Compare revisions

jens.preussner · jens.preussner · a3db7236 · a3db7236 · a3db7236 · a3db7236
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -5,3 +5,6 @@
 ^README\.md
 ^doc$
 ^Meta$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
--- a/.gitignore
+++ b/.gitignore
@@ -4,6 +4,5 @@
 .Ruserdata
 .DS_store
 Thumbs.db
-*.html
-doc
+./*.html
 Meta
--- a/README.md
+++ b/README.md
-# **i2dash**: - **I**nteractive & **i**terative **dash**boards in R <img src="vignettes/images/i2dash_logo.png" align="right" width="150px"/>
+# Interactive & iterative dashboards in R

-
-## Abstract
+## Abstract <img src="vignettes/images/i2dash_logo.png" align="right" width="150px" />

 Scientific communication and data visualization are important aspects to illustrate complex concepts and results from data analyses. The R package **i2dash** provides functionality to create customized, web-based dashboards for data presentation, exploration and sharing. **i2dash** integrates easily into existing data analysis pipelines and can organize scientific findings thematically across different pages and layouts.

 ### Main features

- Easy integration into existing analysis pipelines in R
- Support for multiple components, such as htmlwidgets, tabular data, text, images etc.
+- Easy integration into existing analysis pipelines in R for programmatic dashboard creation
+- Provides a selection of predefined layouts to arrange content
+- Support for multiple components, such as htmlwidgets, tables, text, images etc.
 - Creation of web-based, sharable, static or interactive dashboards
 - Enables a flexible and iterative cycle of dashboard development

-![](man/figures/i2dash_image.jpg)
+![](vignettes/images/i2dash_intro.png)

-*A customized dashboard can be integrated into an existing data analysis pipelines in R (left). After initialization, pages containing components with customized content can be added step-by-step to the dashboard at any stage of the data analysis. The final dashboard is assembled into an R markdown file, and shared together with RDS data files for further use within RStudio, or can also be deployed on a R Shiny Server or as stand-alone HTML file.*
+*(A) dashboard is initialized at the beginning of a data analysis pipeline. During the pipeline run, new content, results, or data visualizations are iteratively added to the dashboard’s pages. The final dashboard is rendered into a static or interactive document. (B) Pages added to the dashboard can be arranged in a flexible manner from a selection of predefined layouts. (C) Examples of programmatically created dashboards. (D) The i2dash docker container, providing all dependencies for interactive, shiny based apps, can be used to easily deploy individual data interpretations on a cloud infrastructure, such as Kubernetes, as a micro service.*

-## Installation:
+## Installation

-The package can be installed with the `r BiocStyle::CRANpkg("remotes")` library:
+The package can be installed with:

-```{r, eval=FALSE}
-remotes::install_git(url = "https://gitlab.gwdg.de/loosolab/software/i2dash.git", repos = BiocManager::repositories())
+```
+install.packages("i2dash")
 ```

 ## Where to start
@@ -36,7 +36,9 @@ It is possible to extend the core functionality of **i2dash** with templates for

 ## How to cite

-Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum.
+If you use **i2dash** or **i2dash.scrnaseq** in your work, please cite:
+
+Ustjanzew A., Preussner J., Bentsen M., Kuenne C., and Looso M. i2dash: creation of flexible, interactive and web-based dashboards from data analysis pipelines. *tba* (2020)

 ## License


--- a/docs/404.html
+++ b/docs/404.html
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+  <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Page not found (404) • i2dash</title>
+
+<!-- favicons -->
+<link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png" />
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png" />
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png" />
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png" />
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="bootstrap-toc.css">
+<script src="bootstrap-toc.js"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="pkgdown.css" rel="stylesheet">
+<script src="pkgdown.js"></script>
+
+
+
+
+<meta property="og:title" content="Page not found (404)" />
+
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+
+  </head>
+
+  <body data-spy="scroll" data-target="#toc">
+    <div class="container template-title-body">
+      <header>
+      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+  <div class="container">
+    <div class="navbar-header">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+      </button>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="index.html">i2dash</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.2</span>
+      </span>
+    </div>
+
+    <div id="navbar" class="navbar-collapse collapse">
+      <ul class="nav navbar-nav">
+        <li>
+  <a href="index.html">
+    <span class="fas fa fas fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
+  <a href="reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+    Articles
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu">
+    <li>
+      <a href="articles/i2dash-intro.html">Creating iterative and interactive dashboards with i2dash</a>
+    </li>
+  </ul>
+</li>
+      </ul>
+      <ul class="nav navbar-nav navbar-right">
+        
+      </ul>
+      
+    </div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+      
+
+      </header>
+
+<div class="row">
+  <div class="contents col-md-9">
+    <div class="page-header">
+      <h1>Page not found (404)</h1>
+    </div>
+
+Content not found. Please use links in the navbar.
+
+  </div>
+
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top">
+      <h2 data-toc-skip>Contents</h2>
+    </nav>
+  </div>
+
+</div>
+
+
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Arsenij Ustjanzew, Jens Preussner, Mario Looso.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+</div>
+
+      </footer>
+   </div>
+
+  
+
+
+  </body>
+</html>
+
+
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+  <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>License • i2dash</title>
+
+<!-- favicons -->
+<link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png" />
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png" />
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png" />
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png" />
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="bootstrap-toc.css">
+<script src="bootstrap-toc.js"></script>
+
+<!-- Font Awesome icons -->
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
+
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
+
+<!-- headroom.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+
+<!-- pkgdown -->
+<link href="pkgdown.css" rel="stylesheet">
+<script src="pkgdown.js"></script>
+
+
+
+
+<meta property="og:title" content="License" />
+
+
+
+
+<!-- mathjax -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+
+  </head>
+
+  <body data-spy="scroll" data-target="#toc">
+    <div class="container template-title-body">
+      <header>
+      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+  <div class="container">
+    <div class="navbar-header">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+      </button>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="index.html">i2dash</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.2</span>
+      </span>
+    </div>
+
+    <div id="navbar" class="navbar-collapse collapse">
+      <ul class="nav navbar-nav">
+        <li>
+  <a href="index.html">
+    <span class="fas fa fas fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
+  <a href="reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+    Articles
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu">
+    <li>
+      <a href="articles/i2dash-intro.html">Creating iterative and interactive dashboards with i2dash</a>
+    </li>
+  </ul>
+</li>
+      </ul>
+      <ul class="nav navbar-nav navbar-right">
+        
+      </ul>
+      
+    </div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+      
+
+      </header>
+
+<div class="row">
+  <div class="contents col-md-9">
+    <div class="page-header">
+      <h1>License</h1>
+    </div>
+
+<pre>MIT License
+
+Copyright (c) 2019 Mario Looso, Jens Preussner and Arsenij Ustjanzew
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+</pre>
+
+  </div>
+
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top">
+      <h2 data-toc-skip>Contents</h2>
+    </nav>
+  </div>
+
+</div>
+
+
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Arsenij Ustjanzew, Jens Preussner, Mario Looso.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+</div>
+
+      </footer>
+   </div>
+
+  
+
+
+  </body>
+</html>
+
+
--- a/docs/android-icon-144x144.png
+++ b/docs/android-icon-144x144.png
--- a/docs/android-icon-192x192.png
+++ b/docs/android-icon-192x192.png
--- a/docs/android-icon-36x36.png
+++ b/docs/android-icon-36x36.png
--- a/docs/android-icon-48x48.png
+++ b/docs/android-icon-48x48.png
--- a/docs/android-icon-72x72.png
+++ b/docs/android-icon-72x72.png
--- a/docs/android-icon-96x96.png
+++ b/docs/android-icon-96x96.png
--- a/docs/apple-icon-114x114.png
+++ b/docs/apple-icon-114x114.png
--- a/docs/apple-icon-120x120.png
+++ b/docs/apple-icon-120x120.png
--- a/docs/apple-icon-144x144.png
+++ b/docs/apple-icon-144x144.png
--- a/docs/apple-icon-152x152.png
+++ b/docs/apple-icon-152x152.png
--- a/docs/apple-icon-180x180.png
+++ b/docs/apple-icon-180x180.png
--- a/docs/apple-icon-57x57.png
+++ b/docs/apple-icon-57x57.png
--- a/docs/apple-icon-60x60.png
+++ b/docs/apple-icon-60x60.png
--- a/docs/apple-icon-72x72.png
+++ b/docs/apple-icon-72x72.png
--- a/docs/apple-icon-76x76.png
+++ b/docs/apple-icon-76x76.png
No results found