Read Arriba PDF File — arriba_pdf

Reads the PDF output by Arriba containing one fusion plot per page and converts each page to a separate PNG file.

Usage

arriba_pdf_read(pdf = NULL, fusions = NULL, outdir = NULL)

Arguments

pdf: Output PDF file from Arriba.
fusions: Tibble with fusions from Arriba.
outdir: Directory to write output PNGs to.

Value

Tibble with paths to the created PNG images and their clean names. If the PDF (or any of the required params) is NULL, returns NULL.

Examples

pdf <- system.file("rawdata/test_data/dragen/arriba/fusions.pdf", package = "RNAsum")
tsv <- system.file("rawdata/test_data/dragen/arriba/fusions.tsv", package = "RNAsum")
fusions <- arriba_tsv_read(tsv)
(pngs <- arriba_pdf_read(pdf, fusions, tempdir()))
#> # A tibble: 4 × 2
#>   nm                                                                 png        
#>   <chr>                                                              <chr>      
#> 1 EP300.AS1__XRCC6_chr22.41195482_chr22.41636113                     /tmp/Rtmpy…
#> 2 LAPTM4A__AC098828.3_chr2.20051410_chr2.20064511                    /tmp/Rtmpy…
#> 3 FNIP1__AC112492.1.83716..DCAF8L1.218._chr5.131642783_chrX.27977775 /tmp/Rtmpy…
#> 4 ZFP64__MORC2_chr20.52096811_chr22.30963497                         /tmp/Rtmpy…