Consolidate some demos

GMOD · Jul 13, 2023 · 4f58970 · 4f58970
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diff --git a/README.Rmd b/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:

diff --git a/README.md b/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}
+}
+```
diff --git a/example_apps/README.md b/example_apps/README.md
@@ -8,14 +8,14 @@ install.packages(c('JBrowseR','crosstalk','DT'))
 ### Deploy
 
 ```R
-
-deployApp('example_apps/basic_usage',account='gmod')
-deployApp('example_apps/bookmarks',account='gmod')
-deployApp('example_apps/custom_theme',account='gmod')
-deployApp('example_apps/hg38_demo',account='gmod')
+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/load_json',account='gmod')
-deployApp('example_apps/multi',account='gmod')
 deployApp('example_apps/skbr3_gene_fusions',account='gmod')
 
 ```
+
+Regex to generate above list of commands
+
+'<,'>s/^\(.\*\)/deployApp('example_apps\/\1',account='gmod')
diff --git a/example_apps/basic_usage/app.R b/example_apps/basic_usage/app.R
diff --git a/example_apps/hg38_demo/app.R → ...le_apps/basic_usage_with_text_index/app.R b/example_apps/hg38_demo/app.R → ...le_apps/basic_usage_with_text_index/app.R
diff --git a/example_apps/bookmarks/app.R b/example_apps/bookmarks/app.R
diff --git a/example_apps/multi/README.md → example_apps/bookmarks_demo/README.md b/example_apps/multi/README.md → example_apps/bookmarks_demo/README.md
diff --git a/example_apps/multi/app.R → example_apps/bookmarks_demo/app.R b/example_apps/multi/app.R → example_apps/bookmarks_demo/app.R
diff --git a/example_apps/custom_theme/app.R b/example_apps/custom_theme/app.R
diff --git a/example_apps/load_json/app.R → example_apps/load_config_json/app.R b/example_apps/load_json/app.R → example_apps/load_config_json/app.R
diff --git a/example_apps/load_json/config.json → example_apps/load_config_json/config.json b/example_apps/load_json/config.json → example_apps/load_config_json/config.json