R/amp_export_long.R
amp_export_long.RdTransforms any ampvis2 object into a long data frame (data.table) to facilitate custom data analysis. Only the elements OTU counts (data$abund), taxonomy (data$tax), and metadata (data$metadata) are used, not phylogenetic tree or DNA sequences.
(required) Data list as loaded with amp_load.
A character vector of sample metadata variables to include from data$metadata, or NULL. The first column (sample IDs) will always be included. Default includes all.
A character vector of taxonomic levels to include from data$tax, or NULL. The OTU column will always be included. Default includes all.
A data.table in long format.
# load minimal example data
d <- amp_load(example_otutable, example_metadata)
# transform d into a long-format data frame
d_long <- amp_export_long(d, metadata_vars = "Date", tax_levels = c("OTU", "Genus"))
# print the data frame (data.table)
d_long
#> SampleID OTU count Date Genus
#> <char> <char> <int> <POSc> <char>
#> 1: 16SAMP_3893 OTU_1 23 2014-02-06 g__Candidatus Amarilinum
#> 2: 16SAMP_3893 OTU_2 675 2014-02-06 g__Tetrasphaera
#> 3: 16SAMP_3893 OTU_3 780 2014-02-06 g__Candidatus Microthrix
#> 4: 16SAMP_3893 OTU_4 272 2014-02-06 g__Dechloromonas
#> 5: 16SAMP_3893 OTU_5 560 2014-02-06 g__Candidatus Villogracilis
#> 6: 16SAMP_3893 OTU_6 906 2014-02-06 g__Trichococcus
#> 7: 16SAMP_3893 OTU_7 297 2014-02-06 g__Candidatus Microthrix
#> 8: 16SAMP_3893 OTU_8 28 2014-02-06 g__Nitrospira
#> 9: 16SAMP_3893 OTU_9 0 2014-02-06 g__QEDR3BF09
#> 10: 16SAMP_3893 OTU_10 373 2014-02-06 g__MK04
#> 11: 16SAMP_3913 OTU_1 15 2014-07-03 g__Candidatus Amarilinum
#> 12: 16SAMP_3913 OTU_2 565 2014-07-03 g__Tetrasphaera
#> 13: 16SAMP_3913 OTU_3 733 2014-07-03 g__Candidatus Microthrix
#> 14: 16SAMP_3913 OTU_4 233 2014-07-03 g__Dechloromonas
#> 15: 16SAMP_3913 OTU_5 339 2014-07-03 g__Candidatus Villogracilis
#> 16: 16SAMP_3913 OTU_6 766 2014-07-03 g__Trichococcus
#> 17: 16SAMP_3913 OTU_7 218 2014-07-03 g__Candidatus Microthrix
#> 18: 16SAMP_3913 OTU_8 8 2014-07-03 g__Nitrospira
#> 19: 16SAMP_3913 OTU_9 0 2014-07-03 g__QEDR3BF09
#> 20: 16SAMP_3913 OTU_10 256 2014-07-03 g__MK04
#> 21: 16SAMP_3941 OTU_1 273 2014-08-19 g__Candidatus Amarilinum
#> 22: 16SAMP_3941 OTU_2 331 2014-08-19 g__Tetrasphaera
#> 23: 16SAMP_3941 OTU_3 405 2014-08-19 g__Candidatus Microthrix
#> 24: 16SAMP_3941 OTU_4 1434 2014-08-19 g__Dechloromonas
#> 25: 16SAMP_3941 OTU_5 509 2014-08-19 g__Candidatus Villogracilis
#> 26: 16SAMP_3941 OTU_6 133 2014-08-19 g__Trichococcus
#> 27: 16SAMP_3941 OTU_7 418 2014-08-19 g__Candidatus Microthrix
#> 28: 16SAMP_3941 OTU_8 155 2014-08-19 g__Nitrospira
#> 29: 16SAMP_3941 OTU_9 9 2014-08-19 g__QEDR3BF09
#> 30: 16SAMP_3941 OTU_10 19 2014-08-19 g__MK04
#> 31: 16SAMP_3946 OTU_1 51 2014-11-13 g__Candidatus Amarilinum
#> 32: 16SAMP_3946 OTU_2 411 2014-11-13 g__Tetrasphaera
#> 33: 16SAMP_3946 OTU_3 199 2014-11-13 g__Candidatus Microthrix
#> 34: 16SAMP_3946 OTU_4 256 2014-11-13 g__Dechloromonas
#> 35: 16SAMP_3946 OTU_5 598 2014-11-13 g__Candidatus Villogracilis
#> 36: 16SAMP_3946 OTU_6 390 2014-11-13 g__Trichococcus
#> 37: 16SAMP_3946 OTU_7 130 2014-11-13 g__Candidatus Microthrix
#> 38: 16SAMP_3946 OTU_8 72 2014-11-13 g__Nitrospira
#> 39: 16SAMP_3946 OTU_9 0 2014-11-13 g__QEDR3BF09
#> 40: 16SAMP_3946 OTU_10 415 2014-11-13 g__MK04
#> 41: 16SAMP_3953 OTU_1 127 2014-02-04 g__Candidatus Amarilinum
#> 42: 16SAMP_3953 OTU_2 430 2014-02-04 g__Tetrasphaera
#> 43: 16SAMP_3953 OTU_3 1346 2014-02-04 g__Candidatus Microthrix
#> 44: 16SAMP_3953 OTU_4 736 2014-02-04 g__Dechloromonas
#> 45: 16SAMP_3953 OTU_5 223 2014-02-04 g__Candidatus Villogracilis
#> 46: 16SAMP_3953 OTU_6 232 2014-02-04 g__Trichococcus
#> 47: 16SAMP_3953 OTU_7 1354 2014-02-04 g__Candidatus Microthrix
#> 48: 16SAMP_3953 OTU_8 156 2014-02-04 g__Nitrospira
#> 49: 16SAMP_3953 OTU_9 19 2014-02-04 g__QEDR3BF09
#> 50: 16SAMP_3953 OTU_10 43 2014-02-04 g__MK04
#> 51: 16SAMP_4591 OTU_1 190 2014-05-05 g__Candidatus Amarilinum
#> 52: 16SAMP_4591 OTU_2 780 2014-05-05 g__Tetrasphaera
#> 53: 16SAMP_4591 OTU_3 1114 2014-05-05 g__Candidatus Microthrix
#> 54: 16SAMP_4591 OTU_4 1338 2014-05-05 g__Dechloromonas
#> 55: 16SAMP_4591 OTU_5 145 2014-05-05 g__Candidatus Villogracilis
#> 56: 16SAMP_4591 OTU_6 1458 2014-05-05 g__Trichococcus
#> 57: 16SAMP_4591 OTU_7 198 2014-05-05 g__Candidatus Microthrix
#> 58: 16SAMP_4591 OTU_8 101 2014-05-05 g__Nitrospira
#> 59: 16SAMP_4591 OTU_9 25 2014-05-05 g__QEDR3BF09
#> 60: 16SAMP_4591 OTU_10 102 2014-05-05 g__MK04
#> 61: 16SAMP_4597 OTU_1 220 2014-08-18 g__Candidatus Amarilinum
#> 62: 16SAMP_4597 OTU_2 699 2014-08-18 g__Tetrasphaera
#> 63: 16SAMP_4597 OTU_3 1630 2014-08-18 g__Candidatus Microthrix
#> 64: 16SAMP_4597 OTU_4 1224 2014-08-18 g__Dechloromonas
#> 65: 16SAMP_4597 OTU_5 212 2014-08-18 g__Candidatus Villogracilis
#> 66: 16SAMP_4597 OTU_6 560 2014-08-18 g__Trichococcus
#> 67: 16SAMP_4597 OTU_7 283 2014-08-18 g__Candidatus Microthrix
#> 68: 16SAMP_4597 OTU_8 151 2014-08-18 g__Nitrospira
#> 69: 16SAMP_4597 OTU_9 58 2014-08-18 g__QEDR3BF09
#> 70: 16SAMP_4597 OTU_10 73 2014-08-18 g__MK04
#> 71: 16SAMP_4603 OTU_1 83 2014-11-12 g__Candidatus Amarilinum
#> 72: 16SAMP_4603 OTU_2 820 2014-11-12 g__Tetrasphaera
#> 73: 16SAMP_4603 OTU_3 112 2014-11-12 g__Candidatus Microthrix
#> 74: 16SAMP_4603 OTU_4 564 2014-11-12 g__Dechloromonas
#> 75: 16SAMP_4603 OTU_5 1619 2014-11-12 g__Candidatus Villogracilis
#> 76: 16SAMP_4603 OTU_6 287 2014-11-12 g__Trichococcus
#> 77: 16SAMP_4603 OTU_7 116 2014-11-12 g__Candidatus Microthrix
#> 78: 16SAMP_4603 OTU_8 25 2014-11-12 g__Nitrospira
#> 79: 16SAMP_4603 OTU_9 0 2014-11-12 g__QEDR3BF09
#> 80: 16SAMP_4603 OTU_10 138 2014-11-12 g__MK04
#> SampleID OTU count Date Genus