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grunwaldlab / metacoder

Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data
http://grunwaldlab.github.io/metacoder_documentation
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Integration in mothur pipeline #146

Closed Wookie777 closed 7 years ago

Wookie777 commented 7 years ago

Hi, I want to integrate metacoder in my mother pipeline but I don't realy know how to deal with.

I have 3 output files from the mothur pipeline: .shared: allocation of samples to number of OTUs .taxonomy: allocation of OTU to taxonomy .tax.summary: matrix of different taxlevels/taxa and number in samples

Which file can I use for the input in the parse_mothur_summary function? Or is it necessary to format every sample back into a FASTA file?

I hope someone can help me!

zachary-foster commented 7 years ago

Hi @Wookie777! Sorry for the delay, I was in the forest with no Internet for the past few days. We should e able to figure this out. Can you attach the first 10 lines or so of each file so I can take a look at how things are formatted? The parse_mothur_summary function will probably work on the .tax.summary file, but I will have to check that.

Wookie777 commented 7 years ago

Thanks for the answer. Here are my first lines of the .tax.summary file (the names in the first row after total are the sample names).

Thanks for your help!

taxlevel    rankID  taxon   daughterlevels  total   A1_10   A1_14   A1_16   A1_2    A1_21   A1_23   A1_28   A1_6    A2_10   A2_14   A2_16   A2_2    A2_21   A2_23   A2_28   A2_6    A3_10   A3_14   A3_16   A3_2    A3_21   A3_23   A3_28   A3_6    B1_10   B1_14   B1_16   B1_2    B1_21   B1_23   B1_28   B1_6    B2_10   B2_14   B2_16   B2_2    B2_21   B2_23   B2_28   B2_6    B3_10   B3_14   B3_16   B3_2    B3_21   B3_23   B3_28   B3_6    C1_10   C1_14   C1_16   C1_2    C1_6    C2_10   C2_14   C2_16   C2_2    C2_6    C3_10   C3_14   C3_16   C3_2    C3_6    D1_10   D1_14   D1_16   D1_2    D1_6    D2_10   D2_14   D2_16   D2_2    D2_6    D3_10   D3_14   D3_16   D3_2    D3_6    S10_1   S10_2   S10_3   S1_1    S1_2    S1_3    S2_1    S2_2    S2_3    S3_1    S3_2    S3_3    S4_1    S4_2    S4_3    S5_1    S5_2    S5_3    S6_1    S6_2    S6_3    S7_1    S7_2    S7_3    S8_1    S8_2    S8_3    S9_1    S9_2    S9_3    SB2_1   SB2_2   SB2_3   SC1_1   SC1_2   SC1_3   raw1    raw2    raw3
0   0   Root    2   11776   1025    1030    904 923 848 1147    1042    1062    913 1034    953 773 1049    1048    1158    1123    930 987 1166    919 1375    1149    1231    1040    886 1057    1059    833 1428    1146    1206    1120    583 909 1093    748 1434    1179    1120    1014    644 941 883 957 832 1148    1033    1025    901 1066    1125    1156    1128    724 838 841 1158    978 831 1023    1091    1104    1038    997 1012    1134    1064    884 920 1004    1026    1121    1049    856 946 1061    1022    938 403 398 466 289 304 98  756 807 645 798 825 901 1906    1823    1968    1094    1027    1127    978 2038    1629    521 483 603 575 654 676 428 422 369 786 846 820 1144    1107    1297    732 802 925
1   0.1 Archaea 3   13  0   0   0   0   1   0   0   1   0   0   0   0   0   1   0   1   0   0   0   0   4   1   0   2   1   0   0   0   3   0   1   0   0   0   0   0   4   0   0   0   0   0   0   0   0   0   0   0   0   1   0   1   0   1   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   1   0   0   1   0   0   0   0   0   1   0   0   1   0   0   1   1   3   3   5   2   3   4   2   3   4   0   0   0   0   0   0   0   0   0   3   3   1   3   2   2   0   0   0
2   0.1.1   Aenigmarchaeota 1   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
3   0.1.1.1 Deep_Sea_Euryarchaeotic_Group(DSEG) 1   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
4   0.1.1.1.1   Deep_Sea_Euryarchaeotic_Group(DSEG)_unclassified    1   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
5   0.1.1.1.1.1 Deep_Sea_Euryarchaeotic_Group(DSEG)_unclassified    1   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
6   0.1.1.1.1.1.1   Deep_Sea_Euryarchaeotic_Group(DSEG)_unclassified    0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
2   0.1.2   Thaumarchaeota  3   10  0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   1   0   0   0   0   3   1   0   2   1   0   0   0   3   0   1   0   0   0   0   0   4   0   0   0   0   0   0   0   0   0   0   0   0   1   0   1   0   1   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   1   0   0   1   0   0   0   0   0   1   0   0   1   0   0   1   1   3   3   4   2   3   3   2   3   4   0   0   0   0   0   0   0   0   0   3   3   1   3   2   2   0   0   0
3   0.1.2.1 AK31    1   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
4   0.1.2.1.1   AK31_unclassified   1   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
5   0.1.2.1.1.1 AK31_unclassified   1   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
6   0.1.2.1.1.1.1   AK31_unclassified   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
3   0.1.2.2 Marine_Group_I  2   5   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   1   0   0   0   0   2   0   0   2   1   0   0   0   3   0   0   0   0   0   0   0   2   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   1   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   1   0   0   1   0   0   0   0   2   2   3   2   3   3   2   3   2   0   0   0   0   0   0   0   0   0   1   3   1   3   2   2   0   0   0
4   0.1.2.2.1   Marine_Group_I_unclassified 1   2   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   1   1   1   1   0   0   0   0
5   0.1.2.2.1.1 Marine_Group_I_unclassified 1   2   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   1   1   1   1   0   0   0   0
6   0.1.2.2.1.1.1   Marine_Group_I_unclassified 0   2   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   1   1   1   1   0   0   0   0
4   0.1.2.2.2   Unknown_Order   1   3   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   1   0   0   0   0   2   0   0   2   1   0   0   0   2   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   1   0   0   1   0   0   0   0   2   2   3   2   3   3   2   3   2   0   0   0   0   0   0   0   0   0   0   2   0   2   1   2   0   0   0
5   0.1.2.2.2.1 Unknown_Family  3   3   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   1   0   0   0   0   2   0   0   2   1   0   0   0   2   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   1   0   0   1   0   0   0   0   2   2   3   2   3   3   2   3   2   0   0   0   0   0   0   0   0   0   0   2   0   2   1   2   0   0   0
6   0.1.2.2.2.1.1   Candidatus_Nitrosoarchaeum  0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   1   0   0   1   0   0   0   0   1   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   1   1   1   1   1   1   1   1   1   0   0   0   0   0   0   0   0   0   0   1   0   1   0   1   0   0   0
6   0.1.2.2.2.1.2   Candidatus_Nitrosopelagicus 0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   1   1   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
6   0.1.2.2.2.1.3   Unknown_Family_unclassified 0   1   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   1   0   0   0   0   1   1   1   1   1   1   1   1   1   0   0   0   0   0   0   0   0   0   0   1   0   1   1   1   0   0   0
3   0.1.2.3 Soil_Crenarchaeotic_Group(SCG)  2   4   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   1   0   0   0   0   0   0   0   0   1   0   0   0   0   0   2   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   1   0   1   1   0   0   0   0   0   2   0   0   0   0   0   0   0   0   0   2   0   0   0   0   0   0   0   0
4   0.1.2.3.1   Soil_Crenarchaeotic_Group(SCG)_unclassified 1   3   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   1   0   0   0   0   0   0   0   0   1   0   0   0   0   0   2   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   1   0   1   1   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   2   0   0   0   0   0   0   0   0
5   0.1.2.3.1.1 Soil_Crenarchaeotic_Group(SCG)_unclassified 1   3   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   1   0   0   0   0   0   0   0   0   1   0   0   0   0   0   2   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   1   0   1   1   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   2   0   0   0   0   0   0   0   0
6   0.1.2.3.1.1.1   Soil_Crenarchaeotic_Group(SCG)_unclassified 0   3   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   1   0   0   0   0   0   0   0   0   1   0   0   0   0   0   2   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   1   0   1   1   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   2   0   0   0   0   0   0   0   0
4   0.1.2.3.2   Unknown_Order   1   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
5   0.1.2.3.2.1 Unknown_Family  1   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
6   0.1.2.3.2.1.1   Candidatus_Nitrososphaera   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
2   0.1.3   Woesearchaeota_(DHVEG-6)    1   2   0   0   0   0   1   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
3   0.1.3.1 Woesearchaeota_(DHVEG-6)_unclassified   1   2   0   0   0   0   1   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
4   0.1.3.1.1   Woesearchaeota_(DHVEG-6)_unclassified   1   2   0   0   0   0   1   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
5   0.1.3.1.1.1 Woesearchaeota_(DHVEG-6)_unclassified   1   2   0   0   0   0   1   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
6   0.1.3.1.1.1.1   Woesearchaeota_(DHVEG-6)_unclassified   0   2   0   0   0   0   1   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
1   0.2 Bacteria    51  11763   1025    1030    904 923 847 1147    1042    1061    913 1034    953 773 1049    1047    1158    1122    930 987 1166    919 1371    1148    1231    1038    885 1057    1059    833 1425    1146    1205    1120    583 909 1093    748 1430    1179    1120    1014    644 941 883 957 832 1148    1033    1025    901 1065    1125    1155    1128    723 838 841 1158    978 831 1023    1091    1103    1038    997 1012    1134    1064    884 920 1004    1026    1121    1049    855 946 1061    1021    938 403 398 466 289 303 98  756 806 645 798 824 900 1903    1820    1963    1092    1024    1123    976 2035    1625    521 483 603 575 654 676 428 422 369 783 843 819 1141    1105    1295    732 802 925
2   0.2.1   Acetothermia    1   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   1   1   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
3   0.2.1.1 Acetothermia_unclassified   1   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   1   1   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
4   0.2.1.1.1   Acetothermia_unclassified   1   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   1   1   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
5   0.2.1.1.1.1 Acetothermia_unclassified   1   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   1   1   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
6   0.2.1.1.1.1.1   Acetothermia_unclassified   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   1   1   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
2   0.2.2   Acidobacteria   21  550 26  30  22  19  27  26  21  38  27  25  32  13  25  27  32  44  23  27  44  23  88  21  39  42  30  33  36  22  98  49  55  29  20  20  32  22  110 39  41  22  22  18  30  20  17  29  33  19  20  32  44  42  25  18  15  30  37  23  23  28  41  42  23  25  33  48  34  22  25  23  33  29  27  29  29  41  31  25  9   8   20  34  33  5   80  66  67  73  75  82  169 178 172 119 112 112 117 193 165 10  8   17  25  21  23  19  13  10  53  57  54  88  89  93  14  11  25
3   0.2.2.1 AT-s3-28    1   23  0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   3   0   0   0   0   1   0   0   0   1   0   0   0   2   0   0   0   1   0   0   0   3   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   1   0   8   4   6   5   6   4   10  11  8   8   7   5   4   11  10  0   0   0   0   0   0   0   0   0   0   0   0   9   7   7   0   0   0
4   0.2.2.1.1   AT-s3-28_unclassified   1   23  0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   3   0   0   0   0   1   0   0   0   1   0   0   0   2   0   0   0   1   0   0   0   3   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   1   0   8   4   6   5   6   4   10  11  8   8   7   5   4   11  10  0   0   0   0   0   0   0   0   0   0   0   0   9   7   7   0   0   0
5   0.2.2.1.1.1 AT-s3-28_unclassified   1   23  0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   3   0   0   0   0   1   0   0   0   1   0   0   0   2   0   0   0   1   0   0   0   3   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   1   0   8   4   6   5   6   4   10  11  8   8   7   5   4   11  10  0   0   0   0   0   0   0   0   0   0   0   0   9   7   7   0   0   0
6   0.2.2.1.1.1.1   AT-s3-28_unclassified   0   23  0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   3   0   0   0   0   1   0   0   0   1   0   0   0   2   0   0   0   1   0   0   0   3   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   1   0   8   4   6   5   6   4   10  11  8   8   7   5   4   11  10  0   0   0   0   0   0   0   0   0   0   0   0   9   7   7   0   0   0
3   0.2.2.2 Acidobacteria   1   9   0   0   0   0   0   1   0   0   1   0   1   0   0   1   0   0   0   0   0   0   1   0   1   0   0   0   0   0   2   1   1   0   0   0   0   0   2   0   0   0   0   0   0   0   0   1   0   0   1   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   1   0   1   0   0   0   0   0
4   0.2.2.2.1   Acidobacteriales    1   9   0   0   0   0   0   1   0   0   1   0   1   0   0   1   0   0   0   0   0   0   1   0   1   0   0   0   0   0   2   1   1   0   0   0   0   0   2   0   0   0   0   0   0   0   0   1   0   0   1   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   1   0   1   0   0   0   0   0
5   0.2.2.2.1.1 Acidobacteriaceae_(Subgroup_1)  3   9   0   0   0   0   0   1   0   0   1   0   1   0   0   1   0   0   0   0   0   0   1   0   1   0   0   0   0   0   2   1   1   0   0   0   0   0   2   0   0   0   0   0   0   0   0   1   0   0   1   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   1   0   1   0   0   0   0   0
6   0.2.2.2.1.1.1   Acidobacteriaceae_(Subgroup_1)_unclassified 0   6   0   0   0   0   0   0   0   0   1   0   1   0   0   0   0   0   0   0   0   0   1   0   1   0   0   0   0   0   1   1   1   0   0   0   0   0   2   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   1   0   1   0   0   0   0   0
6   0.2.2.2.1.1.2   Acidobacterium  0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
6   0.2.2.2.1.1.3   Candidatus_Koribacter   0   2   0   0   0   0   0   1   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   1   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
3   0.2.2.3 Acidobacteria_unclassified  1   3   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   1   0   1   1   1   1   0   1   1   0   2   0   0   0   0   0   0   0   0   0   0   0   0   0   1   2   1   0   0   0
4   0.2.2.3.1   Acidobacteria_unclassified  1   3   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   1   0   1   1   1   1   0   1   1   0   2   0   0   0   0   0   0   0   0   0   0   0   0   0   1   2   1   0   0   0
5   0.2.2.3.1.1 Acidobacteria_unclassified  1   3   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   1   0   1   1   1   1   0   1   1   0   2   0   0   0   0   0   0   0   0   0   0   0   0   0   1   2   1   0   0   0
6   0.2.2.3.1.1.1   Acidobacteria_unclassified  0   3   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   1   0   1   1   1   1   0   1   1   0   2   0   0   0   0   0   0   0   0   0   0   0   0   0   1   2   1   0   0   0
3   0.2.2.4 Blastocatellia  1   85  6   7   7   4   5   5   5   5   8   9   5   4   7   4   9   6   5   8   13  6   10  5   5   7   7   10  9   4   12  17  16  8   6   6   5   6   11  11  10  5   8   5   7   5   4   4   9   7   8   11  9   5   6   8   4   7   9   6   7   8   11  8   4   6   10  12  8   5   7   4   5   3   7   9   10  8   7   6   2   2   7   4   5   0   9   11  10  13  12  14  20  20  21  7   13  12  11  25  24  4   5   6   6   6   6   3   4   5   15  16  12  16  18  18  1   2   5
4   0.2.2.4.1   Blastocatellales    1   85  6   7   7   4   5   5   5   5   8   9   5   4   7   4   9   6   5   8   13  6   10  5   5   7   7   10  9   4   12  17  16  8   6   6   5   6   11  11  10  5   8   5   7   5   4   4   9   7   8   11  9   5   6   8   4   7   9   6   7   8   11  8   4   6   10  12  8   5   7   4   5   3   7   9   10  8   7   6   2   2   7   4   5   0   9   11  10  13  12  14  20  20  21  7   13  12  11  25  24  4   5   6   6   6   6   3   4   5   15  16  12  16  18  18  1   2   5
5   0.2.2.4.1.1 Blastocatellaceae_(Subgroup_4)  7   85  6   7   7   4   5   5   5   5   8   9   5   4   7   4   9   6   5   8   13  6   10  5   5   7   7   10  9   4   12  17  16  8   6   6   5   6   11  11  10  5   8   5   7   5   4   4   9   7   8   11  9   5   6   8   4   7   9   6   7   8   11  8   4   6   10  12  8   5   7   4   5   3   7   9   10  8   7   6   2   2   7   4   5   0   9   11  10  13  12  14  20  20  21  7   13  12  11  25  24  4   5   6   6   6   6   3   4   5   15  16  12  16  18  18  1   2   5
zachary-foster commented 7 years ago

Thanks @Wookie777! Yep, that is pretty straight forward. See:

library(metacoder)
data <- parse_mothur_summary("example.tax.summary")
heat_tree(data, node_color = total, node_size = total, node_label = taxon)

rplot

Wookie777 commented 7 years ago

Thanks a lot for your help and I hope you can help me again for another problem: I want to calculate the Read abundance like in the Human microbiome example but I get this error: Error in FUN(X[[i]], ...) : only defined on a data frame with all numeric variables.

Here is my code for the example above:

moth_test <- parse_mothur_summary("~/moth_test.tax.summary")
calculate_abundance(moth_test)
zachary-foster commented 7 years ago

Hi @Wookie777, It looks to me that the mothur file already has the totals of reads per sample for each taxon. in the HMP example, the source data started out as read counts per OTU, which then needed to be summed per taxon. I dont think you need to do that here. Make sense?

Wookie777 commented 7 years ago

Sorry but I don't really know what you mean. In my opinion I have to normalize the different samples to compare them. One option is the sub-sampling in the mothur pipeline; the other one is to calculate the abundance of every taxon in every sample.

zachary-foster commented 7 years ago

Sorry about the confusion. The abundance of every taxon in every sample is already in the input file, and therefore in the parsed taxmap object as well. For example, if we look at the first few lines:

taxlevel    rankID  taxon   daughterlevels  total   A1_10   A1_14   A1_16   A1_2    A1_21   A1_23   A1_28   A1_6    A2_10   A2_14   A2_16   A2_2    A2_21   A2_23   A2_28   A2_6    A3_10   A3_14   A3_16   A3_2    A3_21   A3_23   A3_28   A3_6    B1_10   B1_14   B1_16   B1_2    B1_21   B1_23   B1_28   B1_6    B2_10   B2_14   B2_16   B2_2    B2_21   B2_23   B2_28   B2_6    B3_10   B3_14   B3_16   B3_2    B3_21   B3_23   B3_28   B3_6    C1_10   C1_14   C1_16   C1_2    C1_6    C2_10   C2_14   C2_16   C2_2    C2_6    C3_10   C3_14   C3_16   C3_2    C3_6    D1_10   D1_14   D1_16   D1_2    D1_6    D2_10   D2_14   D2_16   D2_2    D2_6    D3_10   D3_14   D3_16   D3_2    D3_6    S10_1   S10_2   S10_3   S1_1    S1_2    S1_3    S2_1    S2_2    S2_3    S3_1    S3_2    S3_3    S4_1    S4_2    S4_3    S5_1    S5_2    S5_3    S6_1    S6_2    S6_3    S7_1    S7_2    S7_3    S8_1    S8_2    S8_3    S9_1    S9_2    S9_3    SB2_1   SB2_2   SB2_3   SC1_1   SC1_2   SC1_3   raw1    raw2    raw3
0   0   Root    2   11776   1025    1030    904 923 848 1147    1042    1062    913 1034    953 773 1049    1048    1158    1123    930 987 1166    919 1375    1149    1231    1040    886 1057    1059    833 1428    1146    1206    1120    583 909 1093    748 1434    1179    1120    1014    644 941 883 957 832 1148    1033    1025    901 1066    1125    1156    1128    724 838 841 1158    978 831 1023    1091    1104    1038    997 1012    1134    1064    884 920 1004    1026    1121    1049    856 946 1061    1022    938 403 398 466 289 304 98  756 807 645 798 825 901 1906    1823    1968    1094    1027    1127    978 2038    1629    521 483 603 575 654 676 428 422 369 786 846 820 1144    1107    1297    732 802 925
1   0.1 Archaea 3   13  0   0   0   0   1   0   0   1   0   0   0   0   0   1   0   1   0   0   0   0   4   1   0   2   1   0   0   0   3   0   1   0   0   0   0   0   4   0   0   0   0   0   0   0   0   0   0   0   0   1   0   1   0   1   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   1   0   0   1   0   0   0   0   0   1   0   0   1   0   0   1   1   3   3   5   2   3   4   2   3   4   0   0   0   0   0   0   0   0   0   3   3   1   3   2   2   0   0   0

we can see that "Archaea" have 13 reads total (all samples) and 1 read for sample "A_14". After parsing the data, that information is still present:

> library(metacoder)
> data <- parse_mothur_summary("example.tax.summary")
Removed 0 unclassified rows.
57 inputs used to classify 57 observations by 57 taxa.
> data
`taxmap` object with data for 57 taxa and 57 observations:

---------------------------------------------------------------------- taxa ----------------------------------------------------------------------
1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18 ... 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57

------------------------------------------------------------------- taxon_data -------------------------------------------------------------------
# A tibble: 57 x 124
  taxon_ids supertaxon_ids  name taxlevel                               taxon daughterlevels total A1_10 A1_14 A1_16  A1_2 A1_21 A1_23 A1_28  A1_6 A2_10 A2_14
      <chr>          <chr> <dbl>    <dbl>                               <chr>          <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1         1           <NA>     0        0                                Root              2 11776  1025  1030   904   923   848  1147  1042  1062   913  1034
2         2              1     1        1                             Archaea              3    13     0     0     0     0     1     0     0     1     0     0
3         3              1     2        1                            Bacteria             51 11763  1025  1030   904   923   847  1147  1042  1061   913  1034
4         4              2     1        2                     Aenigmarchaeota              1     1     0     0     0     0     0     0     0     0     0     0
5         5              2     2        2                      Thaumarchaeota              3    10     0     0     0     0     0     0     0     1     0     0
6         6              2     3        2            Woesearchaeota_(DHVEG-6)              1     2     0     0     0     0     1     0     0     0     0     0
7         7              4     1        3 Deep_Sea_Euryarchaeotic_Group(DSEG)              1     1     0     0     0     0     0     0     0     0     0     0
# ... with 50 more rows, and 107 more variables: A2_16 <dbl>, A2_2 <dbl>, A2_21 <dbl>, A2_23 <dbl>, A2_28 <dbl>, A2_6 <dbl>, A3_10 <dbl>, A3_14 <dbl>,
#   A3_16 <dbl>, A3_2 <dbl>, A3_21 <dbl>, A3_23 <dbl>, A3_28 <dbl>, A3_6 <dbl>, B1_10 <dbl>, B1_14 <dbl>, B1_16 <dbl>, B1_2 <dbl>, B1_21 <dbl>, B1_23 <dbl>,
#   B1_28 <dbl>, B1_6 <dbl>, B2_10 <dbl>, B2_14 <dbl>, B2_16 <dbl>, B2_2 <dbl>, B2_21 <dbl>, B2_23 <dbl>, B2_28 <dbl>, B2_6 <dbl>, B3_10 <dbl>, B3_14 <dbl>,
#   B3_16 <dbl>, B3_2 <dbl>, B3_21 <dbl>, B3_23 <dbl>, B3_28 <dbl>, B3_6 <dbl>, C1_10 <dbl>, C1_14 <dbl>, C1_16 <dbl>, C1_2 <dbl>, C1_6 <dbl>, C2_10 <dbl>,
#   C2_14 <dbl>, C2_16 <dbl>, C2_2 <dbl>, C2_6 <dbl>, C3_10 <dbl>, C3_14 <dbl>, C3_16 <dbl>, C3_2 <dbl>, C3_6 <dbl>, D1_10 <dbl>, D1_14 <dbl>, D1_16 <dbl>,
#   D1_2 <dbl>, D1_6 <dbl>, D2_10 <dbl>, D2_14 <dbl>, D2_16 <dbl>, D2_2 <dbl>, D2_6 <dbl>, D3_10 <dbl>, D3_14 <dbl>, D3_16 <dbl>, D3_2 <dbl>, D3_6 <dbl>,
#   S10_1 <dbl>, S10_2 <dbl>, S10_3 <dbl>, S1_1 <dbl>, S1_2 <dbl>, S1_3 <dbl>, S2_1 <dbl>, S2_2 <dbl>, S2_3 <dbl>, S3_1 <dbl>, S3_2 <dbl>, S3_3 <dbl>,
#   S4_1 <dbl>, S4_2 <dbl>, S4_3 <dbl>, S5_1 <dbl>, S5_2 <dbl>, S5_3 <dbl>, S6_1 <dbl>, S6_2 <dbl>, S6_3 <dbl>, S7_1 <dbl>, S7_2 <dbl>, S7_3 <dbl>,
#   S8_1 <dbl>, S8_2 <dbl>, S8_3 <dbl>, S9_1 <dbl>, S9_2 <dbl>, S9_3 <dbl>, SB2_1 <dbl>, SB2_2 <dbl>, ...

-------------------------------------------------------------------- obs_data --------------------------------------------------------------------
# A tibble: 57 x 1
  obs_taxon_ids
          <chr>
1             1
2             2
3             4
4             7
5             8
6             9
7            10
# ... with 50 more rows

------------------------------------------------------------------- taxon_funcs -------------------------------------------------------------------
n_obs, n_obs_1, n_supertaxa, n_subtaxa, n_subtaxa_1, hierarchies, all

in regards to normalizing samples to compare them, that can be done by calculating read proportion by dividing each sample column by the total number of reads in the "Root" taxon, or rarefying using a package like vegan. Since the first is pretty easy and the second is implemented in other packages, metacoder does not have functions for either right now, but it might in the future once I get to it. Hope this helps

Wookie777 commented 7 years ago

This helps a lot. Thanks for your good explanation. Now I get clear and can proceed my data visualization by calculating the read proportion.

zachary-foster commented 7 years ago

Glad to hear it. Is this issue done then? Mind if I close?