Development#16
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Pull request overview
This PR updates the Breedverse Shiny app to integrate the VIEWpoly module (install UI + server wiring), expands in-app help content (including GenoBrew and VIEWpoly materials), and refreshes UI styling/JS behavior alongside a version bump to 0.4.0.
Changes:
- Add VIEWpoly installation card + installer logic and wire VIEWpoly modules into the app UI/server.
- Expand Help Documentation UI to include GenoBrew and VIEWpoly help materials (conditional on module availability).
- Update custom JS/CSS and bump package metadata/version (DESCRIPTION, NEWS, NAMESPACE).
Reviewed changes
Copilot reviewed 9 out of 11 changed files in this pull request and generated 6 comments.
Show a summary per file
| File | Description |
|---|---|
| R/mod_install.R | Adds VIEWpoly install card + install handler; updates GenoBrew feature text. |
| R/mod_help.R | Major rewrite/expansion of help UI; adds GenoBrew + VIEWpoly help sections. |
| R/app_ui.R | Adds VIEWpoly navigation + tabItems; updates module gating and formatting. |
| R/app_server.R | Adds VIEWpoly module server wiring and install flags; updates Familia naming. |
| NEWS.md | Adds 0.4.0 release notes for VIEWpoly/help/CSS changes. |
| NAMESPACE | Removes shinydisconnect import (disconnectMessage). |
| inst/app/www/custom.js | Simplifies header cursor logic and generalizes tab “active” handling. |
| inst/app/www/custom.css | Moves cursor styling to CSS; expands card/tab styling and adds accessibility skip-link styles. |
| DESCRIPTION | Bumps to 0.4.0; updates module list/remotes/suggests and removes shinydisconnect. |
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| conditionalPanel( | ||
| condition = "output.genobrewInstalled == true", | ||
| box( | ||
| title = "Select Markers", id = "Inputs_box", width = 12, collapsible = TRUE, collapsed = TRUE, status = "info", solidHeader = TRUE, |
| conditionalPanel( | ||
| condition = "output.viewpolyInstalled == true", | ||
| box( | ||
| title = "Input Data", id = "Inputs_box", width = 12, collapsible = TRUE, collapsed = TRUE, status = "info", solidHeader = TRUE, |
| ) | ||
| ), | ||
| box( | ||
| title = "CNV Profiles", id = "QTL_box", width = 12, collapsible = TRUE, collapsed = TRUE, status = "info", solidHeader = TRUE, |
| ) | ||
| ), | ||
| box( | ||
| title = "ViewQTL", id = "QTL_box", width = 12, collapsible = TRUE, collapsed = TRUE, status = "info", solidHeader = TRUE, |
| ), | ||
| box( | ||
| title = "Genomic Prediction", id = "Genomic_Prediction_box", width = 12, collapsible = TRUE, collapsed = TRUE, status = "info", solidHeader = TRUE, | ||
| "his tab estimates the trait and estimated-breeding-values (EBVs) for either all individuals in a genomic dataset, or by training the model with one genomic dataset to predict the values in another.", |
| tags$li("Test marker panel performance with historical data"), | ||
| tags$li("Markers basic filters"), | ||
| tags$li("Interactive visualization of Qploidy2 CNV profiles results"), | ||
| tags$li("Find copy number variation hostspots in the genome") |
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