Merge branch 'update0.1' into 'master'

Update0.1

See merge request !35

DESCRIPTION

 Package: i2dash
 Type: Package
 Title: Iterative and Interactive Dashboards
-Version: 0.2
+Version: 0.2.1
 Authors@R: c(
     person(given = "Arsenij", family = "Ustjanzew", email = "arsenij.ustjanzew@mpi-bn.mpg.de", role = c("aut", "cre", "cph")),
     person(given = "Jens", family = "Preussner", email = "jens.preussner@mpi-bn.mpg.de", role = c("aut", "cph"), comment = c(ORCID = "0000-0003-1927-3458")),

README.md

@@ -34,6 +34,18 @@ It is possible to extend the core functionality of **i2dash** with templates for
 
 - [**i2dash.scrnaseq**](https://gitlab.gwdg.de/loosolab/software/i2dash.scrnaseq) enables an enhanced user interactivity and contains simple but effective tools for the creation of an i2dashboard with focus on single-cell RNA-sequencing data visualization and exploration.
 
+## Run i2dash using Docker
+
+At first, install [Docker](https://docs.docker.com/engine/install/). Then pull the image of **i2dash**:
+
+`docker pull docker.gitlab.gwdg.de/loosolab/container/i2dash.deployment:r3.6.3_bioc3.10`
+
+The next step is to run a container and simultaneously load the dashboard files (the `.Rmd` file and all files of the `datadir(dashboard)` directory) into the container. To mount custom data into the container, make use of Docker's `-v` parameter to mount a host directory into the container. Inside the container, **i2dash** looks for external datasets in `/srv/shiny-server/`. Use the following code, where you exchange `/path/to/dashboard/files` with the respective path to the directory containing the `.Rmd` file and all files of the `datadir(dashboard)` directory.
+
+```docker run -d -p 3838:3838 -v '/path/to/dashboard/files':'/srv/shiny-server' docker.gitlab.gwdg.de/loosolab/container/i2dash.deployment:r3.6.3_bioc3.10```
+
+Now, view the dashboard with your browser at `3838:3838`.
+
 ## How to cite
 
 If you use **i2dash** or **i2dash.scrnaseq** in your work, please cite:
@@ -43,3 +55,7 @@ Ustjanzew A., Preussner J., Bentsen M., Kuenne C., and Looso M. i2dash: creation
 ## License
 
 This project is licensed under the MIT license.
+
+## FAQ
+
+- **The Rmd file of the dashboard contains pages and components but after rendering the dashboard remains empty:** Make sure you have a current version of pandoc installed and view the dashboard only with a modern browser.

docs/authors.html

@@ -142,15 +142,15 @@
 
     <ul class="list-unstyled">
       <li>
-        <p><strong>Arsenij Ustjanzew</strong>. Author, maintainer. 
+        <p><strong>Arsenij Ustjanzew</strong>. Author, maintainer, copyright holder. 
         </p>
       </li>
       <li>
-        <p><strong>Jens Preussner</strong>. Author. <a href='https://orcid.org/0000-0003-1927-3458' target='orcid.widget' aria-label='ORCID'><span class='fab fa-orcid orcid' aria-hidden='true'></span></a>
+        <p><strong>Jens Preussner</strong>. Author, copyright holder. <a href='https://orcid.org/0000-0003-1927-3458' target='orcid.widget' aria-label='ORCID'><span class='fab fa-orcid orcid' aria-hidden='true'></span></a>
         </p>
       </li>
       <li>
-        <p><strong>Mario Looso</strong>. Author. <a href='https://orcid.org/0000-0003-1495-9530' target='orcid.widget' aria-label='ORCID'><span class='fab fa-orcid orcid' aria-hidden='true'></span></a>
+        <p><strong>Mario Looso</strong>. Author, copyright holder. <a href='https://orcid.org/0000-0003-1495-9530' target='orcid.widget' aria-label='ORCID'><span class='fab fa-orcid orcid' aria-hidden='true'></span></a>
         </p>
       </li>
     </ul>

docs/index.html

@@ -5,7 +5,7 @@
 <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>Iterative and Interactive Dashboards in R • i2dash</title>
+<title>Iterative and Interactive Dashboards • 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">
@@ -17,8 +17,8 @@
 <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="Iterative and Interactive Dashboards in R">
-<meta property="og:description" content="Easily build dashboards from individual components in HTML and Shiny.">
+<script src="pkgdown.js"></script><meta property="og:title" content="Iterative and Interactive Dashboards">
+<meta property="og:description" content="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.">
 <!-- 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>
@@ -77,12 +77,12 @@
 
       </header><div class="row">
   <div class="contents col-md-9">
-<div id="interactive-iterative-dashboards-in-r" class="section level1">
+<div id="interactive--iterative-dashboards-in-r" class="section level1">
 <div class="page-header"><h1 class="hasAnchor">
-<a href="#interactive-iterative-dashboards-in-r" class="anchor"></a>Interactive &amp; iterative dashboards in R</h1></div>
-<div id="abstract" class="section level2">
+<a href="#interactive--iterative-dashboards-in-r" class="anchor"></a>Interactive &amp; iterative dashboards in R</h1></div>
+<div id="abstract-" class="section level2">
 <h2 class="hasAnchor">
-<a href="#abstract" class="anchor"></a>Abstract <img src="articles/images/i2dash_logo.png" align="right" width="150px">
+<a href="#abstract-" class="anchor"></a>Abstract <img src="articles/images/i2dash_logo.png" align="right" width="150px">
 </h2>
 <p>Scientific communication and data visualization are important aspects to illustrate complex concepts and results from data analyses. The R package <strong>i2dash</strong> provides functionality to create customized, web-based dashboards for data presentation, exploration and sharing. <strong>i2dash</strong> integrates easily into existing data analysis pipelines and can organize scientific findings thematically across different pages and layouts.</p>
 <div id="main-features" class="section level3">
@@ -112,6 +112,23 @@
 <a href="https://gitlab.gwdg.de/loosolab/software/i2dash.scrnaseq"><strong>i2dash.scrnaseq</strong></a> enables an enhanced user interactivity and contains simple but effective tools for the creation of an i2dashboard with focus on single-cell RNA-sequencing data visualization and exploration.</li>
 </ul>
 </div>
+<div id="run-i2dash-using-docker" class="section level2">
+<h2 class="hasAnchor">
+<a href="#run-i2dash-using-docker" class="anchor"></a>Run i2dash using Docker</h2>
+<p>At first, install <a href="https://docs.docker.com/engine/install/">Docker</a>. Then pull the image of <strong>i2dash</strong>:</p>
+<p><code>docker pull docker.gitlab.gwdg.de/loosolab/container/i2dash.deployment:r3.6.3_bioc3.10</code></p>
+<p>The next step is to run a container and simultaneously load the dashboard files (the <code>.Rmd</code> file and all files of the <code><a href="reference/i2dashboard-methods.html">datadir(dashboard)</a></code> directory) into the container. To mount custom data into the container, make use of Docker’s <code>-v</code> parameter to mount a host directory into the container. Inside the container, <strong>i2dash</strong> looks for external datasets in <code>/srv/shiny-server/</code>. Use the following code, where you exchange <code>/path/to/dashboard/files</code> with the respective path to the directory containing the <code>.Rmd</code> file and all files of the <code><a href="reference/i2dashboard-methods.html">datadir(dashboard)</a></code> directory.</p>
+<p><code>docker run -d -p 3838:3838 -v '/path/to/dashboard/files':'/srv/shiny-server' docker.gitlab.gwdg.de/loosolab/container/i2dash.deployment:r3.6.3_bioc3.10</code></p>
+<p>Now, view the dashboard with your browser at <code>3838:3838</code>.</p>
+</div>
+<div id="faq" class="section level2">
+<h2 class="hasAnchor">
+<a href="#faq" class="anchor"></a>FAQ</h2>
+<ul>
+<li>
+<strong>The Rmd file of the dashboard contains pages and components but after rendering the dashboard remains empty:</strong> Make sure you have a current version of pandoc installed and view the dashboard only with a modern browser.</li>
+</ul>
+</div>
 </div>
   </div>
 
@@ -119,6 +136,8 @@
     <div class="links">
 <h2>Links</h2>
 <ul class="list-unstyled">
+<li>Download from CRAN at <br><a href="https://cloud.r-project.org/package=i2dash">https://​cloud.r-project.org/​package=i2dash</a>
+</li>
 <li>Visit our webpage at <br><a href="https://loosolab.mpi-bn.mpg.de">https://​loosolab.mpi-bn.mpg.de</a>
 </li>
 </ul>
@@ -139,9 +158,9 @@
 <div class="developers">
 <h2>Developers</h2>
 <ul class="list-unstyled">
-<li>Arsenij Ustjanzew <br><small class="roles"> Author, maintainer </small>  </li>
-<li>Jens Preussner <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0003-1927-3458" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
-<li>Mario Looso <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0003-1495-9530" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
+<li>Arsenij Ustjanzew <br><small class="roles"> Author, maintainer, copyright holder </small>  </li>
+<li>Jens Preussner <br><small class="roles"> Author, copyright holder </small> <a href="https://orcid.org/0000-0003-1927-3458" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
+<li>Mario Looso <br><small class="roles"> Author, copyright holder </small> <a href="https://orcid.org/0000-0003-1495-9530" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
 </ul>
 </div>
 

inst/templates/vis_object.Rmd

@@ -12,8 +12,10 @@ vis_<% component_id %> <- readRDS(file.path(datadir, '<% component_id %>.rds'))
 # workaround for plotly dependencies issue (https://github.com/ropensci/plotly/issues/1044)
 # 
 fix_dependency <- function(dependency){
-  if(dependency$name == "jquery") dependency$src$file <- file.path(system.file(package ="crosstalk"), "lib/jquery")
-  if(dependency$name == "crosstalk") dependency$src$file <- file.path(system.file(package ="crosstalk"), "www")
+  if(dependency$name == "crosstalk" & dependency$version == "1.1.0"){
+    if(dependency$name == "jquery") dependency$src$file <- file.path(system.file(package ="crosstalk"), "lib/jquery")
+    if(dependency$name == "crosstalk") dependency$src$file <- file.path(system.file(package ="crosstalk"), "www")
+  }
   return(dependency)
 }
 if ("<% package %>" == "plotly"){

pkgdown/index.md

@@ -26,3 +26,18 @@ It is possible to extend the core functionality of **i2dash** with templates for
 
 - [**i2dash.scrnaseq**](https://gitlab.gwdg.de/loosolab/software/i2dash.scrnaseq) enables an enhanced user interactivity and contains simple but effective tools for the creation of an i2dashboard with focus on single-cell RNA-sequencing data visualization and exploration.
 
+## Run i2dash using Docker
+
+At first, install [Docker](https://docs.docker.com/engine/install/). Then pull the image of **i2dash**:
+
+`docker pull docker.gitlab.gwdg.de/loosolab/container/i2dash.deployment:r3.6.3_bioc3.10`
+
+The next step is to run a container and simultaneously load the dashboard files (the `.Rmd` file and all files of the `datadir(dashboard)` directory) into the container. To mount custom data into the container, make use of Docker's `-v` parameter to mount a host directory into the container. Inside the container, **i2dash** looks for external datasets in `/srv/shiny-server/`. Use the following code, where you exchange `/path/to/dashboard/files` with the respective path to the directory containing the `.Rmd` file and all files of the `datadir(dashboard)` directory.
+
+```docker run -d -p 3838:3838 -v '/path/to/dashboard/files':'/srv/shiny-server' docker.gitlab.gwdg.de/loosolab/container/i2dash.deployment:r3.6.3_bioc3.10```
+
+Now, view the dashboard with your browser at `3838:3838`.
+
+## FAQ
+
+- **The Rmd file of the dashboard contains pages and components but after rendering the dashboard remains empty:** Make sure you have a current version of pandoc installed and view the dashboard only with a modern browser.

tests/testthat/test-assemble.R

@@ -13,8 +13,7 @@ test_that("Assembling dashboard is correct",{
   writeLines(new_rmd, temp)
 
   ref_hash <- digest::digest(file = temp, serialize = F, seed = 100)
-
-  expect_true(stringi::stri_detect_regex(ref_hash, "(1055ed29147446902eb224e7c17c52af|442bef06307bb6dea490435230f7e22e|11a5a0938212656d1fbb02496fb7cfa0)"))
+  expect_true(stringi::stri_detect_regex(ref_hash, "(1055ed29147446902eb224e7c17c52af|442bef06307bb6dea490435230f7e22e|11a5a0938212656d1fbb02496fb7cfa0|48152155fd455e7642da35e03f404dd5)"))
 
   expect_warning(assemble(dashboard, file = temp, pages = "page1"), "i2dashboard dashboard does not contain a page named 'page1'")
 })

vignettes/i2dash-intro.Rmd

@@ -93,7 +93,7 @@ With several accessor methods, it is also possible to change the slots `interact
 
 ```{r, eval=FALSE}
 interactivity(dashboard) <- TRUE
-datadir(dashboard) <- "getwd()"
+datadir(dashboard) <- getwd()
 theme(dashboard) <- "cosmo"
 author(dashboard) <- "John Doe, MaxMustermann"
 title(dashboard) <- "New dashboard title"