Generate Quarto report chunks for a GWAS meta-analysis trait

Generates quarto-compatible R code chunks as a character string for inclusion in multi-trait reports. Manhattan plots use knitr::include_graphics() with high-DPI PNG file targets for native HTML rendering at full width. Loci tables are rendered with DT::datatable() with a CSV export button. Precision plots and LDSC heatmaps use native tar_read() calls. Sections with per-ancestry results (LDSC heatmaps, Manhattan plots) are organized using Quarto tabset panels.

Usage

generate_report_chunks(
  trait,
  manifest_df,
  include_loci = TRUE,
  output_file = NULL
)

Arguments

trait

Trait name (e.g. "CAD").

manifest_df

A data frame with at least ancestry and cohort columns. Same manifest passed to generate_gwas_meta_pipeline(). Used to determine which ancestries have per-ancestry meta-analysis targets (only ancestries with 2+ cohorts).

include_loci

Logical; whether to include genome-wide significant loci table chunks. Default TRUE.

output_file

Optional file path to write the generated chunks to. When provided, parent directories are created automatically and the string is returned invisibly. When NULL (default), the string is returned visibly.

Value

A length-1 character string containing quarto markdown with embedded R code chunks.

Examples

if (FALSE) { # \dontrun{
manifest <- data.frame(
  path     = c("/data/UKBB_EUR.txt.gz", "/data/MVP_AFR.txt.gz",
               "/data/BioVU_EUR.txt.gz"),
  file     = c("UKBB_EUR.txt.gz", "MVP_AFR.txt.gz", "BioVU_EUR.txt.gz"),
  cohort   = c("UKBB", "MVP", "BioVU"),
  ancestry = c("EUR", "AFR", "EUR"),
  study    = c("UKBB", "MVP", "BioVU"),
  stringsAsFactors = FALSE
)
cat(generate_report_chunks("CAD", manifest))
} # }