🕸 linxreport - LINX HTML Reporter

{linxreport} is an R package for generating a HTML report with results from the LINX structural variant tool from the Hartwig Medical Foundation - see documentation for LINX at https://github.com/hartwigmedical/hmftools/tree/master/linx.

For useful functions for parsing and processing LINX results, see https://umccr.github.io/linxreport/reference.

Note

{linxreport} does not run any analyses! It simply parses the outputs from LINX and displays them in tables and tabs. No optimisations are performed.

Caution

The HTML report size depends on the number of LINX plots! We have encountered samples with hundreds of plots which has resulted in HTML files in excess of 200Mb in size.

📦 Installation

• Install current main version from GitHub with:

remotes::install_github("umccr/linxreport")

• Or if used inside a conda environment:

conda install r-linxreport -c conda-forge -c bioconda

✨ Usage

You can generate a HTML report within an R session, or from the command line.

R

The linx_rmd function takes as inputs the directories to the LINX tables and plots, along with the file prefix (sample) and the path to output the HTML to. See ?linx_rmd for more.

d <- system.file("extdata", package = "linxreport")
linxreport::linx_rmd(
  sample = "subject_a.tumor",
  table_dir = file.path(d, "tables"),
  plot_dir = file.path(d, "plots"),
  out_file = tempfile(fileext = ".html"),
  quiet = TRUE
)

CLI

The linxreport.R script is available to generate the HTML report via the command line. Quick example:

linxreport.R \
  --sample subject_a.tumor \
  --plot inst/extdata/plots \
  --table inst/extdata/tables \
  --out subject_a.tumor_linx_report.html

Tip

If you’re using the conda package, the linxreport.R command will already be set up inside an activated conda environment. If you’re not using the conda package, you need to export the linxreport/inst/cli/ directory to your PATH in order to use linxreport.R.

See below for required arguments.

linxr_cli=$(Rscript -e 'x <- system.file("cli", package = "linxreport"); cat(x, "\n")' | xargs)
export PATH="${linxr_cli}:${PATH}"

linxreport.R --version
0.1.0.9000 

linxreport.R --help
Usage
=====
 
linxreport/cli/linxreport.R [options]


Options
=======
--sample=SAMPLE
        Sample name (REQUIRED).

--plot=PLOT
        Path to LINX plot directory (REQUIRED).

--table=TABLE
        Path to LINX table directory (REQUIRED).

--out=OUT
        HTML output file name [def: linx_{sample}.html].

--quiet
        Suppress log printing during rendering.

--version, -v
        Print version and exit.

--help, -h
        Show this help message and exit