Generate LINX HTML Report — linx

Generates a LINX HTML report. It does so with the following steps:

recursively copy the table and plot directories into tmp/plot and tmp/table
copy the rmd into tmp/linx.Rmd
render the rmd inside tmp/
return the path to the output HTML

Usage

linx_rmd(sample, table_dir, plot_dir, out_file = NULL, quiet = FALSE)

Arguments

sample: Name of sample.
table_dir: Path to LINX table directory.
plot_dir: Path to LINX plot directory.
out_file: Path to output HTML file (needs '.html' suffix).
quiet: Suppress printing during rendering.

Value

Path to rendered HTML report.

Examples

d <- system.file("extdata", package = "linxreport")
outd <- tempdir()
linx_rmd(
  sample = "COLO829v003T",
  table_dir = file.path(d, "tables"),
  plot_dir = file.path(d, "plots"),
  out_file = file.path(outd, "test1.html"),
  quiet = FALSE
)
#> 
#> 
#> processing file: linxreport.Rmd
#> 1/75                      
#> 2/75 [knitr_opts]         
#> 3/75                      
#> 4/75 [load_pkgs]          
#> 5/75                      
#> 6/75 [funcs]              
#> 7/75                      
#> 8/75 [read_tables]        
#> Error: ncol(d) not equal to length(nm)
#> 9/75                      
#> 10/75 [svs0]               
#> Error: object 'tabs' not found
#> 11/75                      
#> Error in eval(parse_only(code), envir = envir): object 'l' not found
#> 
#> Quitting from linxreport.Rmd:75-75