## ----setup, include = FALSE-----------------------------------------------------------------------
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    crop = NULL ## Related to https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016656.html
)

## ----eval=!exists("SCREENSHOT"), include=FALSE----------------------------------------------------
#  SCREENSHOT <- function(x, ...) knitr::include_graphics(x)

## ----vignetteSetup, echo=FALSE, message=FALSE, warning = FALSE------------------------------------
## Track time spent on making the vignette
startTime <- Sys.time()

## Bib setup
library("RefManageR")

## Write bibliography information
bib <- c(
    R = citation(),
    BiocStyle = citation("BiocStyle")[1],
    knitr = citation("knitr")[1],
    RefManageR = citation("RefManageR")[1],
    rmarkdown = citation("rmarkdown")[1],
    sessioninfo = citation("sessioninfo")[1],
    testthat = citation("testthat")[1],
    iSEEindex = citation("iSEEindex")[1]
)

## ----"install", eval = FALSE----------------------------------------------------------------------
#  if (!requireNamespace("BiocManager", quietly = TRUE)) {
#        install.packages("BiocManager")
#    }
#  
#  BiocManager::install("iSEEindex")
#  
#  ## Check that you have a valid Bioconductor installation
#  BiocManager::valid()

## ----"citation"-----------------------------------------------------------------------------------
## Citation info
citation("iSEEindex")

## ----"start", message=FALSE, warning=FALSE--------------------------------------------------------
library("iSEEindex")
library("BiocFileCache")

bfc <- BiocFileCache(cache = tempdir())

dataset_fun <- function() {
    x <- yaml::read_yaml(system.file(package="iSEEindex", "example.yaml"))
    x$datasets
}

initial_fun <- function() {
    x <- yaml::read_yaml(system.file(package="iSEEindex", "example.yaml"))
    x$initial
}

app <- iSEEindex(bfc, dataset_fun, initial_fun)

if (interactive()) {
  shiny::runApp(app, port = 1234)
}

## ----echo=FALSE-----------------------------------------------------------------------------------
SCREENSHOT("screenshots/landing_page.png", delay=20)

## ----createVignette, eval=FALSE-------------------------------------------------------------------
#  ## Create the vignette
#  library("rmarkdown")
#  system.time(render("iSEEindex.Rmd", "BiocStyle::html_document"))
#  
#  ## Extract the R code
#  library("knitr")
#  knit("iSEEindex.Rmd", tangle = TRUE)

## ----reproduce1, echo=FALSE-----------------------------------------------------------------------
## Date the vignette was generated
Sys.time()

## ----reproduce2, echo=FALSE-----------------------------------------------------------------------
## Processing time in seconds
totalTime <- diff(c(startTime, Sys.time()))
round(totalTime, digits = 3)

## ----reproduce3, echo=FALSE-----------------------------------------------------------------------
## Session info
library("sessioninfo")
options(width = 100)
session_info()

## ----vignetteBiblio, results = "asis", echo = FALSE, warning = FALSE, message = FALSE-------------
## Print bibliography
PrintBibliography(bib, .opts = list(hyperlink = "to.doc", style = "html"))