Scenario gallery: committed witness census, provenance-stamped
Source:vignettes/scenarios-gallery.Rmd
scenarios-gallery.Rmdmsuiter’s application-scenario drivers
(bench/scenarios/run_atlas.R, run_hrd.R,
run_treatment.R) persist their evidence tables under
bench/scenarios/out/. This page galleries every committed
witness there: one card per file, each carrying an in-process sha256
provenance stamp, a row/column census and a verbatim excerpt of the
leading data rows. No number on this page is hand-typed:
tools/scenarios-gallery.R re-derives every digit from the
committed bytes at build time, and the testthat law
tests/testthat/test-scenarios-gallery.R audits that every
card names its witness and that every stamp and census matches the disk
bytes – a tampered witness, a dropped card or an empty witness tree
reddens the lane.
witnesses=12 rows-total=344 columns-total=124
association.csv
sha256
d267e597d9fbdad6ec1ebce64595c06b188bc91d58db847cdbc814a6caeb56c7
rows=14 cols=7
| signature | median_group1 | median_group2 | statistic | p_raw | p_bh | pass_bh |
|---|---|---|---|---|---|---|
| SBS1 | 234.185314628885 | 234.192676003428 | 68 | 0.817361331385177 | 0.862490230135922 | FALSE |
| SBS5 | 504.758112723486 | 177.797647504167 | 144 | 3.22564145624377e-05 | 0.000193538487374626 | TRUE |
| SBS22a | 233.101945076628 | 234.520364323503 | 75 | 0.862490230135922 | 0.862490230135922 | FALSE |
| SBS2 | 0 | 0 | 90 | 0.0706255684331111 | 0.141251136866222 | FALSE |
| SBS13 | 0 | 0 | 90 | 0.0706255684331111 | 0.141251136866222 | FALSE |
compare_sweep.csv
sha256
366ad13d8acaf29fb338f02af36de53442a4af9f2592be771f8ff14cf5efa5bf
rows=4 cols=9
| tau | tp | fp | fn | precision | recall | f1 | split | merge |
|---|---|---|---|---|---|---|---|---|
| 0.7 | 5 | 0 | 0 | 1 | 1 | 1 | 0 | 0 |
| 0.8 | 5 | 0 | 0 | 1 | 1 | 1 | 0 | 0 |
| 0.9 | 3 | 2 | 2 | 0.6 | 0.6 | 0.6 | 0 | 0 |
counts_dbs.csv
sha256
a2faa938d8733f0b11b622b063555a64b3e2bd86d6abbfb204d0a0716f5d46a9
rows=79 cols=25
| A01 | A02 | A03 | A04 | A05 | A06 | A07 | A08 | A09 | A10 | A11 | A12 | A13 | A14 | A15 | A16 | A17 | A18 | A19 | A20 | A21 | A22 | A23 | A24 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| AC>CA | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| AC>CG | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| AC>CT | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| AC>GA | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| AC>GG | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
counts_sbs.csv
sha256
28784938c3708dfadbffe88e2c1850b0a3c365fc235b4c9bf508c2acb5d9fdaf
rows=97 cols=25
| A01 | A02 | A03 | A04 | A05 | A06 | A07 | A08 | A09 | A10 | A11 | A12 | A13 | A14 | A15 | A16 | A17 | A18 | A19 | A20 | A21 | A22 | A23 | A24 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| A[C>A]A | 9 | 9 | 8 | 10 | 8 | 10 | 6 | 9 | 7 | 8 | 10 | 7 | 4 | 4 | 5 | 4 | 5 | 4 | 4 | 4 | 5 | 4 | 5 | 4 |
| A[C>A]C | 6 | 6 | 5 | 7 | 6 | 6 | 5 | 7 | 5 | 6 | 7 | 4 | 3 | 2 | 3 | 3 | 3 | 2 | 3 | 3 | 3 | 3 | 3 | 2 |
| A[C>A]G | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| A[C>A]T | 5 | 5 | 4 | 5 | 4 | 5 | 4 | 5 | 4 | 4 | 5 | 4 | 2 | 2 | 3 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 3 | 2 |
| A[C>G]A | 7 | 7 | 6 | 9 | 7 | 8 | 5 | 7 | 6 | 6 | 8 | 5 | 3 | 3 | 4 | 3 | 4 | 3 | 3 | 3 | 3 | 3 | 4 | 3 |
hrd_report.csv
sha256
32c321b79a1477e9c5e8b7e20912039fc4d5614756c49d44b9173ebfffb2672a
rows=5 cols=11
| sample | genome | caller | assay | ploh_fraction | aneuploidy_count | hrd_score | evidence_tier | n_windows_scored | coverage_note | ploidy_source |
|---|---|---|---|---|---|---|---|---|---|---|
| H1 | GRCh37 | ascat | wgs | 5 | 5 | 1 | standard | 10 | ploidy-source=caller; denominator=injected; aneuploidy=scored | caller |
| H2 | GRCh37 | ascat | wgs | 0.45 | 0 | 0 | standard | 1 | ploidy-source=caller; denominator=injected; aneuploidy=scored | caller |
| H3 | GRCh37 | ascat | wgs | 0 | 5 | 0 | standard | 10 | ploidy-source=caller; denominator=injected; aneuploidy=scored | caller |
| H4 | GRCh37 | ascat | wgs | 0 | 0 | 0 | standard | 2 | ploidy-source=caller; denominator=injected; aneuploidy=scored | caller |
pbr.csv
sha256
d701579f06ad5771d9756f712e7daa0f449c6b2d60027060370cab4ef868e84a
rows=25 cols=3
| sample | pbr | n |
|---|---|---|
| A01 | 0.975819635464902 | 1403.57900863254 |
| A02 | 0.987404204601453 | 1237.44644722619 |
| A03 | 0.970445237158261 | 1229.19637393672 |
| A04 | 0.988225150597043 | 1463.86027319685 |
| A05 | 0.972262150890656 | 1178.10169856176 |
presence.csv
sha256
82bf4b337c5aa1c5a1e794b3682b4ffddf5091f186903ceba64770ac94df3a38
rows=6 cols=5
| signature | stat | p_raw | p_bh | pass_bh |
|---|---|---|---|---|
| SBS1 | 6436.76300302252 | 0 | 0 | TRUE |
| SBS5 | 9617.87413670036 | 0 | 0 | TRUE |
| SBS22a | 6830.71169289432 | 0 | 0 | TRUE |
| SBS2 | 473.643168324866 | 2.68867700987004e-90 | 2.68867700987004e-90 | TRUE |
| SBS13 | 733.320572037617 | 5.98642586200459e-145 | 7.48303232750574e-145 | TRUE |
prevalence.csv
sha256
6480fc04ebdbd2ecfd1af3c5fdc1924f6957cb29c0175312060b44414a5d0452
rows=14 cols=2
| prevalence | |
|---|---|
| SBS1 | 1 |
| SBS5 | 1 |
| SBS22a | 1 |
| SBS2 | 0.125 |
| SBS13 | 0.125 |
qc_report.csv
sha256
3b0a46a8f74bd1fcd3fa84d9e362e109753ca7c2cffe1048ed6025531c07ada9
rows=25 cols=10
| sample | total | log10_total | burden_class | gt_share | ct_share | strand_bias_p | artifact_share | artifact_sigs | qc_flag |
|---|---|---|---|---|---|---|---|---|---|
| A01 | 1406 | 3.1479853206838 | standard | 0.0526315789473684 | 0.537695590327169 | NA | NA | NA | watch |
| A02 | 1239 | 3.09307130637606 | standard | 0.0613397901533495 | 0.506860371267151 | NA | NA | NA | watch |
| A03 | 1232 | 3.09061070782841 | standard | 0.0503246753246753 | 0.511363636363636 | NA | NA | NA | watch |
| A04 | 1467 | 3.16643011384328 | standard | 0.0920245398773006 | 0.328561690524881 | NA | NA | NA | ok |
| A05 | 1179 | 3.07151380509509 | standard | 0.0949957591178965 | 0.272264631043257 | NA | NA | NA | ok |
synth-cn.tsv
sha256
b8513d8f2490db141993ccd191df3111554519efe1d9508241d90d103ecc037d
rows=49 cols=6
| chromosome | chromosome_start | chromosome_end | copy_number | mutation_type | sample |
|---|---|---|---|---|---|
| chr1 | 1 | 1023 | 1 | loss | A01 |
| chr1 | 1024 | 2048 | 3 | gain | A01 |
| chr1 | 1 | 1023 | 1 | loss | A02 |
| chr1 | 1024 | 2048 | 3 | gain | A02 |
| chr1 | 1 | 1023 | 1 | loss | A03 |
treatment_association.csv
sha256
aac8e83be72453a2ae4a75ba5f1073a7b5d3890e99a4202f8f1859613b2cd873
rows=13 cols=12
| treatment | signature | n_exposed | n_unexposed | prevalence_exposed | prevalence_unexposed | mean_exposed | mean_unexposed | contrast | contrast_lower | contrast_upper | is_associated |
|---|---|---|---|---|---|---|---|---|---|---|---|
| temozolomide | SBS11 | 4 | 5 | 1 | 1 | 559.03583215219 | 18.9325414508716 | 540.103290701319 | 488.832976255401 | 582.719269257673 | TRUE |
| temozolomide | SBS31 | 4 | 5 | 1 | 1 | 51.0858403212427 | 16.2127430064597 | 34.873097314783 | 5.40424907559841 | 74.4800714533771 | FALSE |
| temozolomide | SBS32 | 4 | 5 | 1 | 1 | 47.2511888545141 | 23.2459609319126 | 24.0052279226015 | -9.8676787698153 | 65.777400136769 | FALSE |
| temozolomide | SBS35 | 4 | 5 | 0.5 | 1 | 5.69198425743698 | 22.6087546107561 | -16.9167703533191 | -26.0064203969415 | -0.290449991053495 | FALSE |
| platinum | SBS11 | 4 | 5 | 0.5 | 1 | 13.0486976007475 | 18.9325414508716 | -5.88384385012411 | -21.0632735917649 | 15.4390070294653 | FALSE |
treatment_timing.csv
sha256
2d2e7c40ee9eb5b471fb0b22ec0c68713098082b80de825f27d790c10e96d1ec
rows=13 cols=9
| treatment | signature | n_exposed | exposure_pre | exposure_post | pre_lower | pre_upper | post_lower | post_upper |
|---|---|---|---|---|---|---|---|---|
| temozolomide | SBS11 | 4 | 279.517916076095 | 279.517916076095 | 253.971959676777 | 299.130457563726 | 253.971959676777 | 299.130457563726 |
| temozolomide | SBS31 | 4 | 25.5429201606214 | 25.5429201606214 | 11.5960761437721 | 46.1651053487118 | 11.5960761437721 | 46.1651053487118 |
| temozolomide | SBS32 | 4 | 23.625594427257 | 23.625594427257 | 7.13674719059398 | 42.5306620436252 | 7.13674719059398 | 42.5306620436252 |
| temozolomide | SBS35 | 4 | 2.84599212871849 | 2.84599212871849 | 0 | 10.175153131152 | 0 | 10.175153131152 |
| platinum | SBS11 | 4 | 6.52434880037375 | 6.52434880037375 | 0 | 15.8797897515838 | 0 | 15.8797897515838 |
Every stamp above is recomputed from the file bytes the moment this
page builds; to re-derive the census yourself, run
Rscript tools/scenarios-gallery.R --out=<dir> from
the repository root and diff its manifest.tsv against what
you see here.