1 Custom header and footer

1.1 Overview

By default, iSEEindex creates a minimal landing page presenting users with a fluid row that contains two shinydashboard::box():

On the left, users can select a data set.
On the right, users can select an initial configuration and launch the main app interface.

iSEEindex offers the opportunity for app maintainers to add content above (i.e., header) and below (i.e., footer) that row.

That header and footer space may contain any valid UI element that will be displayed in the application UI as is.

1.2 Implementation

The function iSEEindex() accepts header and footer content through its arguments body.header= and body.footer=.

We recommend wrapping header and footer content in shiny::fluidRow(), to fit naturally with the main fluid row (see above).

2 Example

First, let us set up the core elements of a simple application (see ?iSEEindex).

library("BiocFileCache")

##
# BiocFileCache ----
##

library(BiocFileCache)
bfc <- BiocFileCache(cache = tempdir())

##
# iSEEindex ----
##

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
}

Then, we design header and footer content, each wrapped in a shiny::fluidRow().

library("shiny")
header <- fluidRow(shinydashboard::box(width = 12L, 
  column(width = 10,
    p(strong("Welcome to this demonstration app!")),
    p(
      "This is an example header that demonstrate how to use the functionality.",
      "A great place for branding and intros.",
    ),
    p("On the right, we demonstrate how other content such as images can be added to this header.")
  ),
  column(width = 2, img(src="www/iSEE.png", width = "100px", height = "120px"))
))
footer <- fluidRow(shinydashboard::box(width = 12L,
  p("This is a example footer. A great place for copyright statements and outros.", style="text-align: center;"),
  p(
    "© 2023 iSEE.",
    a("Artistic-2.0", href = "https://opensource.org/license/artistic-2-0/"),
    style="text-align: center;")
  ))

For the image file to be found, the containing directory must be added to the Shiny resource path as follows:

library("shiny")
addResourcePath("www", system.file(package = "iSEEindex"))

Finally, we supply the custom header and footer to iSEEindex().

library("iSEEindex")
app <- iSEEindex(bfc, dataset_fun, initial_fun,
  body.header = header, body.footer = footer
)

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

3 Reproducibility

The iSEEindex package (Rue-Albrecht and Marini, 2024) was made possible thanks to:

R (R Core Team, 2024)
BiocStyle (Oleś, 2024)
knitr (Xie, 2024)
RefManageR (McLean, 2017)
rmarkdown (Allaire, Xie, Dervieux, McPherson, Luraschi, Ushey, Atkins, Wickham, Cheng, Chang, and Iannone, 2024)
sessioninfo (Wickham, Chang, Flight, Müller, and Hester, 2021)
testthat (Wickham, 2011)

This package was developed using biocthis.

Code for creating the vignette

## Create the vignette
library("rmarkdown")
system.time(render("header.Rmd", "BiocStyle::html_document"))

## Extract the R code
library("knitr")
knit("header.Rmd", tangle = TRUE)

Date the vignette was generated.

#> [1] "2024-10-29 18:00:29 EDT"

Wallclock time spent generating the vignette.

#> Time difference of 10.666 secs

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R Under development (unstable) (2024-10-21 r87258)
#>  os       Ubuntu 24.04.1 LTS
#>  system   x86_64, linux-gnu
#>  ui       X11
#>  language (EN)
#>  collate  C
#>  ctype    en_US.UTF-8
#>  tz       America/New_York
#>  date     2024-10-29
#>  pandoc   3.1.3 @ /usr/bin/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────
#>  package              * version date (UTC) lib source
#>  abind                  1.4-8   2024-09-12 [2] CRAN (R 4.5.0)
#>  backports              1.5.0   2024-05-23 [2] CRAN (R 4.5.0)
#>  bibtex                 0.5.1   2023-01-26 [2] CRAN (R 4.5.0)
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Adding a custom header and footer to the landing page

29 October 2024

Package

1 Custom header and footer

1.1 Overview

1.2 Implementation

2 Example

3 Reproducibility