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update snapshots
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@jeffkimbrel
jeffkimbrel committed Oct 24, 2024
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176 changes: 8 additions & 168 deletions tests/testthat/_snaps/qsip_data.md
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Original file line number Diff line number Diff line change
Expand Up @@ -6,172 +6,12 @@
There are 15 source_mat_ids, and they are all shared between the source and sample objects
There are 284 sample_ids, and they are all shared between the sample and feature objects
Output
<qsip_data>
@ source_data : <qsip_source_data>
.. @ data : tibble [15 x 6] (S3: tbl_df/tbl/data.frame)
$ isotope : chr [1:15] "12C" "12C" "12C" "12C" ...
$ isotopolog : chr [1:15] "glucose" "glucose" "glucose" "glucose" ...
$ source_mat_id : chr [1:15] "S149" "S150" "S151" "S152" ...
$ total_copies_per_g: num [1:15] 34838665 53528072 95774992 9126192 41744046 ...
$ total_dna : num [1:15] 74.5 109 182.2 23.7 67.6 ...
$ Moisture : chr [1:15] "Normal" "Normal" "Normal" "Normal" ...
.. @ isotope : chr "Isotope"
.. @ isotopolog : chr "isotopolog"
.. @ source_mat_id : chr "source"
.. @ time : chr "NULL"
.. @ total_abundance: chr "NULL"
@ sample_data : <qsip_sample_data>
.. @ data : tibble [284 x 7] (S3: tbl_df/tbl/data.frame)
$ sample_id : chr [1:284] "149_F1" "149_F2" "149_F3" "149_F4" ...
$ source_mat_id : chr [1:284] "S149" "S149" "S149" "S149" ...
$ gradient_position : int [1:284] 1 2 3 4 5 6 7 8 9 10 ...
$ gradient_pos_density: num [1:284] 1.78 1.77 1.77 1.76 1.75 ...
$ gradient_pos_amt : num [1:284] 4474 987 4003 3960 5726 ...
$ gradient_pos_rel_amt: num [1:284] 1.28e-04 2.83e-05 1.15e-04 1.14e-04 1.64e-04 ...
$ dna_conc : num [1:284] 0 0 0 0 0.00124 ...
.. @ sample_id : chr "sample"
.. @ source_mat_id : chr "source"
.. @ gradient_position : chr "Fraction"
.. @ gradient_pos_density: chr "density_g_ml"
.. @ gradient_pos_amt : chr "avg_16S_g_soil"
.. @ gradient_pos_rel_amt: chr "gradient_pos_rel_amt"
@ feature_data : <qsip_feature_data>
.. @ data : tibble [2,030 x 285] (S3: tbl_df/tbl/data.frame)
$ feature_id: chr [1:2030] "ASV_1" "ASV_2" "ASV_3" "ASV_4" ...
$ 149_F1 : num [1:2030] 1245 1471 342 288 317 ...
$ 149_F2 : num [1:2030] 376 569 152 119 108 73 82 47 74 58 ...
$ 149_F3 : num [1:2030] 582 830 211 161 95 130 102 52 89 73 ...
$ 149_F4 : num [1:2030] 1258 1373 389 294 292 ...
$ 149_F5 : num [1:2030] 692 737 218 157 164 112 136 90 83 64 ...
$ 149_F6 : num [1:2030] 1482 1777 461 381 310 ...
$ 149_F7 : num [1:2030] 812 2086 304 242 216 ...
$ 149_F8 : num [1:2030] 743 2603 293 219 188 ...
$ 149_F9 : num [1:2030] 285 3375 134 135 83 ...
$ 149_F10 : num [1:2030] 47 1145 30 27 27 ...
$ 149_F11 : num [1:2030] 265 2236 187 147 80 ...
$ 149_F12 : num [1:2030] 434 982 221 215 110 85 86 79 171 94 ...
$ 149_F13 : num [1:2030] 773 436 446 378 303 141 34 26 153 72 ...
$ 149_F14 : num [1:2030] 4695 829 1702 1520 1237 ...
$ 149_F15 : num [1:2030] 3967 918 1065 844 795 ...
$ 149_F16 : num [1:2030] 2295 1077 721 561 549 ...
$ 149_F17 : num [1:2030] 1411 974 536 498 413 ...
$ 149_F18 : num [1:2030] 780 584 335 223 244 121 36 34 93 56 ...
$ 149_F19 : num [1:2030] 2000 1626 836 734 646 ...
$ 150_F1 : num [1:2030] 197 2006 111 81 79 ...
$ 150_F2 : num [1:2030] 131 1445 76 85 53 ...
$ 150_F3 : num [1:2030] 177 1854 113 110 71 ...
$ 150_F4 : num [1:2030] 384 1844 163 118 105 ...
$ 150_F5 : num [1:2030] 543 5403 340 327 211 ...
$ 150_F6 : num [1:2030] 591 5568 343 344 261 ...
$ 150_F7 : num [1:2030] 472 5450 345 291 205 97 143 159 222 158 ...
$ 150_F8 : num [1:2030] 536 6331 384 332 236 ...
$ 150_F9 : num [1:2030] 330 4722 277 227 151 ...
$ 150_F10 : num [1:2030] 409 5425 317 295 184 ...
$ 150_F11 : num [1:2030] 313 3498 248 202 137 ...
$ 150_F12 : num [1:2030] 229 1762 149 148 84 ...
$ 150_F13 : num [1:2030] 616 2329 460 397 249 ...
$ 150_F14 : num [1:2030] 1339 2197 715 728 406 ...
$ 150_F15 : num [1:2030] 1986 1647 787 724 541 ...
$ 150_F16 : num [1:2030] 2581 1996 1003 897 661 ...
$ 150_F17 : num [1:2030] 1869 1970 757 679 468 ...
$ 150_F18 : num [1:2030] 1069 1384 494 436 304 ...
$ 150_F19 : num [1:2030] 1627 2266 706 595 486 ...
$ 151_F1 : num [1:2030] 392 1920 104 94 103 0 70 59 81 89 ...
$ 151_F2 : num [1:2030] 300 1581 121 76 95 ...
$ 151_F3 : num [1:2030] 140 1539 64 44 26 ...
$ 151_F4 : num [1:2030] 250 1681 92 92 62 ...
$ 151_F5 : num [1:2030] 232 1953 113 107 99 ...
$ 151_F6 : num [1:2030] 220 1612 85 86 95 ...
$ 151_F7 : num [1:2030] 292 3057 89 108 93 ...
$ 151_F8 : num [1:2030] 256 4118 117 120 86 ...
$ 151_F9 : num [1:2030] 179 3199 67 59 56 ...
$ 151_F10 : num [1:2030] 142 3265 75 51 53 ...
$ 151_F11 : num [1:2030] 56 1393 0 42 30 ...
$ 151_F12 : num [1:2030] 102 1280 65 53 38 0 48 44 94 53 ...
$ 151_F13 : num [1:2030] 462 1588 290 258 172 ...
$ 151_F14 : num [1:2030] 1462 1001 618 511 401 ...
$ 151_F15 : num [1:2030] 2670 819 636 594 699 390 26 26 136 80 ...
$ 151_F16 : num [1:2030] 3248 1404 747 576 498 ...
$ 151_F17 : num [1:2030] 1070 736 292 201 258 165 22 34 77 49 ...
$ 151_F18 : num [1:2030] 1154 1249 361 325 335 ...
$ 151_F19 : num [1:2030] 846 1084 288 222 237 ...
$ 152_F1 : num [1:2030] 505 259 78 67 92 73 40 27 57 49 ...
$ 152_F2 : num [1:2030] 1258 1063 248 232 381 ...
$ 152_F3 : num [1:2030] 1964 1848 437 388 379 ...
$ 152_F4 : num [1:2030] 2236 2235 439 424 494 ...
$ 152_F5 : num [1:2030] 2223 3934 525 467 561 ...
$ 152_F6 : num [1:2030] 2921 4021 691 494 814 ...
$ 152_F7 : num [1:2030] 1187 1133 182 203 270 ...
$ 152_F8 : num [1:2030] 1236 1993 191 267 336 ...
$ 152_F9 : num [1:2030] 507 1611 92 107 114 ...
$ 152_F10 : num [1:2030] 345 4983 112 90 127 ...
$ 152_F11 : num [1:2030] 248 5557 111 76 83 ...
$ 152_F12 : num [1:2030] 330 5867 158 120 152 ...
$ 152_F13 : num [1:2030] 1083 5397 427 384 498 ...
$ 152_F14 : num [1:2030] 7262 6213 1988 1983 2577 ...
$ 152_F15 : num [1:2030] 11167 2384 1984 1833 3347 ...
$ 152_F16 : num [1:2030] 7663 1320 1036 893 2256 ...
$ 152_F17 : num [1:2030] 3701 844 495 397 1022 ...
$ 152_F18 : num [1:2030] 2590 2182 489 429 792 ...
$ 152_F19 : num [1:2030] 3171 3549 658 574 969 ...
$ 161_F1 : num [1:2030] 752 887 208 175 135 132 168 74 81 57 ...
$ 161_F2 : num [1:2030] 458 469 106 122 132 118 93 45 45 51 ...
$ 161_F3 : num [1:2030] 1530 1710 447 330 297 210 277 147 125 127 ...
$ 161_F4 : num [1:2030] 1790 1348 678 762 835 ...
$ 161_F5 : num [1:2030] 1262 1607 309 245 319 ...
$ 161_F6 : num [1:2030] 1056 1237 254 266 258 ...
$ 161_F7 : num [1:2030] 306 618 92 82 82 66 96 34 62 44 ...
$ 161_F8 : num [1:2030] 586 622 181 144 144 90 76 62 101 42 ...
$ 161_F9 : num [1:2030] 497 2950 159 128 93 87 329 200 88 84 ...
$ 161_F10 : num [1:2030] 260 2219 105 102 78 ...
$ 161_F11 : num [1:2030] 316 4221 166 168 136 ...
$ 161_F12 : num [1:2030] 628 3171 382 363 252 ...
$ 161_F13 : num [1:2030] 2514 2370 1206 1179 710 ...
$ 161_F14 : num [1:2030] 4013 1308 1252 1162 992 ...
$ 161_F15 : num [1:2030] 2254 593 594 473 455 ...
$ 161_F16 : num [1:2030] 4370 1733 896 827 920 ...
$ 161_F17 : num [1:2030] 1025 886 268 240 228 ...
$ 161_F18 : num [1:2030] 1855 1789 499 503 524 ...
$ 161_F19 : num [1:2030] 2467 3394 754 622 629 ...
$ 162_F1 : num [1:2030] 272 1115 137 126 92 ...
$ 162_F2 : num [1:2030] 214 355 64 86 85 44 578 160 82 32 ...
$ 162_F3 : num [1:2030] 529 920 239 217 216 ...
[list output truncated]
.. @ feature_id: chr "ASV"
.. @ taxonomy :'data.frame': 0 obs. of 0 variables
.. @ type : chr "counts"
@ shared :List of 2
.. $ source_mat_ids:List of 3
.. ..$ shared : chr [1:15] "S149" "S150" "S151" "S152" ...
.. ..$ source_data: NULL
.. ..$ sample_data: NULL
.. $ sample_ids :List of 3
.. ..$ shared : chr [1:284] "149_F1" "149_F2" "149_F3" "149_F4" ...
.. ..$ sample_data : NULL
.. ..$ feature_data: NULL
@ tube_rel_abundance : tibble [39,183 x 6] (S3: tbl_df/tbl/data.frame)
$ feature_id : chr [1:39183] "ASV_1" "ASV_1" "ASV_1" "ASV_1" ...
$ sample_id : chr [1:39183] "149_F1" "149_F2" "149_F3" "149_F4" ...
$ source_mat_id : chr [1:39183] "S149" "S149" "S149" "S149" ...
$ tube_rel_abundance : num [1:39183] 1.80e-05 4.11e-06 1.60e-05 1.67e-05 2.82e-05 ...
$ gradient_pos_density: num [1:39183] 1.78 1.77 1.77 1.76 1.75 ...
$ gradient_pos_rel_amt: num [1:39183] 1.28e-04 2.83e-05 1.15e-04 1.14e-04 1.64e-04 ...
@ wads : tibble [9,282 x 4] (S3: tbl_df/tbl/data.frame)
$ feature_id : chr [1:9282] "ASV_1000" "ASV_1001" "ASV_1001" "ASV_1001" ...
$ source_mat_id: chr [1:9282] "S203" "S149" "S164" "S179" ...
$ WAD : num [1:9282] 1.71 1.75 1.76 1.69 1.73 ...
$ n_fractions : int [1:9282] 1 1 1 1 1 1 1 1 1 1 ...
@ source_wads : tibble [15 x 2] (S3: tbl_df/tbl/data.frame)
$ source_mat_id: chr [1:15] "S149" "S150" "S151" "S152" ...
$ WAD : num [1:15] 1.71 1.71 1.71 1.71 1.71 ...
@ fraction_counts : tibble [30,450 x 3] (S3: tbl_df/tbl/data.frame)
$ feature_id : chr [1:30450] "ASV_1" "ASV_1" "ASV_1" "ASV_1" ...
$ source_mat_id: chr [1:30450] "S203" "S149" "S164" "S179" ...
$ n_fractions : int [1:30450] 19 19 19 16 19 19 18 19 15 19 ...
@ filtered_feature_data:'data.frame': 0 obs. of 0 variables
@ filtered_wad_data :'data.frame': 0 obs. of 0 variables
@ filter_results : list()
@ resamples : list()
@ EAF :'data.frame': 0 obs. of 0 variables
@ growth : list()
<qSIP2::qsip_data>
group: none
feature_id count: 2030 of 2030
sample_id count: 284
filtered: FALSE
resampled: FALSE
EAF: FALSE
growth: FALSE

36 changes: 6 additions & 30 deletions tests/testthat/_snaps/qsip_sample_data.md
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Expand Up @@ -5,21 +5,9 @@
gradient_position = "Fraction", gradient_pos_density = "density_g_ml",
gradient_pos_amt = "avg_16S_g_soil", gradient_pos_rel_amt = "gradient_pos_rel_amt")
Output
<qsip_sample_data>
@ data : tibble [284 x 7] (S3: tbl_df/tbl/data.frame)
$ sample_id : chr [1:284] "149_F1" "149_F2" "149_F3" "149_F4" ...
$ source_mat_id : chr [1:284] "S149" "S149" "S149" "S149" ...
$ gradient_position : int [1:284] 1 2 3 4 5 6 7 8 9 10 ...
$ gradient_pos_density: num [1:284] 1.78 1.77 1.77 1.76 1.75 ...
$ gradient_pos_amt : num [1:284] 4474 987 4003 3960 5726 ...
$ gradient_pos_rel_amt: num [1:284] 1.28e-04 2.83e-05 1.15e-04 1.14e-04 1.64e-04 ...
$ dna_conc : num [1:284] 0 0 0 0 0.00124 ...
@ sample_id : chr "sample"
@ source_mat_id : chr "source"
@ gradient_position : chr "Fraction"
@ gradient_pos_density: chr "density_g_ml"
@ gradient_pos_amt : chr "avg_16S_g_soil"
@ gradient_pos_rel_amt: chr "gradient_pos_rel_amt"
<qSIP2::qsip_sample_data>
source_material_id count: 15
sample_id count: 284

# no gradient_pos_rel_amt given will autocalculate

Expand All @@ -30,19 +18,7 @@
Message
<gradient_pos_rel_amt> not specified. Calculating using avg_16S_g_soil column
Output
<qsip_sample_data>
@ data : tibble [284 x 7] (S3: tbl_df/tbl/data.frame)
$ sample_id : chr [1:284] "149_F1" "149_F2" "149_F3" "149_F4" ...
$ source_mat_id : chr [1:284] "S149" "S149" "S149" "S149" ...
$ gradient_position : int [1:284] 1 2 3 4 5 6 7 8 9 10 ...
$ gradient_pos_density: num [1:284] 1.78 1.77 1.77 1.76 1.75 ...
$ gradient_pos_amt : num [1:284] 4474 987 4003 3960 5726 ...
$ gradient_pos_rel_amt: num [1:284] 1.28e-04 2.83e-05 1.15e-04 1.14e-04 1.64e-04 ...
$ dna_conc : num [1:284] 0 0 0 0 0.00124 ...
@ sample_id : chr "sample"
@ source_mat_id : chr "source"
@ gradient_position : chr "Fraction"
@ gradient_pos_density: chr "density_g_ml"
@ gradient_pos_amt : chr "avg_16S_g_soil"
@ gradient_pos_rel_amt: chr "gradient_pos_rel_amt"
<qSIP2::qsip_sample_data>
source_material_id count: 15
sample_id count: 284

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