Deploy demos to shinyapps.io (#24)

* Move files around

* Consolidate some demos

README.Rmd

@@ -27,7 +27,6 @@ Using JBrowseR, you can:
 - Deploy a genome browser directly from the R console to view your data
 - Customize your genome browser to display your own data
 
-With this functionality, you can deploy a first-class genome browser with your data in just a few lines of R code!
 
 ## Installation
 
@@ -49,8 +48,7 @@ This line of code can be used to launch a genome browser from your R console:
 
 ```{r example, eval=FALSE}
 library(JBrowseR)
-JBrowseR("ViewHg19",
- location = "10:29,838,737..29,838,819")
+JBrowseR("ViewHg19", location = "10:29,838,737..29,838,819")
 ```
 
 <img src="man/figures/README-example-1.png" width="100%" />
@@ -64,6 +62,40 @@ In order to get started with JBrowseR, please refer to the vignette that best su
 - [JSON configuration tutorial](https://gmod.github.io/JBrowseR/articles/json-tutorial.html)
 - [Creating URLS](https://gmod.github.io/JBrowseR/articles/creating-urls.html)
 
+## Live demos
+
+
+### Basic usage including text search index
+
+Allows you to search by gene name
+
+https://gmod.shinyapps.io/basic_usage_with_text_index
+
+### Multi purpose demo app
+
+Shows a "bookmark" type feature, loading data from data frame, and buttons to navigate to genes of interest
+
+https://gmod.shinyapps.io/bookmarks_demo
+
+### Load config.json file
+
+Shows loading a config.json file
+
+https://gmod.shinyapps.io/load_config_json
+
+### Load data frame
+
+Simple example showing a data frame as a track
+
+https://gmod.shinyapps.io/load_data_frame
+
+### Gene fusion example
+
+Shows putative gene fusions in the SKBR3 breast cancer cell line
+
+https://gmod.shinyapps.io/skbr3_gene_fusions
+
+
 ## Citation
 
 If you use JBrowseR in your research, please cite the following publication:

README.md

@@ -1,72 +1,105 @@
+---
+output: github_document
+---
+
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
+
+
 # JBrowseR <img src='man/figures/logo.png' align="right" height="136" />
 
 <!-- badges: start -->
-
 [![R-CMD-check](https://github.com/GMOD/JBrowseR/workflows/R-CMD-check/badge.svg)](https://github.com/gmod/JBrowseR/actions)
-[![CRAN
-status](https://www.r-pkg.org/badges/version/JBrowseR)](https://CRAN.R-project.org/package=JBrowseR)
-
+[![CRAN status](https://www.r-pkg.org/badges/version/JBrowseR)](https://CRAN.R-project.org/package=JBrowseR)
 <!-- badges: end -->
 
-JBrowseR is an R package that provides a simple and clean interface to
-[JBrowse 2](https://jbrowse.org/jb2/) for R users. Using JBrowseR, you can:
+JBrowseR is an R package that provides a simple and clean interface to [JBrowse 2](https://jbrowse.org/jb2/) for R users.
+Using JBrowseR, you can:
 
-- Embed the JBrowse 2 genome browser in **R Markdown** documents and **Shiny
- applications**
+- Embed the JBrowse 2 genome browser in **R Markdown** documents and **Shiny applications**
 - Deploy a genome browser directly from the R console to view your data
 - Customize your genome browser to display your own data
 
-With this functionality, you can deploy a first-class genome browser with your
-data in just a few lines of R code!
 
 ## Installation
 
-You can install the released version of JBrowseR from
-[CRAN](https://CRAN.R-project.org) with:
+You can install the released version of JBrowseR from [CRAN](https://CRAN.R-project.org) with:
 
-```r
+``` r
 install.packages("JBrowseR")
 ```
 
 And the development version from [GitHub](https://github.com/) with:
 
-```r
+``` r
 # install.packages("devtools")
 devtools::install_github("gmod/JBrowseR")
 ```
-
 ## Example
 
 This line of code can be used to launch a genome browser from your R console:
 
+
 ```r
 library(JBrowseR)
-JBrowseR("ViewHg19",
- location = "10:29,838,737..29,838,819")
+JBrowseR("ViewHg19", location = "10:29,838,737..29,838,819")
 ```
 
 <img src="man/figures/README-example-1.png" width="100%" />
 
 ## Getting started
 
-In order to get started with JBrowseR, please refer to the vignette that best
-suits your needs:
+In order to get started with JBrowseR, please refer to the vignette that best suits your needs:
 
 - [Introduction](https://gmod.github.io/JBrowseR/articles/JBrowseR.html)
 - [Custom browser tutorial](https://gmod.github.io/JBrowseR/articles/custom-browser-tutorial.html)
 - [JSON configuration tutorial](https://gmod.github.io/JBrowseR/articles/json-tutorial.html)
-- [Creating URLs](https://gmod.github.io/JBrowseR/articles/creating-urls.html)
+- [Creating URLS](https://gmod.github.io/JBrowseR/articles/creating-urls.html)
+
+## Live demos
+
+
+### Basic usage including text search index
+
+Allows you to search by gene name
+
+https://gmod.shinyapps.io/basic_usage_with_text_index
+
+### Multi purpose demo app
+
+Shows a "bookmark" type feature, loading data from data frame, and buttons to navigate to genes of interest
+
+https://gmod.shinyapps.io/bookmarks_demo
+
+### Load config.json file
+
+Shows loading a config.json file
+
+https://gmod.shinyapps.io/load_config_json
+
+### Load data frame
+
+Simple example showing a data frame as a track
+
+https://gmod.shinyapps.io/load_data_frame
+
+### Gene fusion example
+
+Shows putative gene fusions in the SKBR3 breast cancer cell line
+
+https://gmod.shinyapps.io/skbr3_gene_fusions
+
 
 ## Citation
 
 If you use JBrowseR in your research, please cite the following publication:
 
 [Hershberg et al., 2021. JBrowseR: An R Interface to the JBrowse 2 Genome Browser](https://doi.org/10.1093/bioinformatics/btab459)
 
- @article{hershberg2021jbrowser,
-  title={JBrowseR: An R Interface to the JBrowse 2 Genome Browser},
-  author={Hershberg, Elliot A and Stevens, Garrett and Diesh, Colin and Xie, Peter and De Jesus Martinez, Teresa and Buels, Robert and Stein, Lincoln and Holmes, Ian},
-  journal={Bioinformatics}
- }
+```
+@article{hershberg2021jbrowser,
+ title={JBrowseR: An R Interface to the JBrowse 2 Genome Browser},
+ author={Hershberg, Elliot A and Stevens, Garrett and Diesh, Colin and Xie, Peter and De Jesus Martinez, Teresa and Buels, Robert and Stein, Lincoln and Holmes, Ian},
+ journal={Bioinformatics}
+}
+```

example_apps/.gitignore

@@ -0,0 +1 @@
+*.dcf

example_apps/README.md

@@ -0,0 +1,21 @@
+## Install deps
+
+```R
+
+install.packages(c('JBrowseR','crosstalk','DT'))
+```
+
+### Deploy
+
+```R
+deployApp('example_apps/basic_usage_with_text_index',account='gmod')
+deployApp('example_apps/bookmarks_demo',account='gmod')
+deployApp('example_apps/load_config_json',account='gmod')
+deployApp('example_apps/load_data_frame',account='gmod')
+deployApp('example_apps/skbr3_gene_fusions',account='gmod')
+
+```
+
+Regex to generate above list of commands
+
+'<,'>s/^\(.\*\)/deployApp('example_apps\/\1',account='gmod')

example_apps/hg38_index_app.R → example_apps/basic_usage_with_text_index/app.R

@@ -1,8 +1,13 @@
 library(shiny)
 library(JBrowseR)
+library(bslib)
 
-ui <- fluidPage(titlePanel("JBrowseR Example"),
- JBrowseROutput("widgetOutput"))
+ui <- fluidPage(
+ # Overriding the default bootstrap theme is needed to get proper font size
+ theme = bs_theme(version = 5),
+ titlePanel("JBrowseR Example"),
+ JBrowseROutput("widgetOutput")
+)
 
 server <- function(input, output, session) {
  hg38 <- assembly(

example_apps/bookmarks_demo/README.md

@@ -0,0 +1,16 @@
+# JBrowse R Demo (with Shiny)
+
+See this app running at https://cbridge.shinyapps.io/jbrowse-r-shiny/
+
+This demo is originally by
+[Caroline Bridge](https://github.com/carolinebridge-oicr) with components by
+[Elliot Hershberg](https://github.com/elliothershberg).
+
+Download this directory from the monorepo using
+https://download-directory.github.io/?url=https://github.com/GMOD/jbrowse-components/tree/main/embedded_demos/jbrowse-r-shiny
+
+## Usage
+
+On the command line:
+
+`Rscript app.R`