Implement UI and madc2vcf updates with GS-Amat support#155
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alex-sandercock wants to merge 10 commits into
Open
Implement UI and madc2vcf updates with GS-Amat support#155alex-sandercock wants to merge 10 commits into
alex-sandercock wants to merge 10 commits into
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updated minor edits
include main updates
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
madc2vcf updates
Merge GS-Amat support to development
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Pull request overview
This PR bumps BIGapp to v1.8.0 and primarily expands the mod_dosage2vcf module with GS-Amat / microhaplotype support (new "Microhaplotypes" marker type, additional species, advanced-options modal, real-time log with download), refreshes UI footer/branding (2026, UF|IFAS), supports both raw and fixed-allele MADC example downloads, and streamlines VCF sanity checks by removing phased_GT from error_if_true across several analysis modules. A handful of small UX/whitespace cleanups and a doc rewrite of the DArT_Report2VCF help round out the change.
Changes:
- Major refactor of
mod_dosage2vcfUI/server (logging, advanced options, microhaplotypes, new species, switch from local example files to GitHub-hosted assets on thelong_seqbranch). - Remove
phased_GTfrom VCFerror_if_truechecks in PCA, GWAS, GSAcc, GS, Filtering, Diversity, DAPC (partially). - Footer/branding updates (UF|IFAS logo, 2026), version bump to 1.8.0, RoxygenNote 7.3.3, max upload size reduced from 1000GB→100GB, README author spelling fix (Tanigut→Taniguti), and substantial expansion of the
DArT_Report2VCF_par.Rmdhelp.
Reviewed changes
Copilot reviewed 13 out of 15 changed files in this pull request and generated 12 comments.
Show a summary per file
| File | Description |
|---|---|
| DESCRIPTION | Version bump to 1.8.0 and RoxygenNote to 7.3.3 |
| README.md | Spelling correction in citation (Taniguti) |
| R/app_server.R | Reduce shiny.maxRequestSize from 1000GB to 100GB |
| R/app_ui.R | Footer year/funding update, add UF |
| R/mod_dosage2vcf.R | Major UI/server overhaul: logging, advanced options, microhaplotypes, new species, GitHub-hosted assets |
| R/mod_dapc.R | Add VCF_compressed to one check block; only one of two blocks had phased_GT removed (other still includes it) |
| R/mod_diversity.R | Remove phased_GT from error_if_true; whitespace cleanup |
| R/mod_Filtering.R | Remove phased_GT from error_if_true; whitespace cleanup |
| R/mod_GS.R | Remove phased_GT from error_if_true; whitespace cleanup |
| R/mod_GSAcc.R | Remove phased_GT; whitespace cleanup |
| R/mod_gwas.R | Remove phased_GT; whitespace cleanup |
| R/mod_PCA.R | Remove phased_GT; whitespace cleanup |
| man/polyRAD2vcf.Rd | Expanded roxygen-generated documentation |
| inst/help_files/DArT_Report2VCF_par.Rmd | Substantially rewritten help with HTML requirement tables |
Files not reviewed (1)
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| error_if_true <- c( | ||
| "multiallelics", "phased_GT", "mixed_ploidies", |
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| } else if(input$snp_type == "multiallelic"){ | ||
| madc2vcf_multi( | ||
| madc_file = read_madc, | ||
| botloci_file = botloci, | ||
| outfile = output_name, | ||
| markers_info = markers_info, | ||
| ploidy = 4L, | ||
| verbose = TRUE | ||
| ) |
| verbose = TRUE) | ||
| } else if(input$snp_type == "target"){ | ||
| madc2vcf_targets(read_madc, output_name, get_REF_ALT = as.logical(input$ref_alt), botloci_file = botloci, | ||
| markers_info = markers_info, collapse_matches_counts = input$collapse_matches_counts) |
| fileInput(ns("hapDB_file"), "Upload haplotype database file (fasta) (optional)"), | ||
| fileInput(ns("markers_info_file"), "Upload markers information (_lut.csv from HapApp) (optional)"), | ||
| ) | ||
| ) |
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| radioButtons(ns("collapse_matches_counts"), | ||
| label = "Collapse Matches Counts:", | ||
| choices = list("Yes"= TRUE, "No" = FALSE), | ||
| selected = FALSE), | ||
| conditionalPanel(condition = "input.species == 'other'", | ||
| ns = ns, | ||
| radioButtons(ns("ref_alt"), | ||
| label = "Extract REF and ALT info:", | ||
| choices = list("Yes"= "TRUE", "No" = "FALSE"), | ||
| selected = "TRUE"), | ||
| choices = list("Yes"= TRUE, "No" = FALSE), | ||
| selected = TRUE), |
| selectInput(ns('species'), | ||
| label = 'Species', | ||
| choices = c("alfalfa","blueberry", "cranberry", "cucumber", "lettuce", "pecan", "sweetpotato", "other"), | ||
| choices = c("alfalfa", "blueberry", "cranberry", "cucumber", "pecan", "potato", "strawberry", "sweetpotato", "other"), |
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| @@ -464,7 +622,7 @@ mod_dosage2vcf_server <- function(input, output, session, parent_session){ | |||
| sep = "" | |||
| ) | |||
| } | |||
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| * **Target vs. Off-Target SNPs** | ||
|
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| ### **Target vs. Off-Target SNPs** vs. **Microhaplotypes** |
| text = "This MADC file has not been processed by the updated Breeding Insight fixed allele ID pipeline.", | ||
| size = "m", | ||
| title = "Missing input!", | ||
| text = "Upload MADC and/or define a output file name", |
| @@ -268,106 +431,101 @@ mod_dosage2vcf_server <- function(input, output, session, parent_session){ | |||
| showCancelButton = FALSE, | |||
| animation = TRUE | |||
| ) | |||
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This pull request introduces several improvements and updates to the BIGapp Shiny application, focusing on enhanced user experience, expanded data format support, improved logging and status reporting, and updated institutional branding. The most significant changes are grouped below:
User Interface and Experience Enhancements:
The
mod_dosage2vcfmodule UI now includes a real-time log display, a "Download Log" button, and a more informative "Status & Log" box for better user feedback during file conversions. The advanced options modal has been added, allowing users to customize conversion parameters. Several input fields have been clarified, new options (such as "Microhaplotypes") and additional species have been added, and layout improvements were made for clarity and usability. [1] [2] [3] [4]The footer in the UI has been updated to reflect the new year ("2026 Breeding Insight") and new funding attribution ("Funded by USDA through UF|IFAS"), and the UF|IFAS logo has been added alongside the Cornell logo. [1] [2]
Data Handling and Format Support:
The file input section for DArT reports now supports "DArT Dosage/SNP Report" (renamed from "DArT Dosage Reports"), and the UI and download handlers have been updated to provide both "Raw" and "Fixed Allele" MADC example files, with the latter downloaded from an external GitHub source. [1] [2]
The marker type selection now supports "Microhaplotypes," and the species selection list has been expanded to include "potato" and "strawberry." Additional optional file inputs are now available for more flexible analysis.
Validation and Error Handling:
error_if_truelists, reducing unnecessary validation failures for phased genotypes. [1] [2] [3] [4] [5] [6]General Updates:
The app version is incremented to 1.8.0, and the
RoxygenNoteis updated to 7.3.3 in theDESCRIPTIONfile. [1] [2]The maximum upload size is reduced from 1000GB to 100GB to better align with practical server resource limits.
Minor Improvements:
These updates collectively improve usability, flexibility, and maintainability of the application.