First scetch of the vignette

.Rbuildignore

 ^.*\.Rproj$
 ^\.Rproj\.user$
+^doc$
+^Meta$

.gitignore

@@ -4,3 +4,5 @@
 .Ruserdata
 .DS_store
 *.html
+doc
+Meta

DESCRIPTION

@@ -11,12 +11,14 @@ License: MIT
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 6.1.1
+VignetteBuilder: knitr
 Imports: 
     magrittr,
     knitr,
     flexdashboard,
     yaml,
-    assertive.sets
+    assertive.sets,
+    rmarkdown
 Suggests: 
     highcharter,
     plotly,
@@ -29,7 +31,9 @@ Suggests:
     visNetwork,
     d3heatmap,
     metricsgraphics,
-    diagrammeR
+    diagrammeR,
+    BiocStyl,
+    knitr
 Collate: 
     'i2dashboard.R'
     'AllGenerics.R'

vignettes/basic.Rmd

+---
+title: "An introduction to i2dash"
+author:
+- name: Jens Preussner
+  affiliation: 
+  email: jens.preussner@mpi-bn.mpg.de
+- name: Arsenij Ustjanzew
+  affiliation: 
+  email: arsenij.ustjanzew@mpi-bn.mpg.de
+date: "`r BiocStyle::doc_date()`"
+package: "`r BiocStyle::pkg_ver('i2dash')`"
+output: 
+  BiocStyle::html_document:
+    toc_float: true
+vignette: >
+  %\VignetteIndexEntry{1. An introduction to i2dash}
+  %\VignettePackage{i2dash}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+**Compiled date**: `r Sys.Date()`
+
+**Last edited**: 26.08.2019
+
+**License**: `r packageDescription("i2dash")[["LICENSE"]]`
+
+```{r style, echo = FALSE, results = 'asis'}
+  BiocStyle::markdown()
+```
+
+```{r setup, include = FALSE}
+knitr::opts_chunk$set(
+    collapse = TRUE,
+    comment = "#>",
+    error = FALSE,
+    warning = FALSE,
+    message = FALSE
+)
+stopifnot(requireNamespace("htmltools"))
+htmltools::tagList(rmarkdown::html_dependency_font_awesome())
+```
+
+```{r, echo=FALSE, out.width='50%', fig.align='center'}
+knitr::include_graphics(path = system.file(package="i2dash", "/www/logo-placeholder.png", mustWork=TRUE))
+```
+
+
+# Introduction 
+
+i2dash (Iterative & Interactive dashboards in R) is a package that provides the functionality to create a customized dashboard, which can be static (a standart HTML page) or dynamic with R Studio's [Shiny](https://shiny.rstudio.com/). The layout of the dashboard is based on R Studio's [flexdashboard](https://rmarkdown.rstudio.com/flexdashboard/), where the content (e.g. [htmlwidgets](http://www.htmlwidgets.org/), tabular data or graphical output) is organized into "components". i2dash stores the provided content in a S4 class `i2dashboard` object. The single pages and components are added iteratively to the `i2dashboard` object which enables the implementation into a bigger pipeline.
+
+Instructions to install the package are available ...
+Once installed, the package can be loaded and attached to your current workspace as follows:
+
+```{r library}
+library(i2dash)
+```
+
+# Workflow for creating a dashboard with i2dash
+
+At first you need to create a an instance of the `i2dashboard` class with `new()` and fill the basic slots. With `title` you set the dashboards title that will be displayed in the left corner of the navigation bar. The name of the author of the dashboard will be shown in the navigation bar, if `author` is provided. If the argument `interactive` is set to `TRUE` a shiny-based dashboard will be created, else a static dashboard will be created. You can change the apperance of your dashboard by selecting a valid `theme`. See the variety of themes [here](https://rmarkdown.rstudio.com/flexdashboard/using.html#appearance).
+and change 
+#' @slot datadir Path to the directory, where report data is stored.
+#' @slot file Filename of the resulting report Rmd file.
+#' @slot pages A list of dashboard pages
+
+```{r}
+dashboard <- new("i2dashboard",
+             title = "Name of the dashboard",
+             author = "John Doe",
+             interactive = TRUE,
+             theme = "yeti",
+             datadir = "P:/scRNA_test/package_test",
+             file = "final_report.Rmd")
+```
+
+
+## Creating an `i2dashboard` object
+
+## Adding & removing pages
+
+### Existing page layouts
+
+## Adding components
+
+### Valid objects to add as components
+
+## Assembling pages
+
+
+
+
+
+
+
+
+
+# Additional information
+
+Bug reports can be raised as issues in the `r #Githubpkg("csoneson/iSEE")` GitHub repository.
+The GitHub repository also contains the development version of the package, where new functionality is added over time.
+The authors appreciate well-considered suggestions for improvements or new features, or even better, pull requests.
+
+If you use `r Biocpkg("iSEE")` for your analysis, please cite it as shown below:
+
+```{r citation}
+#citation("iSEE")
+```
+
+# Session Info {.unnumbered}
+
+```{r sessioninfo}
+sessionInfo()
+```
+
+# References {.unnumbered}
\ No newline at end of file