Add ped cleaner

[josuechinchilla]

added ped_cleaner, css and restructured help module and sections

[Copilot]

Pull request overview

Adds a Pedigree Cleaner workflow, reorganizes app navigation/help content around pedigree and composition tools, and updates shared UI styling/resources.

Changes:

• Adds mod_ped_cleaner plus dedicated help content for Pedigree Cleaner, SNMF, and PolyBreedTools.
• Reworks app sidebar/tab wiring and removes the Genomic Diversity module from the active app.
• Adds custom CSS/JS for dashboard theming and card/tab behavior.

Reviewed changes

Copilot reviewed 17 out of 22 changed files in this pull request and generated 10 comments.

Show a summary per file

File	Description
R/mod_SNMF.R	Adds module help button and image export support; mostly reformats existing SNMF UI/server.
R/mod_polybreedtools.R	Adds help button/content integration and reorganizes UI layout.
R/mod_ped_cleaner.R	New Pedigree Cleaner UI/server module.
R/mod_Home.R	Removes/comment-disables the tutorials value box.
R/mod_help.R	Replaces old help page with accordion-based help for new supported modules.
R/mod_diversity.R	Deletes the Genomic Diversity module.
R/help_SNMF.R	Adds reusable SNMF help content.
R/help_polybreedtools.R	Adds reusable PolyBreedTools help content.
R/help_ped_cleaner.R	Adds reusable Pedigree Cleaner help content.
R/app_ui.R	Adds Pedigree Cleaner tab, updates sidebar/menu/source link, and injects CSS/JS.
R/app_server.R	Wires Pedigree Cleaner and Help servers; removes active Diversity server wiring.
NAMESPACE	Removes unused includeMarkdown import.
inst/app/www/custom.js	Adds card-header collapse behavior and tab active-state sync.
inst/app/www/custom.css	Adds dashboard color/theme overrides and UI styling.
inst/.gitignore	Ignores an SNMF test VCF under inst.
.Rhistory	Updates tracked interactive R history.
.Rbuildignore	Adds local AI tool directories to build ignore.
.gitignore	Ignores .positai.

Comments suppressed due to low confidence (1)

R/mod_SNMF.R:759

• The exported ancestry plot is rebuilt independently from output$snmf_q_plot, duplicating the reshape/theme logic. Sharing a single plot helper would prevent the downloaded image from diverging from the on-screen plot when future changes are made.

        q      <- q_matrix()
        df     <- data.frame(ID = rownames(q), q, check.names = FALSE)
        q_cols <- colnames(q)
        long   <- stats::reshape(df, varying = q_cols, v.names = "Q", timevar = "Cluster",
                                 times = q_cols, direction = "long")
        long$ID      <- factor(long$ID,      levels = unique(df$ID))
        long$Cluster <- factor(long$Cluster, levels = q_cols)
        ggplot(long, ggplot2::aes(x = ID, y = Q, fill = Cluster)) +
          geom_col(width = 0.9) +
          scale_y_continuous(labels = scales::percent_format(accuracy = 1)) +
          labs(x = "Individual", y = "Ancestry proportion", fill = "Cluster") +
          theme_minimal() +
          theme(axis.text.x = element_text(angle = 45, hjust = 1, vjust = 1, size = 8),
                panel.grid.major.x = element_blank())
      }

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[Copilot]

Pull request overview

Copilot reviewed 18 out of 23 changed files in this pull request and generated 7 comments.

[Copilot]

Pull request overview

Copilot reviewed 18 out of 23 changed files in this pull request and generated 8 comments.

[Copilot]

Pull request overview

Copilot reviewed 18 out of 23 changed files in this pull request and generated 10 comments.

[Copilot]

Pull request overview

Copilot reviewed 18 out of 23 changed files in this pull request and generated 5 comments.

Comments suppressed due to low confidence (1)

R/mod_ped_cleaner.R:235

• shinyjs::enable("download_results") will not work reliably in a module because the actual DOM id is namespaced. Enable the button using the namespaced id (e.g., shinyjs::enable(session$ns("download_results"))) so downloads are re-enabled after a successful run.

        shinyWidgets::updateProgressBar(
          session = session, id = "pb_ped",
          value = 100, status = "success",
          title = "Finished"
        )
        shinyjs::enable("download_results")
        

[Copilot]

Pull request overview

Copilot reviewed 18 out of 23 changed files in this pull request and generated 3 comments.

Comments suppressed due to low confidence (1)

R/mod_ped_cleaner.R:398

• These section titles are hard-coded as "Conflicting Trios Resolved" even though correction is optional. If the user disables correction, the table should not be labeled as "resolved" (same for any other conditionally-corrected issue types). Suggest making the title conditional on the run settings or using a neutral label like "Conflicting Trios".

      render_if("Exact Duplicates Removed",       report$exact_duplicates)
      render_if("Conflicting Trios Resolved",      report$conflicting_trios)
      render_if("Inconsistent Sex Roles",          report$inconsistent_sex_roles)
      render_if("Missing Parents Added",           report$missing_parents)

[Copilot]

Pull request overview

Copilot reviewed 18 out of 23 changed files in this pull request and generated 2 comments.