ggiraph package 0.8.11 compatibility - #27
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ltalignani
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Jul 22, 2026
Adds fieldSelectorModule.R — a reusable moduleServer providing current_group/current_indiv/current_locus reactives, to be consumed by the upcoming Genotype Call (#25/#26) and Criteria Cutoff (#27) tabs. Key decision: selection state is tracked in server-side reactiveVal()s rather than read directly off input$group/input$indiv/input$locus. updateSelectInput() only pushes a value to the browser widget — it never loops back into input$<id> outside a real browser round-trip, so shiny::testServer() can't observe the effect of updateSelectInput() on input$x. Routing all reads/writes through reactiveVal()s makes the "changing group resets individual to first of group" and prev/next navigation logic directly testable, while updateSelectInput() calls remain as a one-way sync to keep the real browser widgets in sync. Files changed: - app/R/fieldSelectorModule.R (new): fieldSelectorUI/fieldSelectorServer - app/app.R: source the new module (not yet wired into the navbar — #25 will add the Genotype Call tab that consumes it) - tests/testthat/test-field-selector-server.R (new): 6 testServer cycles covering population from haplo_data, group-change reset, individual and locus prev/next navigation with clamping, manual dropdown selection, and the no-data state Verification: full R test suite run — 417 pass, 1 pre-existing unrelated failure in test-input-validation.R:118 (BAI path matching, present before this change). Blockers/notes for next iteration: #25 (Genotype Call > AR Refinement) and #26 (Summaries) are unblocked by this and should add a "Genotype Call" nav_panel in app.R wiring fieldSelectorUI/fieldSelectorServer alongside their own sub-tab content. #27 (Criteria Cutoff) is independently unblocked and does not need this module (reads haplo_data directly). Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
ltalignani
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in ltalignani/microhaplot-2
Jul 22, 2026
…ofiling Adds a new "Criteria Cutoff" navbar tab reading haplo_data directly (no blockers). Global sliders (min.depth.homo, min.depth.het, min.ar) drive three plots: read depth histogram with threshold lines, rank-2 allele ratio histogram with threshold line, and an individual x locus coverage heatmap (pass/fail/missing). Key decisions: - Coverage status per individual x locus picks min_depth_het when a rank-2 haplotype was observed for that combo (heterozygote candidate), else min_depth_homo — mirrors how Genotype Call (#25) will classify homozygote vs heterozygote calls. - locus_coverage_status() builds the full id x locus grid via expand.grid so combos absent from haplo_data show up as "missing" rather than being silently dropped, which a plain group_by/summarise would do. - Threshold values are read straight from sliders via input$ (not routed through reactiveVal() like fieldSelectorModule/#24) because shiny::testServer correctly reflects direct input$ writes via session$setInputs() — the updateSelectInput() round-trip problem from #24 only applies to select/updateSelectInput, not sliders. Files changed: - app/R/criteria_cutoff.R (new): default_criteria_params(), total_depth_by_indiv_locus(), rank2_ar_values(), locus_coverage_status() - app/R/criteriaCutoffModule.R (new): criteriaCutoffUI/criteriaCutoffServer — exposes $thresholds and $has_data reactives for downstream consumers - app/app.R: source new files, add "Criteria Cutoff" nav_panel, wire criteriaCutoffServer in the main server function - tests/testthat/test-criteria-cutoff.R (new): 8 tests for the pure aggregation/classification helpers - tests/testthat/test-criteria-cutoff-server.R (new): 4 testServer cycles covering threshold defaults, slider reactivity, and has_data state Verification: full R test suite — 447 pass, 1 pre-existing unrelated failure in test-input-validation.R:118 (BAI path matching, present before this change). Blockers/notes for next iteration: criteria_res$thresholds is returned from criteriaCutoffServer in app.R but not yet consumed by the filtering pipeline or Genotype Call tab, since #25/#26 (Genotype Call) don't exist yet — same "computed but not yet wired downstream" pattern #24 used for fieldSelectorModule. When #25/#26 land, thread criteria_res$thresholds() into their diplotype-calling logic, and consider feeding it into filterAnnotationServer's global params as the new baseline. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
ltalignani
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in ltalignani/microhaplot-2
Jul 22, 2026
Key decisions: - criteriaCutoffModule now receives filter_params (per-locus, from #30) and current_locus (from #29) as reactive args instead of owning its own min_depth_homo/min_depth_het/min_ar sliders — those and the "Save thresholds" button are removed along with the old locus_coverage heatmap. - Two bslib::navset_tab sub-tabs: Global Scope (allReadDepth/allAllelicRatio histograms across all id x locus with a dashed threshold line from the active locus's filter_params row; haplabel/hapReadDepth/hapAllelicRatio per-haplotype views + RDnARplot scatter, all scoped to current_locus) and Quality Profiling (sliderTextInput("rdMin") + Update button drives ambigIndivPlot/ambigLociPlot with an x-brush, and indivProfileTbl DT). - "Ambiguous" id x locus combos are defined as more ranks passing rdMin than the locus's n.alleles cap (from filter_params) — a stand-in for the v1 "> n.alleles qualified haplotypes" semantics, since #30 replaced the old global thresholds with per-locus filter_params. - Located the legacy v1 plot logic (ggiraph/shinyBS-based) in upstream commit 2554654 and used it to understand intent, not ported verbatim — reimplemented with this project's ggplot2/DT/bslib conventions instead. - total_depth_by_indiv_locus() and rank2_ar_values() are kept from #27 and repurposed to feed the new Global Scope histograms; default_criteria_params() and locus_coverage_status() are removed as superseded. Files changed: app/app.R, app/R/criteria_cutoff.R, app/R/criteriaCutoffModule.R, tests/testthat/test-criteria-cutoff.R, tests/testthat/test-criteria-cutoff-server.R, CHANGELOG.md, issues/32-criteria-cutoff-v1-plots.md -> issues/done/ Full suite: 639 PASS, 1 pre-existing FAIL (test-input-validation.R:118, unrelated BAI path matching), 21 WARN (pre-existing Bioc version mismatches). Blockers/notes for next iteration: no open issues remain in issues/ — all AFK tasks (#21-#32) are complete. The brush inputs on ambigIndivPlot/ ambigLociPlot are wired but not yet consumed downstream (no exclusion action); a future issue could wire them to an exclusion reactive if needed. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Hello,
The ggiraph R package changed the names of some function calls and I have updated these in a fork of the microhaplot code to make it compatible with ggiraph v0.8.11. The function
ggiraphOutputis nowgirafeOutputandrenderggiraphis nowrenderGirafe.Thank you for your consideration in adding these updates,
-Steve