.16651981277506, 1.83077776355542, 0.337793998293254,
0.0253298729109259, 0, 0.0184171892314341, 0.00447120679268883,
0.0102552900209923, 0), NGS41 = c(0.0133008743459121, 48.6773410850511,
1.3556896461801, 5.51281277318208, 0.129259627734828, 0.00143876103833793,
2.82238457369471, 0, 3.07104499014821, 0.0485765044782552,
0, 36.0761340141425, 0.614499627318652, 0.0913422676789195,
0, 0.00136039493697304, 0.0182150660355393, 0.0103534449778949,
0.00808298456621801, 0), NGS42 = c(0.00833564556055011, 0.0572938262507176,
0.943125790806968, 11.8118252123699, 0.0244660698072901,
0.00130114661365017, 0.861095763108183, 0.0054203056785881,
0.191846196978028, 1.23401223126569, 0, 63.1102184492069,
0.391040702219935, 13.7913418203266, 0, 0, 0.0266821746860153,
0.00602979890494902, 6.33948689784295, 0), NGS43 = c(1.85840966734622,
0.353610069968206, 13.181616997741, 9.10266081276299, 0.562382732976902,
0.225910535399374, 5.8851121278011, 0.830513445343487, 14.9498856759981,
6.83452662330844, 0, 29.6310890716873, 8.36434215687838,
0.593165034193873, 0.698037013942465, 0, 0.0296214919862156,
0.146568658639062, 0.0293772620212207, 0.374520362270232),
NGS44 = c(8.98357766336455, 0.589318063929205, 0.561058789856876,
6.26961311341626, 0.514784226319922, 0.046999556166536, 0.328513475771223,
0, 61.0746683872156, 0.330067912326817, 0.00287856725561097,
14.5717153784831, 1.85571576986379, 1.17765452253105, 0.152312796725635,
0, 0.0899808521638762, 0.289230095503815, 1.7740213493065,
0.213706162886409), NGS45 = c(0.00628075967437536, 0, 0,
1.46198077035109, 0, 0.0167400761510954, 21.7812870990465,
0, 52.5240752549622, 0, 0, 0.0159884851452056, 0.564837244497352,
0, 0, 0, 0.0308269626567839, 0.374807830958602, 0, 0.0578890858616403
), NGS46 = c(7.76086880356853, 0.14534983778136, 0.346542099683442,
3.69773967872993, 0, 0.0465164490894812, 0.583143119204788,
0, 65.6370271479614, 0.193627680309858, 0.00353838527659947,
12.584056074471, 2.39483006636567, 0.79813108049551, 0, 0,
0.0773077697032965, 0.0825342088535844, 1.95439048298546,
0), NGS47 = c(0.789438602727383, 44.5981995002164, 2.6949855169119,
4.97115908383563, 37.8108060507954, 0.103522196389958, 2.04295949705074,
1.12244459968807, 0.174087842241501, 0.2350316425656, 0,
0.0398888568016094, 0.0419399897826563, 0, 5.74158766569327,
0, 0.024183222326248, 0, 0, 0), NGS48 = c(15.3597635277663,
62.0666163108133, 0.191264922880888, 1.07297041022047, 0.184062955782019,
0.0340051078988955, 1.7935310171756, 0.0223205914836636,
2.66784410905841, 0.0596624635854359, 0.000950953086560778,
0.163080593024591, 0.135021670372934, 0, 3.12674045074837,
0.0113326188961648, 0.181219223293187, 18.1252004899456,
0, 0), NGS49 = c(16.8191116279315, 47.6631722592845, 3.23927443486789,
1.63679045126097, 0.0873853764447723, 0.0276415711824677,
3.4717915406365, 0, 5.79383032055487, 0.17439740838611, 0.000524209929433917,
2.25447389864684, 1.84097821491911, 0, 0.790064717350159,
0.0102224796503141, 2.4778163938617, 0.181051116354679, 0,
0.0670936287726436), Taxa.1 = c("Ulnaria_ulna", "Achnanthidium_minutissimum",
"Nitzschia_palea", "Navicula_veneta", "Nitzschia_paleacea",
"Melosira_varians", "Fistulifera_saprophila", "Planothidium_lanceolatum",
"Mayamaea_permitis", "Cyclotella_meneghiniana", "Amphora_copulata",
"Craticula_buderi", "Nitzschia_inconspicua", "Nitzschia_capitellata",
"Nitzschia_fonticola", "Rhoicosphenia_abbreviata", "Achnanthidium_pyrenaicum",
"Navicula_tripunctata", "Nitzschia_frustulum", "Achnanthidium_eutrophilum"
), Taxonomy1 = c(0, 86.6141732283464, 0, 0.78740157480315,
0.26246719160105, 0, 0, 0.26246719160105, 2.88713910761155,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0.26246719160105, 0), Taxonomy2 = c(1.06100795755968,
1.3262599469496, 0, 0.795755968169761, 0.795755968169761,
0, 0, 0.26525198938992, 39.5225464190981, 0, 0, 0, 0.530503978779841,
0, 0, 0, 0, 0, 0, 0), Taxonomy3 = c(0L, 100L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L
), Taxonomy4 = c(0, 30.9090909090909, 0.727272727272727,
2.54545454545454, 46.5454545454545, 0.363636363636364, 0,
0, 1.45454545454545, 0.363636363636364, 0, 0, 0.363636363636364,
0, 0, 0, 0, 0, 0, 0), Taxonomy5 = c(0, 9.88700564971751,
0.282485875706215, 22.316384180791, 0, 0, 0.564971751412429,
0, 7.34463276836158, 2.25988700564972, 0, 0, 16.1016949152542,
0, 5.64971751412429, 0, 0, 0.282485875706215, 0, 0), Taxonomy6 = c(0,
0, 0, 14.6529562982005, 8.48329048843188, 0, 0.51413881748072,
0, 16.452442159383, 7.7120822622108, 0, 0, 26.9922879177378,
0, 0, 0, 0, 0, 0, 0), Taxonomy7 = c(0, 0, 0, 0, 0, 0, 0,
0, 7.45501285347044, 0.25706940874036, 0, 0, 25.9640102827763,
0, 0, 0, 0, 4.11311053984576, 0, 0.25706940874036), Taxonomy8 = c(0,
0, 0, 2.3121387283237, 13.5838150289017, 0.578034682080925,
9.53757225433526, 0, 7.22543352601156, 0, 0, 0, 0, 2.60115606936416,
1.44508670520231, 0.289017341040462, 0, 0.578034682080925,
0, 0), Taxonomy9 = c(1.98817738959961, 31.1455339059451,
6.42519426128803, 2.21958063376199, 30.1598330522632, 0.331734375729987,
3.2766681157527, 0, 2.60804216179849, 0.00681150359517639,
0, 0.0294051872966077, 0.0197212942792069, 0, 13.5523522332935,
0.00153701299028779, 0.0399936075982398, 0.00589345607230487,
0, 4.77922705812871), Taxonomy10 = c(0, 0, 0, 0.263157894736842,
0, 0, 10.2631578947368, 0, 30.7894736842105, 0, 0, 0, 0.789473684210526,
0, 0, 0, 0, 0, 0, 0), Taxonomy11 = c(0.337837837837838, 2.7027027027027,
0, 0, 7.43243243243243, 0.337837837837838, 0, 0, 0, 0.675675675675676,
0, 0, 23.9864864864865, 0, 4.39189189189189, 0, 0, 0, 0,
0), Taxonomy12 = c(0, 0, 0, 1.44927536231884, 0, 0, 0, 0,
0, 0, 0, 0, 1.93236714975845, 0, 0, 0, 0, 0, 0, 0), Taxonomy13 = c(0,
95.8448753462604, 1.10803324099723, 0.554016620498615, 0,
0, 0, 0, 0.554016620498615, 0, 0, 0, 0.277008310249307, 0,
0, 0, 0, 0, 0, 0), Taxonomy14 = c(2.18579234972678, 5.46448087431694,
1.09289617486339, 1.63934426229508, 2.18579234972678, 1.09289617486339,
1.09289617486339, 0, 0.546448087431694, 0, 0, 0, 2.73224043715847,
0.546448087431694, 0, 0, 0, 0, 0, 0), Taxonomy15 = c(0, 0,
0, 0.510204081632653, 0.510204081632653, 0, 0, 0, 56.1224489795919,
0.255102040816327, 0, 0, 13.265306122449, 0, 0, 4.59183673469388,
0, 0.255102040816327, 0, 0), Taxonomy16 = c(0, 0, 0, 1.57728706624606,
0.315457413249211, 0, 0, 0, 14.8264984227129, 0, 0.315457413249211,
0, 18.2965299684543, 0, 0, 0, 0, 0.315457413249211, 0, 0),
Taxonomy17 = c(0.557103064066852, 0.835654596100279, 0, 11.6991643454039,
4.17827298050139, 0, 11.4206128133705, 0, 23.3983286908078,
0.557103064066852, 0, 10.8635097493036, 10.3064066852368,
0, 0, 0, 0, 0, 0, 0), Taxonomy18 = c(0, 0, 0, 1.69971671388102,
0, 0, 1.69971671388102, 0, 6.23229461756374, 1.13314447592068,
0, 0, 0, 0, 10.1983002832861, 0, 0, 0, 0.28328611898017,
0), Taxonomy19 = c(0, 1.26582278481013, 0, 1.26582278481013,
0.253164556962025, 0, 0.759493670886076, 0, 0.759493670886076,
2.0253164556962, 0, 0, 0, 0, 0.759493670886076, 0, 0, 0,
3.54430379746835, 0), Taxonomy20 = c(0, 0, 0, 2.96495956873315,
0, 0, 0, 0, 2.69541778975741, 0.269541778975741, 0, 0, 56.3342318059299,
0, 0, 0, 0, 4.31266846361186, 0, 0), Taxonomy21 = c(0, 0,
0, 3.1413612565445, 3.92670157068063, 0, 1.30890052356021,
0, 17.2774869109948, 0.261780104712042, 0, 0, 2.61780104712042,
0, 0, 0, 0, 0, 0, 0), Taxonomy22 = c(0, 1.50753768844221,
0, 8.29145728643216, 0.50251256281407, 0, 0, 0, 3.51758793969849,
0, 0, 0, 26.6331658291457, 0, 2.51256281407035, 0, 0, 2.01005025125628,
0, 0), Taxonomy23 = c(1.52671755725191, 55.3435114503817,
0.381679389312977, 0, 0, 0.381679389312977, 0, 1.90839694656488,
0, 0.381679389312977, 0, 1.52671755725191, 0, 0, 0, 0, 0,
0.381679389312977, 0, 0), Taxonomy24 = c(0, 20.1058201058201,
1.58730158730159, 2.64550264550265, 0.529100529100529, 0,
16.1375661375661, 0, 18.7830687830688, 0.264550264550265,
0, 0, 3.17460317460317, 0, 0, 0, 0, 0, 0, 0), Taxonomy25 = c(0,
9.67741935483871, 0, 1.34408602150538, 0, 1.0752688172043,
4.3010752688172, 0, 29.3010752688172, 0, 0, 0, 0.806451612903226,
0, 0, 0, 0, 7.79569892473118, 0, 0), Taxonomy26 = c(0, 4.52674897119342,
0, 1.23456790123457, 0, 0, 0, 0, 0, 0, 0, 1.23456790123457,
0.823045267489712, 0, 0, 0, 0, 0, 0, 0), Taxonomy27 = c(0.377358490566038,
0, 0.377358490566038, 17.3584905660377, 0.377358490566038,
10.5660377358491, 0, 0, 12.8301886792453, 0, 0, 7.16981132075472,
0.754716981132076, 2.64150943396226, 0, 0, 0, 0, 0, 0), Taxonomy28 = c(0,
0, 0, 6.79611650485437, 50.4854368932039, 0, 0, 0, 23.7864077669903,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Taxonomy29 = c(1.31926121372032,
0.527704485488127, 0.527704485488127, 25.065963060686, 3.16622691292876,
0, 0, 0, 5.54089709762533, 0, 0, 0, 25.8575197889182, 1.84696569920844,
0, 0, 0.527704485488127, 0, 0, 0), Taxonomy30 = c(0, 0.522193211488251,
0, 1.82767624020888, 0, 0, 0, 0, 95.3002610966058, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0), Taxonomy31 = c(0, 0, 0, 18.0156657963446,
0, 0, 0.522193211488251, 0, 53.2637075718016, 0, 0, 0, 5.48302872062663,
0, 0, 0, 0, 0, 0, 0), Taxonomy32 = c(0, 0, 0, 0, 0, 0, 1.98511166253102,
0, 27.2952853598015, 0, 0, 0, 1.98511166253102, 0, 0.248138957816377,
0, 0, 0, 0, 0), Taxonomy33 = c(0, 2.81329923273657, 0, 1.0230179028133,
0, 0, 0, 0, 3.32480818414322, 0.51150895140665, 0, 0, 23.2736572890026,
0, 1.79028132992327, 0.255754475703325, 0, 0.255754475703325,
0, 0), Taxonomy34 = c(0.31055900621118, 30.1242236024845,
0.62111801242236, 7.7639751552795, 3.72670807453416, 0, 0,
0.31055900621118, 4.6583850931677, 0, 0, 0, 7.14285714285714,
0, 0, 0, 0, 0, 0, 4.03726708074534), Taxonomy35 = c(0, 43.0517711171662,
0, 3.81471389645776, 1.63487738419618, 0, 0, 0, 4.63215258855586,
0, 0.272479564032697, 0, 1.63487738419618, 0, 0, 1.90735694822888,
0, 0, 0, 0.272479564032697), Taxonomy36 = c(0, 1.01351351351351,
0, 0.675675675675676, 0, 0, 1.01351351351351, 0, 5.74324324324324,
1.01351351351351, 0, 0, 9.7972972972973, 0, 0, 0, 0, 0, 1.01351351351351,
0), Taxonomy37 = c(0.255102040816327, 28.5714285714286, 0,
3.8265306122449, 47.1938775510204, 0, 1.02040816326531, 0,
0.76530612244898, 0, 0, 0.255102040816327, 0.76530612244898,
0, 0, 0, 0, 0, 0, 0), Taxonomy38 = c(0, 58.974358974359,
0, 0, 0, 0, 0, 0, 0, 0, 2.56410256410256, 0, 0, 0, 0, 0,
0, 0, 0, 0), Taxonomy39 = c(0, 0, 0, 7.52688172043011, 15.3225806451613,
0, 0.537634408602151, 0, 21.2365591397849, 0.537634408602151,
0, 0, 3.76344086021505, 0, 0, 0, 0, 0, 0, 0), Taxonomy40 = c(0,
0.584795321637427, 0, 4.3859649122807, 0, 0, 2.92397660818713,
0, 58.187134502924, 2.33918128654971, 0, 0.87719298245614,
0, 0.584795321637427, 0, 0, 0, 0, 0, 0), Taxonomy41 = c(0,
59.6825396825397, 4.44444444444444, 10.7936507936508, 0,
0, 0, 0, 0, 0, 0, 9.20634920634921, 2.85714285714286, 0,
0, 0, 0, 0, 0, 0), Taxonomy42 = c(0, 0, 0, 21.256038647343,
0, 0, 0, 0, 0, 0.241545893719807, 0, 1.69082125603865, 3.3816425120773,
16.4251207729469, 0, 0, 0, 0, 38.6473429951691, 0), Taxonomy43 = c(0,
0, 0.26525198938992, 9.81432360742705, 0, 0, 0, 0, 6.36604774535809,
15.6498673740053, 0, 2.38726790450928, 30.5039787798408,
0.26525198938992, 0, 0, 0, 0, 0, 0), Taxonomy44 = c(0, 0,
0, 0.251256281407035, 0, 0, 0, 0, 6.28140703517588, 0, 0,
0, 2.26130653266332, 0, 0, 0, 0, 0, 0, 0), Taxonomy45 = c(0,
0, 0, 1.02040816326531, 0.255102040816327, 0, 0, 0, 4.59183673469388,
0, 0, 0, 9.69387755102041, 0, 0, 0, 0, 0, 0, 0), Taxonomy46 = c(0,
0, 0.2710027100271, 1.3550135501355, 5.14905149051491, 1.3550135501355,
0, 0, 0.2710027100271, 0, 0, 0, 0.813008130081301, 0, 1.0840108401084,
1.8970189701897, 0, 1.3550135501355, 1.6260162601626, 1.3550135501355
), Taxonomy47 = c(0.302114803625378, 57.0996978851964, 0,
5.13595166163142, 24.4712990936556, 0.302114803625378, 0,
0, 3.62537764350453, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Taxonomy48 = c(0.520833333333333,
82.8125, 0.520833333333333, 1.04166666666667, 1.5625, 0,
0, 0, 0, 0.520833333333333, 0, 0.520833333333333, 0.520833333333333,
0, 2.08333333333333, 0, 0, 0, 0.520833333333333, 0), Taxonomy49 = c(0,
98.7616099071207, 0.309597523219814, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0)), row.names = c(NA, 20L), class = "data.frame")

dromano · April 2, 2024, 1:25pm

Perfect! And just using the code block (as you did earlier), without any "details" code would be fine, too — I just happened give you incomplete instructions by accident.

Patrizia · April 2, 2024, 1:31pm

Thank you so much! I will try to follow your code right now and see what kind of outputs (boxplots etc) I get.!!

jrkrideau · April 2, 2024, 3:01pm

@ dromano beat me to it. I realized this morning that we could "melt" / "pivot_longer" in one step.
Slightly revised code and an extra plot.

suppressMessages(library(data.table)); 
suppressMessages(library(tidyverse))

dat1 <- read.csv("raw.data.csv")  # read in data
DT  <- as.data.table(dat1)  # Convert to data.table focmat. 

DT <- DT[, !c("X", "Taxa.1")]   # Drop unneeded variables. 

## Convert from 'wide' to 'long' format to plot.
DT1 <- melt(DT,
            id.vars       = "Taxa",
            variable.name = "Sample",
            value.name    = "Value")

## Subset the data for ploting. 
T1 <- DT1[Sample == "NGS1" | Sample == "Taxonomy1",]


p1 <- ggplot(T1 , aes(Taxa, Value, colour = Sample, shape = Sample)) +
       geom_point() +
      coord_flip() + 
       theme(legend.position = "top") + 
           geom_jitter() 
p1


T2 <- DT1[Taxa == "Ulnaria_ulna"  & (Sample == "NGS1" | Sample == "Taxonomy1"),]

p2 <- ggplot(T2 , aes(Taxa, Value, colour = Sample, shape = Sample)) +
       geom_point() +
      coord_flip() + 
       theme(legend.position = "top") + 
           geom_jitter() 
p2

dromano · April 2, 2024, 3:14pm

Not really :). Your code is suited for Patrizia's original submission, whereas I making a suggestion for how to go from excel to R, so slightly different purpose, and complementary toolkit!