grabear
commented
6 years ago > length(m$data$diff_table$wilcox_p_value)
[1] 420
> length(m$taxon_ids())
[1] 239
> length(unique(m$data$diff_table$taxon_id))
[1] 239
> m
<Taxmap>
239 taxa: ac. Bacteria, af. Firmicutes ... ff. Anaeroplasmataceae, ky. Anaeroplasma
239 edges: NA->ac, ac->af, af->av, av->bu, bu->dc ... ac->at, at->bs, bs->da, da->ff, ff->ky
6 data sets:
otu_table:
# A tibble: 1,866 x 49
taxon_id Sample_1 Sample_2 Sample_3 Sample_6 Sample_9 Sample_10 Sample_13 Sample_14 Sample_17
<chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 fh 0.000438 0.0000118 0.000435 0.0000257 0.000245 0.0000896 0.0000253 0 0.00000735
2 fi 0.0000438 0.0000589 0.000814 0.000103 0.000768 0.000381 0.000160 0.0000110 0.00000735
3 fi 0.000728 0 0.000860 0.00237 0.000309 0.000179 0.0000422 0 0.0000294
# ... with 1,863 more rows, and 39 more variables: Sample_21 <dbl>, Sample_22 <dbl>,
# Sample_24 <dbl>, Sample_25 <dbl>, Sample_26 <dbl>, Sample_30 <dbl>, Sample_50 <dbl>,
# Sample_59 <dbl>, Sample_60 <dbl>, Sample_61 <dbl>, Sample_7 <dbl>, Sample_27 <dbl>,
# Sample_45 <dbl>, Sample_5 <dbl>, Sample_57 <dbl>, Sample_20 <dbl>, Sample_29 <dbl>,
# Sample_11 <dbl>, Sample_12 <dbl>, Sample_15 <dbl>, Sample_16 <dbl>, Sample_18 <dbl>,
# Sample_19 <dbl>, Sample_23 <dbl>, Sample_28 <dbl>, Sample_31 <dbl>, Sample_35 <dbl>,
# Sample_40 <dbl>, Sample_41 <dbl>, Sample_46 <dbl>, Sample_47 <dbl>, Sample_51 <dbl>,
# Sample_55 <dbl>, Sample_56 <dbl>, Sample_58 <dbl>, Sample_8 <dbl>, Sample_4 <dbl>,
# Sample_52 <dbl>, Sample_36 <dbl>
tax_data:
# A tibble: 1,866 x 8
taxon_id Kingdom Phylum Class Order Family Genus Species
<chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 fh Bacteria Firmicutes Negativicutes Selenomonadales Veillonellaceae Megamonas uncultur~
2 fi Bacteria Firmicutes Negativicutes Selenomonadales Acidaminococcaceae Phascola~ uncultur~
3 fi Bacteria Firmicutes Negativicutes Selenomonadales Acidaminococcaceae Phascola~ uncultur~
# ... with 1,863 more rows
sam_data:
# A tibble: 48 x 9
sample_ids X.SampleID BarcodeSequence LinkerPrimerSeque~ ForwardFastqFile ReverseFastqFile
<chr> <chr> <chr> <chr> <chr> <chr>
1 Sample_1 Sample_1 <NA> <NA> 33749_S1_L001_R1_00~ 33749_S1_L001_R2_0~
2 Sample_2 Sample_2 <NA> <NA> 33739_S2_L001_R1_00~ 33739_S2_L001_R2_0~
3 Sample_3 Sample_3 <NA> <NA> 33737_S3_L001_R1_00~ 33737_S3_L001_R2_0~
# ... with 45 more rows, and 3 more variables: TreatmentGroup <chr>, SampleName <chr>,
# Description <chr>
phylo_tree:
Phylogenetic tree with 1955 tips and 1954 internal nodes.
Tip labels:
New.CleanUp.ReferenceOTU177, New.ReferenceOTU1091, New.ReferenceOTU2352, EU774211.1.1284, New.ReferenceOTU1302, New.ReferenceOTU239, ...
Node labels:
Root, 0.917, 0.794, 0.853, 0.768, 0.880, ...
Rooted; includes branch lengths.
tax_table:
# A tibble: 420 x 49
taxon_id Sample_1 Sample_2 Sample_3 Sample_6 Sample_9 Sample_10 Sample_13 Sample_14 Sample_17
<chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 ac 0.987 0.994 0.982 0.991 0.983 0.988 0.986 0.991 0.988
2 af 0.473 0.370 0.468 0.397 0.392 0.632 0.436 0.363 0.385
3 ag 0.0370 0.131 0.00445 0.0327 0.00695 0.00538 0.00938 0.00385 0.0235
# ... with 417 more rows, and 39 more variables: Sample_21 <dbl>, Sample_22 <dbl>, Sample_24 <dbl>,
# Sample_25 <dbl>, Sample_26 <dbl>, Sample_30 <dbl>, Sample_50 <dbl>, Sample_59 <dbl>,
# Sample_60 <dbl>, Sample_61 <dbl>, Sample_7 <dbl>, Sample_27 <dbl>, Sample_45 <dbl>,
# Sample_5 <dbl>, Sample_57 <dbl>, Sample_20 <dbl>, Sample_29 <dbl>, Sample_11 <dbl>,
# Sample_12 <dbl>, Sample_15 <dbl>, Sample_16 <dbl>, Sample_18 <dbl>, Sample_19 <dbl>,
# Sample_23 <dbl>, Sample_28 <dbl>, Sample_31 <dbl>, Sample_35 <dbl>, Sample_40 <dbl>,
# Sample_41 <dbl>, Sample_46 <dbl>, Sample_47 <dbl>, Sample_51 <dbl>, Sample_55 <dbl>,
# Sample_56 <dbl>, Sample_58 <dbl>, Sample_8 <dbl>, Sample_4 <dbl>, Sample_52 <dbl>,
# Sample_36 <dbl>
diff_table:
# A tibble: 420 x 11
taxon_id treatment_1 treatment_2 log2_median_ratio median_diff mean_diff wilcox_p_value
<chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl>
1 ac Stressed Control 0.00272 0.00186 0.00106 0.313
2 af Stressed Control 0.322 0.0850 0.102 0.0000803
3 ag Stressed Control -0.542 -0.00454 -0.00455 0.219
# ... with 417 more rows, and 4 more variables: hartigan_dip_treat1 <dbl>,
# hartigan_dip_treat2 <dbl>, bimodality_coeff_treat1 <dbl>, bimodality_coeff_treat2 <dbl>
0 functions:
zachary-foster
The taxon_ids that are present in the otu_table/tax_data tables are different, but related to the taxon_ids in the tax_table/diff_tables created by coercing the phyloseq object into a taxmap object as shown here.
While the different taxon_ids are obviously just part of the taxmap heirarchy, the confusion could be remedied by including the OTU label for taxon_ids mentioned in #219 that are legitimately identified/annotated organisms. While intermediate taxon_ids that are used to identify/accumulate data for each of the intermediate taxonomic ranks, are left without this OTU label.
The intermediate taxon_ids could also be given a group OTU label that gives access to the list of OTU labels that are included in that taxonomy.