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barqueReport

Installation

Installing barqueReport

You can install the development version of barqueReport from GitHub with:

install.packages("remotes")
remotes::install_github("taq-community/barqueReport")

Quick Start

Generate a Client Report (PDF)

Generate a professional PDF document with custom cover page focused on 12S analysis for client delivery:

library(barqueReport)

# Generate client report with project metadata
generate_client_report(
  barque_output_folder = "/path/to/barque/12_results",
  samples_ids = c("ST1", "ST2", "ST3", "ST4", "ST5"),
  client_name = "Valérie Langlois",
  geographic_region = "Province du Québec",
  target_species = "Espèces aquatiques (poissons)",
  sample_type = "ADN extrait",
  lab_author = "Julie Couillard",
  bioinfo_author = "Steve Vissault",
  report_author = "Tuan Ahn To",
  output_file = "client_report.pdf"
)

This generates a PDF document with:

  • Custom cover page with background image (automatically detected from inst/images/cover.jpg|png|pdf)
  • Project information and metadata
  • Laboratory methods and parameters
  • Bioinformatics pipeline configuration
  • Sequencing metrics and statistics
  • Species identification results
  • Quality control information
  • Detailed species list with read counts

Note: To use a custom cover image, place your image file (JPG, PNG, or PDF) at inst/images/cover.[jpg|png|pdf] in the package directory. If no image is found, a default gradient background will be used.

Process Species Information

Enhance species data with taxonomic and conservation information:

# Load your species list
species_list <- c("Salmo trutta", "Oncorhynchus mykiss", "Perca flavescens")

# Fetch comprehensive species information
enhanced_species <- process_species_info(species_list)

# View the results
head(enhanced_species)

What does this function?

  • Fetches conservation status from NatureServe Canada
  • Retrieves common names from ITIS (French and English)
  • Adds links to GBIF, Catalogue of Life, and ITIS databases
  • Creates formatted species names with external links

File Structure Requirements

Your barque output folder should be the 12_results folder produce by barque. For Illumina quality analysis, provide the Quality_Metrics.csv file from your sequencer.

Conservation Status Data Sources

These files should be downloaded from their respective sources and placed in inst/extdata/:

  1. CA_especes_en_peril.csv - Canadian species at risk
  2. QC_especes_en_peril.csv - Quebec species at risk