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Generate a publication-ready VISTA workflow report

run_vista_report.Rd

Builds a VISTA object (or uses a precomputed one), computes a comprehensive single-comparison analysis panel, exports publication assets, and renders an automated Quarto HTML/PDF report from YAML-driven parameters.

Usage

run_vista_report(config, output_file = "vista-report.html")

Arguments

config

Path to a YAML config file (see template at inst/reports/vista-report-template.yml) or a named list of parameters.

output_file

Optional output filename overriding config$output_file.

Value

Invisibly, the normalized output report path.

Details

The report focuses on one differential comparison (primary_comparison) and includes:

  • QC plots (PCA, MDS, correlation heatmap),

  • DE plots (volcano, MA, DEG bar/pie/donut summaries),

  • expression-focused views (boxplot, fold-change barplot, expression heatmap),

  • enrichment outputs (MSigDB/GO/KEGG when available),

  • downloadable artifacts (tables + plots + optional zip bundle),

  • interactive HTML tables via DT when installed.

Examples

if (FALSE) { # \dontrun{
data('count_data', package = 'VISTA')
data('sample_metadata', package = 'VISTA')
cfg <- list(
  counts = count_data[1:100, ],
  sample_info = sample_metadata[1:6, ],
  column_geneid = 'gene_id',
  group_column = 'cond_long',
  group_numerator = 'treatment1',
  group_denominator = 'control',
  include_msigdb = FALSE, include_go = FALSE, include_kegg = FALSE
)
if (requireNamespace('quarto', quietly = TRUE)) {
  out <- tempfile(fileext = '.html')
  try(run_vista_report(cfg, output_file = out), silent = TRUE)
}
} # }