Render the template report

Copy the Quarto template to the current working directory and render it using quarto::quarto_render(). The rendered report will be saved in the current working directory. You can specify additional arguments to quarto::quarto_render() to customize the rendering process.

Usage

render_report(
  qmd_template = system.file("quarto", "report.qmd", package = "MOSuite"),
  qmd_src = NULL,
  ...
)

Arguments

qmd_template

Path to the Quarto report file (default is the template report in the package).

qmd_src

Optional path to copy the Quarto report template to before rendering. If NULL (default), the template will be copied to the current working directory with the same filename as the template. If a file already exists at qmd_src, it will not be overwritten.

...

Additional arguments passed to quarto::quarto_render(), such as execute_params (a named list of parameters) or quarto_args (a character vector of CLI flags, e.g. c("--output-dir", "/path/to/out")).

Details

You can edit the copy of report.qmd in the current working directory to customize the report.

Examples

render_report(execute_params = list(
  counts_csv = system.file("extdata", "nidap", "Raw_Counts.csv.gz",
                           package = "MOSuite"),
  samplesheet_csv = system.file("extdata", "nidap",
    "Sample_Metadata_Bulk_RNA-seq_Training_Dataset_CCBR.csv.gz",
    package = "MOSuite")
))
#> 
#> 
#> processing file: report.qmd
#> 1/17                   
#> 2/17 [deps]            
#> 3/17                   
#> 4/17 [initialize]      
#> 5/17                   
#> 6/17 [analyze]         
#> 7/17                   
#> 8/17 [pca_3D]          
#> 9/17                   
#> 10/17 [expr_heatmap]    
#> 11/17                   
#> 12/17 [volcano_summary] 
#> 13/17                   
#> 14/17 [volcano_enhanced]
#> 15/17                   
#> 16/17 [venn_diagram]    
#> 17/17                   
#> output file: report.knit.md
#> 
#> pandoc 
#>   to: html
#>   output-file: report.html
#>   standalone: true
#>   section-divs: true
#>   html-math-method: mathjax
#>   wrap: none
#>   default-image-extension: png
#>   
#> metadata
#>   document-css: false
#>   link-citations: true
#>   date-format: long
#>   lang: en
#>   title: MOSuite analysis report
#>   date: today
#>   
#> Output created: report.html
#> 
#> 

# Render to a specific output directory
render_report(
  quarto_args = c("--output-dir", "./results"),
  execute_params = list(
    counts_csv = system.file("extdata", "nidap", "Raw_Counts.csv.gz",
                             package = "MOSuite"),
    samplesheet_csv = system.file("extdata", "nidap",
      "Sample_Metadata_Bulk_RNA-seq_Training_Dataset_CCBR.csv.gz",
      package = "MOSuite")
  )
)
#> 
#> 
#> processing file: report.qmd
#> 1/17                   
#> 2/17 [deps]            
#> 3/17                   
#> 4/17 [initialize]      
#> 5/17                   
#> 6/17 [analyze]         
#> 7/17                   
#> 8/17 [pca_3D]          
#> 9/17                   
#> 10/17 [expr_heatmap]    
#> 11/17                   
#> 12/17 [volcano_summary] 
#> 13/17                   
#> 14/17 [volcano_enhanced]
#> 15/17                   
#> 16/17 [venn_diagram]    
#> 17/17                   
#> output file: report.knit.md
#> 
#> pandoc 
#>   to: html
#>   output-file: report.html
#>   standalone: true
#>   section-divs: true
#>   html-math-method: mathjax
#>   wrap: none
#>   default-image-extension: png
#>   
#> metadata
#>   document-css: false
#>   link-citations: true
#>   date-format: long
#>   lang: en
#>   title: MOSuite analysis report
#>   date: today
#>   
#> Output created: results/report.html
#> 
#>