## ----options, include = FALSE, echo = FALSE, results = 'asis'-----------------
knitr::opts_chunk$set(
  echo = TRUE,
  collapse = TRUE, 
  comment = "#>",
  
  fig.width = 9,      # Makes the internal plot larger
  fig.height = 6,
  out.width = "100%", # Scales it to fit the screen
  fig.alt = " ",
  fig.align = "center",
  fig.path = 'man/images/'
)
BiocStyle::markdown()

## ----installation, eval = FALSE-----------------------------------------------
# ## GOATEA installation requires R (v4.5.0) and the lastest version of Rtools
# ## Rtools is needed for package compilation, to download and install visit:
# # R: https://cran.r-project.org/mirrors.html
# # Rtools: https://cran.r-project.org/bin/windows/Rtools/
# ## I recommend to run the installation and GUI startup code via Rstudio, to have a nice graphical environment:
# # Rstudio: https://posit.co/downloads/
# 
# ## To install GOATEA from Bioconductor (v3.23) use:
# if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager")
# BiocManager::install("goatea")
# # or via pak
# if ( ! require("pak", quietly = TRUE)) install.packages('pak')
# pak::pkg_install('goatea', dependencies = TRUE, upgrade = TRUE)
# 
# ## goatea requires at least one of the following available organism genome wide annotation packages:
# ### format: organism (taxid): org.Xx.eg.dg
# # Human (9606)--------: org.Hs.eg.db
# # Mouse (10090)-------: org.Mm.eg.db
# # Fruit Fly (7227)----: org.Dm.eg.db
# # Rhesus monkey (9544): org.Mmu.eg.db
# # Rat (10116)---------: org.Rn.eg.db
# # Worm (6239)---------: org.Ce.eg.db
# # Chimpanzee (9598)---: org.Pt.eg.db
# # Zebrafish (7955)----: org.Dr.eg.db
# if ( ! require("pak", quietly = TRUE)) install.packages('pak')
# pak::pkg_install(c(
#   "org.Hs.eg.db",
#   "org.Mm.eg.db",
#   "org.Dm.eg.db",
#   "org.Mmu.eg.db",
#   "org.Rn.eg.db",
#   "org.Ce.eg.db",
#   "org.Pt.eg.db",
#   "org.Dr.eg.db"
# ))

## ----goatea_Shiny, eval=FALSE, message=FALSE, warning=FALSE-------------------
# library(goatea)
# 
# ## customizable coloring
# colors <- list(
#   main_bg = "#222222",
#   darker_bg = "#111111",
#   focus = "#32CD32",
#   hover = "#228B22",
#   border = "#555555",
#   text = "#FFFFFF"
# )
# 
# ## set max file size to ...MB for uploads (default: 100)
# options(shiny.maxRequestSize = 1024^2 * 100)
# 
# ## run the goatea Shiny application
# shiny::shinyApp(
#   ui = goatea_ui,
#   server = function(input, output, session) {
#     goatea_server(
#       input, output, session,
#       css_colors = colors)
#   }
# )

## ----session_info-------------------------------------------------------------
sessionInfo()