In d3b-center/annoFuse: annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions

knitr::opts_chunk$set(
  echo = TRUE, 
  warning = FALSE, 
  message = FALSE,
  error = TRUE
)
# knitr::opts_knit$set(
#   progress = FALSE, 
#   verbose = FALSE
# )

Intro

library("annoFuse")
out_annofuse

Output table

Enhancing with buttons...

# enhancing the content of the table

enhanced_annofuse_tbl <- annofuse_tbl
enhanced_annofuse_tbl$Gene1A <- .multilink(enhanced_annofuse_tbl$Gene1A)
enhanced_annofuse_tbl$Gene1B <- .multilink(enhanced_annofuse_tbl$Gene1B)

## would need to be made unique - and maybe keep frozen while scrolling the table
# rownames(enhanced_annofuse_tbl) <- enhanced_annofuse_tbl$FusionName

And rendering!

DT::datatable(
  enhanced_annofuse_tbl,
  filter = "top",
  selection = "single",
  extensions = c("Buttons"),
  escape = FALSE,
  options = list(
    scrollX = TRUE,
    pageLength = 25,
    lengthMenu = c(5, 10, 25, 50, 100, nrow(enhanced_annofuse_tbl)),
    dom = "Bfrtip",
    buttons = list("copy", "print", list(
        extend = "collection",
        buttons = c("csv", "excel", "pdf"),
        text = "Download"
      )
    )
  )
)

General summary on the standardized fusion file

plot_summary(annofuse_tbl, base_size = 8)

Session info {-}

sessionInfo()

d3b-center/annoFuse documentation built on Oct. 2, 2024, 4:17 a.m.