Merge pull request #1 from NielInfante/16S_interactive_tree

16 s interactive tree
speeding-up-science-workshops · Oct 23, 2019 · 1dc3c11 · 1dc3c11
2 parents d7fc877 + 23f7cb5
commit 1dc3c11
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Showing 13 changed files with 146,739 additions and 13 deletions.
diff --git a/Data_Files/bact_alldata_mapfile.csv b/Data_Files/bact_alldata_mapfile.csv
@@ -0,0 +1,50 @@
+"","BarcodeSequence","LinkerPrimerSequence","IDTplateposition","SampleNo","Project","spatialtree","transecttree","Vertposition","litterorother","BlockNo","grndcnpy","samplelocation","sample_type","Description"
+"230","TTCTCCATCACA","TTCTCCATCACACCGTAAAACGACGGCCAG","C4","230","transects",NA,"6","5","abovelitter",NA,NA,NA,NA,"transects"
+"225","CATACCGTGAGT","CATACCGTGAGTCCGTAAAACGACGGCCAG","E2","225","transects",NA,"5","5","abovelitter",NA,NA,NA,NA,"transects"
+"212","CATTCGTGGCGT","CATTCGTGGCGTCCGTAAAACGACGGCCAG","G4","212","transects",NA,"3","2","abovelitter",NA,NA,NA,NA,"transects"
+"231","CGATAGGCCTTA","CGATAGGCCTTACCCGTAAAACGACGGCCAG","C5","231","transects",NA,"7","1","litter",NA,NA,NA,NA,"transects"
+"241","CTATCATCCTCA","CTATCATCCTCACCCGTAAAACGACGGCCAG","D5","241","transects",NA,"9","1","litter",NA,NA,NA,NA,"transects"
+"232","GAAACATCCCAC","GAAACATCCCACCCGTAAAACGACGGCCAG","C6","232","transects",NA,"7","2","abovelitter",NA,NA,NA,NA,"transects"
+"216","CGCTGTGGATTA","CGCTGTGGATTACCGTAAAACGACGGCCAG","B1","216","transects",NA,"4","1","litter",NA,NA,NA,NA,"transects"
+"206","CACTCATCATTC","CACTCATCATTCCCGTAAAACGACGGCCAG","A1","206","transects",NA,"2","1","litter",NA,NA,NA,NA,"transects"
+"211","ATTCGGTAGTGC","ATTCGGTAGTGCCCGTAAAACGACGGCCAG","A6","211","transects",NA,"3","1","litter",NA,NA,NA,NA,"transects"
+"238","GCATCAGAGTTA","GCATCAGAGTTACCCCGTAAAACGACGGCCAG","D2","238","transects",NA,"8","3","abovelitter",NA,NA,NA,NA,"transects"
+"239","TTAAGACAGTCG","TTAAGACAGTCGCCGTAAAACGACGGCCAG","D3","239","transects",NA,"8","4","abovelitter",NA,NA,NA,NA,"transects"
+"233","ACAACACTCCGA","ACAACACTCCGACCGTAAAACGACGGCCAG","C7","233","transects",NA,"7","3","abovelitter",NA,NA,NA,NA,"transects"
+"243","ACGGGTCATCAT","ACGGGTCATCATCCGTAAAACGACGGCCAG","D7","243","transects",NA,"9","3","abovelitter",NA,NA,NA,NA,"transects"
+"244","GAGAGCAACAGA","GAGAGCAACAGACCGTAAAACGACGGCCAG","D8","244","transects",NA,"9","4","abovelitter",NA,NA,NA,NA,"transects"
+"223","TCAGTTCTCGTT","TCAGTTCTCGTTCCGTAAAACGACGGCCAG","B8","223","transects",NA,"5","3","abovelitter",NA,NA,NA,NA,"transects"
+"207","ACACGCGGTTTA","ACACGCGGTTTACCGTAAAACGACGGCCAG","A2","207","transects",NA,"2","2","abovelitter",NA,NA,NA,NA,"transects"
+"240","GTTCGGTGTCCA","GTTCGGTGTCCACCCGTAAAACGACGGCCAG","D4","240","transects",NA,"8","5","abovelitter",NA,NA,NA,NA,"transects"
+"245","AGCTGCACCTAA","AGCTGCACCTAACGTAAAACGACGGCCAG","E4","245","transects",NA,"9","5","abovelitter",NA,NA,NA,NA,"transects"
+"220","ATTCTCTCACGT","ATTCTCTCACGTCCCGTAAAACGACGGCCAG","B5","220","transects",NA,"4","5","abovelitter",NA,NA,NA,NA,"transects"
+"248","CGCAGATTAGTA","CGCAGATTAGTACCGTAAAACGACGGCCAG","F2","248","transects",NA,"10","3","abovelitter",NA,NA,NA,NA,"transects"
+"249","TTCCTAGGCCAG","TTCCTAGGCCAGCCCGTAAAACGACGGCCAG","F3","249","transects",NA,"10","4","abovelitter",NA,NA,NA,NA,"transects"
+"210","TTCGATGCCGCA","TTCGATGCCGCACCCGTAAAACGACGGCCAG","A5","210","transects",NA,"2","5","abovelitter",NA,NA,NA,NA,"transects"
+"250","GTCTTCAGCAAG","GTCTTCAGCAAGCGTAAAACGACGGCCAG","F4","250","transects",NA,"10","5","abovelitter",NA,NA,NA,NA,"transects"
+"203","GTCGAATTTGCG","GTCGAATTTGCGCCCGTAAAACGACGGCCAG","G3","203","transects",NA,"1","3","abovelitter",NA,NA,NA,NA,"transects"
+"208","TCTGCACTGAGC","TCTGCACTGAGCCCGTAAAACGACGGCCAG","A3","208","transects",NA,"2","3","abovelitter",NA,NA,NA,NA,"transects"
+"215","CGACTCTAAACG","CGACTCTAAACGCCGTAAAACGACGGCCAG","E5","215","transects",NA,"3","5","abovelitter",NA,NA,NA,NA,"transects"
+"234","CCTTGACCGATG","CCTTGACCGATGCCGTAAAACGACGGCCAG","C8","234","transects",NA,"7","4","abovelitter",NA,NA,NA,NA,"transects"
+"219","CTCCCTTTGTGT","CTCCCTTTGTGTCCGTAAAACGACGGCCAG","B4","219","transects",NA,"4","4","abovelitter",NA,NA,NA,NA,"transects"
+"226","TACCGAAGGTAT","TACCGAAGGTATCCGTAAAACGACGGCCAG","E6","226","transects",NA,"6","1","litter",NA,NA,NA,NA,"transects"
+"236","CGTGCTTAGGCT","CGTGCTTAGGCTCCGTAAAACGACGGCCAG","E7","236","transects",NA,"8","1","litter",NA,NA,NA,NA,"transects"
+"237","AGCTGTCAAGCT","AGCTGTCAAGCTCCGTAAAACGACGGCCAG","D1","237","transects",NA,"8","2","abovelitter",NA,NA,NA,NA,"transects"
+"213","GTAAATTCAGGC","GTAAATTCAGGCCCGTAAAACGACGGCCAG","A8","213","transects",NA,"3","3","abovelitter",NA,NA,NA,NA,"transects"
+"218","ACGATTCGAGTC","ACGATTCGAGTCCCGTAAAACGACGGCCAG","B3","218","transects",NA,"4","3","abovelitter",NA,NA,NA,NA,"transects"
+"214","TTCTCTCGACAT","TTCTCTCGACATCCGTAAAACGACGGCCAG","E1","214","transects",NA,"3","4","abovelitter",NA,NA,NA,NA,"transects"
+"229","GTGCAACCAATC","GTGCAACCAATCCCGTAAAACGACGGCCAG","C3","229","transects",NA,"6","4","abovelitter",NA,NA,NA,NA,"transects"
+"246","CGCTCACAGAAT","CGCTCACAGAATCGTAAAACGACGGCCAG","E8","246","transects",NA,"10","1","litter",NA,NA,NA,NA,"transects"
+"242","GTATTTCGGACG","GTATTTCGGACGCCGTAAAACGACGGCCAG","D6","242","transects",NA,"9","2","abovelitter",NA,NA,NA,NA,"transects"
+"221","CGAGCTGTTACC","CGAGCTGTTACCCCCGTAAAACGACGGCCAG","B6","221","transects",NA,"5","1","litter",NA,NA,NA,NA,"transects"
+"228","AGTTGTAGTCCG","AGTTGTAGTCCGCCGTAAAACGACGGCCAG","C2","228","transects",NA,"6","3","abovelitter",NA,NA,NA,NA,"transects"
+"227","ATGTGTGTAGAC","ATGTGTGTAGACCCGTAAAACGACGGCCAG","C1","227","transects",NA,"6","2","abovelitter",NA,NA,NA,NA,"transects"
+"222","TATCTATCCTGC","TATCTATCCTGCCCGTAAAACGACGGCCAG","B7","222","transects",NA,"5","2","abovelitter",NA,NA,NA,NA,"transects"
+"201","AGTAGCGGAAGA","AGTAGCGGAAGACCGTAAAACGACGGCCAG","G1","201","transects",NA,"1","1","litter",NA,NA,NA,NA,"transects"
+"202","CGTACTCTCGAG","CGTACTCTCGAGCCGTAAAACGACGGCCAG","G2","202","transects",NA,"1","2","abovelitter",NA,NA,NA,NA,"transects"
+"204","ACTCTAGCCGGT","ACTCTAGCCGGTCCCCGTAAAACGACGGCCAG","G4","204","transects",NA,"1","4","abovelitter",NA,NA,NA,NA,"transects"
+"205","TACTCGGGAACT","TACTCGGGAACTCCGTAAAACGACGGCCAG","G5","205","transects",NA,"1","5","abovelitter",NA,NA,NA,NA,"transects"
+"217","CCTGCGAAGTAT","CCTGCGAAGTATCCGTAAAACGACGGCCAG","B2","217","transects",NA,"4","2","abovelitter",NA,NA,NA,NA,"transects"
+"235","TTGCCAAGAGTC","TTGCCAAGAGTCCCGTAAAACGACGGCCAG","E3","235","transects",NA,"7","5","abovelitter",NA,NA,NA,NA,"transects"
+"209","ACCGTGCTCACA","ACCGTGCTCACACCCGTAAAACGACGGCCAG","A4","209","transects",NA,"2","4","abovelitter",NA,NA,NA,NA,"transects"
+"247","GCTTGAGCTTGA","GCTTGAGCTTGACCGTAAAACGACGGCCAG","F1","247","transects",NA,"10","2","abovelitter",NA,NA,NA,NA,"transects"