From 853cbfbf11f5d70fa0d13a9e67e63bc862796425 Mon Sep 17 00:00:00 2001 From: Charlotte Soneson Date: Wed, 27 Mar 2024 10:24:05 +0100 Subject: [PATCH] Fix docs (#58) * Rerender documentation * Update to recommended format for package documentation * Version bump --- DESCRIPTION | 4 +-- R/{iSEEindex-pkg.R => iSEEindex-package.R} | 7 ++--- man/iSEEindex-package.Rd | 36 ++++++++++++++++++++++ man/iSEEindex-pkg.Rd | 21 ------------- man/iSEEindex.Rd | 5 +++ 5 files changed, 46 insertions(+), 27 deletions(-) rename R/{iSEEindex-pkg.R => iSEEindex-package.R} (80%) create mode 100644 man/iSEEindex-package.Rd delete mode 100644 man/iSEEindex-pkg.Rd diff --git a/DESCRIPTION b/DESCRIPTION index a94159e..8c25bc3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: iSEEindex Title: iSEE extension for a landing page to a custom collection of data sets -Version: 1.1.1 +Version: 1.1.2 Date: 2024-02-21 Authors@R: c(person("Kevin", "Rue-Albrecht", email = "kevinrue67@gmail.com", @@ -25,7 +25,7 @@ biocViews: Software, Infrastructure Encoding: UTF-8 Roxygen: list(markdown = TRUE) -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.1 Depends: SummarizedExperiment, SingleCellExperiment diff --git a/R/iSEEindex-pkg.R b/R/iSEEindex-package.R similarity index 80% rename from R/iSEEindex-pkg.R rename to R/iSEEindex-package.R index 6abcdb6..86dce78 100644 --- a/R/iSEEindex-pkg.R +++ b/R/iSEEindex-package.R @@ -4,7 +4,7 @@ #' single iSEE web-application. #' The main functionality of this package is to define a custom landing page #' allowing app maintainers to list a custom collection of data sets that users -#' can selected from and directly load objects into an iSEE web-application. +#' can select from and directly load objects into an iSEE web-application. #' #' @seealso #' Useful links: @@ -13,6 +13,5 @@ #' - Report bugs at #' #' @keywords internal -#' @name iSEEindex-pkg -#' @docType package -NULL +#' @aliases iSEEindex-package NULL +"_PACKAGE" diff --git a/man/iSEEindex-package.Rd b/man/iSEEindex-package.Rd new file mode 100644 index 0000000..20e2f89 --- /dev/null +++ b/man/iSEEindex-package.Rd @@ -0,0 +1,36 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/iSEEindex-package.R +\docType{package} +\name{iSEEindex-package} +\alias{iSEEindex-package} +\title{iSEEindex: iSEE extension for a landing page to a custom collection of data sets} +\description{ +This package provides an interface to any collection of data sets within a +single iSEE web-application. +The main functionality of this package is to define a custom landing page +allowing app maintainers to list a custom collection of data sets that users +can select from and directly load objects into an iSEE web-application. +} +\seealso{ +Useful links: +\itemize{ +\item \url{https://github.com/iSEE/iSEEindex} +\item Report bugs at \url{https://support.bioconductor.org/t/iSEEindex} +} +} +\author{ +\strong{Maintainer}: Kevin Rue-Albrecht \email{kevinrue67@gmail.com} (\href{https://orcid.org/0000-0003-3899-3872}{ORCID}) + +Authors: +\itemize{ + \item Federico Marini \email{marinif@uni-mainz.de} (\href{https://orcid.org/0000-0003-3252-7758}{ORCID}) +} + +Other contributors: +\itemize{ + \item Thomas Sandmann \email{tomsing1@gmail.com} (\href{https://orcid.org/0000-0002-6601-8890}{ORCID}) [contributor] + \item Denali Therapeutics [funder] +} + +} +\keyword{internal} diff --git a/man/iSEEindex-pkg.Rd b/man/iSEEindex-pkg.Rd deleted file mode 100644 index 167ba61..0000000 --- a/man/iSEEindex-pkg.Rd +++ /dev/null @@ -1,21 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/iSEEindex-pkg.R -\docType{package} -\name{iSEEindex-pkg} -\alias{iSEEindex-pkg} -\title{iSEEindex: iSEE extension for a landing page to a custom collection of data sets} -\description{ -This package provides an interface to any collection of data sets within a -single iSEE web-application. -The main functionality of this package is to define a custom landing page -allowing app maintainers to list a custom collection of data sets that users -can selected from and directly load objects into an iSEE web-application. -} -\seealso{ -Useful links: -\itemize{ -\item \url{https://github.com/iSEE/iSEEindex} -\item Report bugs at \url{https://support.bioconductor.org/t/iSEEindex} -} -} -\keyword{internal} diff --git a/man/iSEEindex.Rd b/man/iSEEindex.Rd index fefb5d9..e1eb505 100644 --- a/man/iSEEindex.Rd +++ b/man/iSEEindex.Rd @@ -10,6 +10,7 @@ iSEEindex( FUN.initial = NULL, default.add = TRUE, default.position = c("first", "last"), + app.title = NULL, body.header = NULL, body.footer = NULL ) @@ -31,6 +32,10 @@ See \code{\link[=iSEEindex]{iSEEindex()}}.} initial configuration should be added as the \code{"first"} or \code{"last"} option in the Shiny \code{selectizeInput()}.} +\item{app.title}{Character string to specify the desired title to be displayed +in the main window of the dashboard. Defaults to \code{NULL}, which displays some +info on the versions of the \code{iSEEindex} and \code{iSEE} packages.} + \item{body.header}{UI element to display \emph{above} the main landing page body.} \item{body.footer}{UI element to display \emph{below} the main landing page body.}