Skip to contents

Generate Client Report (PDF)

generate_client_report.Rd

Renders a client-focused metabarcoding report in PDF format for 12S analysis using the package template with specified parameters.

Usage

generate_client_report(
  barque_output_folder,
  samples_ids,
  output_file = "client_report.pdf",
  output_dir = getwd(),
  title = "Rapport d'Analyse Métagénomique - 12S",
  subtitle = "",
  lab_author = "",
  bioinfo_author = "",
  report_author = "",
  extraction_author = "",
  title_short = "Rapport 12S",
  client_name = "",
  geographic_region = "",
  target_species = "Espèces aquatiques (poissons)",
  config_file = NULL,
  primer_file = NULL,
  citation_note = NULL
)

Arguments

barque_output_folder

Path to the barque output folder

samples_ids

Vector of sample IDs to include in the analysis

output_file

Output file name (default: "client_report.pdf")

output_dir

Output directory (default: current working directory)

title

Report title (default: "Rapport d'Analyse Metagenomique - 12S")

subtitle

Report subtitle (default: "")

lab_author

Laboratory analysis author(s) (default: "")

bioinfo_author

Bioinformatics analysis author(s) (default: "")

report_author

Report writing author(s) (default: "")

extraction_author

DNA extraction author(s) (default: "")

title_short

Short title for headers (default: "Rapport 12S")

client_name

Client name (default: "")

geographic_region

Geographic region of sampling (default: "")

target_species

Target species description (default: "Especes aquatiques (poissons)")

config_file

Path to barque config file (optional)

primer_file

Path to primers CSV file (optional)

citation_note

Citation note for the report (optional)

Value

Path to the generated report file

Details

The function automatically looks for a cover image in the package directory at inst/images/cover.jpg or inst/images/cover.png. If no cover image is found, a default gradient background will be used in the PDF report.

Examples

if (FALSE) { # \dontrun{
# Basic usage
generate_client_report(
  barque_output_folder = "/path/to/barque/output",
  samples_ids = c("ST1", "ST2", "ST3", "ST4"),
  client_name = "Valerie Langlois",
  geographic_region = "Province du Quebec",
  lab_author = "Julie Couillard",
  bioinfo_author = "Steve Vissault",
  report_author = "Tuan Ahn To"
)
} # }