Use as_tibble() - #28
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ltalignani
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Jul 22, 2026
…d diplotype calling Adds the "Genotype Call" navbar tab with an "AR Refinement" sub-tab: the interactive read-depth x allelic-ratio biplot for visually setting homozygote/heterozygote thresholds per locus, restoring the central analysis view from v1. Key decisions: - classify_call() treats a missing rank-2 haplotype (NA ar) as homozygote unconditionally, since an individual with only a rank-1 call has no second allele to compare against the AR thresholds. - Per-locus thresholds are stored in a moduleServer-local reactiveValues() keyed by locus name (not a data.frame table) — lookup by locus is a single indexed access, and reactiveValuesToList() gives the same "one row per locus" shape the issue asked for when inspected. - Slider lower bound is refreshed via updateSliderInput(min = ...) on every locus change, driven by min_observed_ar() for that locus, per the issue's "slider bounds constrained by minimum observed AR" requirement. - ggiraph was a declared but previously unused Imports entry (from DESCRIPTION) and was not installed in the local dev environment; installed it locally to get real (non-skipped) test coverage of genotypeCallModule.R rather than relying on testthat's silent skip-if-missing behavior. - fieldSelectorServer (#24) is instantiated once for the Genotype Call tab (id "genotype_call_fields") and its $current_locus is threaded into genotypeCallServer — the same instance will drive the Summaries sub-tab (#26) once it exists, so both sub-tabs stay in sync on locus navigation. Files changed: - app/R/genotype_call.R (new): default_ar_params(), classify_call(), locus_biplot_data(), pie_call_counts(), haplotype_distributions(), min_observed_ar() - app/R/genotypeCallModule.R (new): genotypeCallUI/genotypeCallServer — pie chart, ggiraph biplot, DT calls table, per-haplotype depth/AR boxplots, per-locus threshold persistence - app/app.R: source new files, add "Genotype Call" nav_panel (field selector + AR Refinement navset_tab), wire fieldSelectorServer + genotypeCallServer in the main server function - tests/testthat/test-genotype-call.R (new): 31 tests for the pure classification/aggregation helpers - tests/testthat/test-genotype-call-server.R (new): 7 testServer cycles covering default thresholds, save/persist across locus navigation, biplot_data reactivity, and has_data state Verification: full R test suite — 485 pass, 1 pre-existing unrelated failure in test-input-validation.R:118 (BAI path matching, present before this change). Confirmed app.R sources and builds ui/server without error. Blockers/notes for next iteration: #26 (Genotype Call > Summaries) should reuse the same fieldSelectorServer("genotype_call_fields") instance already wired in app.R and add its nav_panel inside the existing navset_tab alongside "AR Refinement". #28's "Genotype call table" view depends on genotypeCallServer's $biplot_data (or a per-locus aggregate built from $saved_thresholds across all loci) — that reactive is only computed for the currently active locus today, so #28 will need to iterate saved_thresholds across all loci to build a full genotype-call table. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
ltalignani
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in ltalignani/microhaplot-2
Jul 22, 2026
… pairwise, by-group, sequence alignment
Adds the "Summaries" sub-tab alongside AR Refinement in the Genotype Call
navbar tab, sharing the existing fieldSelectorServer("genotype_call_fields")
instance and current_locus reactive from #24/#25.
Key decisions:
- Diploid allele counting (haplotype_frequencies / haplotype_frequencies_by_group
in genotype_summaries.R) follows hwe_entropy.R's existing convention: a
homozygous individual (rank-1 only) contributes two copies of its allele,
a heterozygous individual one copy each of rank-1/rank-2 — kept consistent
rather than inventing a second counting rule.
- HWE pairwise plot reuses haplo_freq_tbl() (hwe_entropy.R) via a thin
locus_hwe_pairs() wrapper instead of recomputing observed/expected
diplotype frequencies — that logic already existed and is tested.
- Haplotype frequency plot uses ggiraph (already a project dependency from
#25's biplot) with opts_selection(type = "single") for bar-click
highlighting; input$hapFreq_selected is exposed via a plain reactive
(selected_haplo) that filters the sequence alignment display, mirroring
how #25 wired ggiraph interactivity.
- Haplotype sequence alignment is long-format (haplo x position x base) from
strsplit() on each unique haplotype string, rendered as geom_tile() —
works for any haplotype length without hardcoding SNP count.
Files changed:
- app/R/genotype_summaries.R (new): haplotype_frequencies(),
haplotype_frequencies_by_group(), locus_hwe_pairs(), haplotype_sequences()
- app/R/genotypeSummariesModule.R (new): genotypeSummariesUI/Server —
hapFreq ggiraph bar chart, PairWiseHap scatter, hapByGroupPlot, hapSeq tile
display
- app/app.R: source new files, add "Summaries" nav_panel inside the
Genotype Call navset_tab, wire genotypeSummariesServer with the shared
field selector and result$color_map
- tests/testthat/test-genotype-summaries.R (new): 23 assertions for the
pure aggregation helpers
- tests/testthat/test-genotype-summaries-server.R (new): 9 testServer
cycles covering has_data, hap_freq/hwe_pairs/hap_freq_by_group/hap_seq
reactivity, and ggiraph selection wiring
- CHANGELOG.md: document the new sub-tab
Verification: full R test suite — 517 pass, 1 pre-existing unrelated
failure in test-input-validation.R:118 (BAI path matching, present before
this change). Confirmed app.R sources and builds ui/server without error.
Blockers/notes for next iteration: #28 (Table view types + About tab) is
unblocked — its "Genotype call table" view needs to iterate
genotypeCallServer's saved_thresholds across all loci (not just the active
one) to build a full per-individual-per-locus call table, as noted when
#25 shipped.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
ltalignani
referenced
this pull request
in ltalignani/microhaplot-2
Jul 22, 2026
…ummary, session info Adds a radioButtons selector to the Download/Table tab for three views (Haplotype / Summary / Genotype call) and a new About tab as the last navbar item, closing the final open issue in the v1 feature-restoration backlog. Key decisions: - genotype_call_table() (genotype_call.R) iterates every locus in haplo_data, applying saved_thresholds[[locus]] where present and default_ar_params() otherwise, reusing locus_biplot_data()/classify_call() rather than reimplementing diplotype logic. Table columns are id, locus, h1, h2, depth, ar, status, max_ar_hm, min_ar_hz. - summary_table_wide() (output_utils.R) is a straight pivot_wider() on (id, locus) x haplo -> depth across the whole dataset — matches microhaplot::tableIndLocus() semantics without hardcoding haplotype columns per locus. - Dropped outputServer()'s filtered_data argument: the old "filtered diploid" view is subsumed by the genotype call table (same diploid pairing plus AR-based call status), so app.R now threads genotypeCallServer's saved_thresholds reactive into outputServer instead. app.R previously discarded genotypeCallServer's return value entirely — now captured as genotype_call_res. - Genotype call view is gated behind an info message until at least one locus's thresholds have been saved (acceptance criteria requirement), rather than silently falling back to defaults for every locus. - Internal reactives not part of a module's public return (current_table, has_thresholds) are tested by calling them directly inside shiny::testServer(), following the existing pattern in test-pop-genetics-server.R rather than session$returned$. - app_metadata() reads name/version/license/url from DESCRIPTION via read.dcf() rather than hardcoding, so the About tab stays in sync with package metadata. Files changed: - app/R/output_utils.R: add summary_table_wide() - app/R/genotype_call.R: add genotype_call_table() - app/R/outputModule.R: rewritten — radioButtons view selector, single download button/preview, field selector only for the haplotype view - app/R/aboutModule.R (new): app_metadata(), aboutUI/aboutServer — metadata card, citation, license, GitHub link, collapsible sessionInfo() - app/app.R: source aboutModule.R, add "About" nav_panel as last item, capture genotypeCallServer's return as genotype_call_res and thread saved_thresholds into outputServer, wire aboutServer - tests/testthat/test-output-utils.R: 4 new tests for summary_table_wide() - tests/testthat/test-genotype-call.R: 5 new tests for genotype_call_table() - tests/testthat/test-output-server.R (new): 10 testServer cycles covering view switching, field selection, and threshold gating - tests/testthat/test-about.R (new): app_metadata() assertions - CHANGELOG.md: document the new views and About tab - issues/28-table-types-about-tab.md moved to issues/done/ Verification: full R test suite — 547 pass, 1 pre-existing unrelated failure in test-input-validation.R:118 (BAI path matching, present before this change). Confirmed app.R sources and builds ui/server without error. Blockers/notes for next iteration: none — this was the last open issue in the backlog (issues/ is now empty except issues/done/). Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Hi there, we are working on the next version of dplyr and your package was flagged in our reverse dependency checks.
We've advanced our deprecation of
dplyr::as.tbl()anddplyr::tbl_df(), both of which have been deprecated since dplyr 1.0.0 in 2020.You'll need to update your package to use
tibble::as_tibble()instead to stay on CRAN.dplyr will be released on January 31, 2026. If you could please send an update of your package to CRAN before then, that would help us out a lot! Thanks!