{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.

• 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

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

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 )

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

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