Rename to JBrowseR

.Rbuildignore

@@ -1,4 +1,4 @@
-^RBrowse\.Rproj$
+^JBrowseR\.Rproj$
 ^\.Rproj\.user$
 ^node_modules$
 ^srcjs$
@@ -7,7 +7,7 @@
 ^webpack\.config\.js$
 ^yarn\.lock$
 ^LICENSE\.md$
-^inst/htmlwidgets/RBrowse\.js\.map$
+^inst/htmlwidgets/JBrowseR\.js\.map$
 ^config\.json$
 ^custom_app\.R$
 ^json_app\.R$

DESCRIPTION

@@ -1,13 +1,17 @@
-Package: RBrowse
-Title: What the Package Does (One Line, Title Case)
-Version: 0.0.0.9000
+Package: JBrowseR
+Title: An R interface to the JBrowse 2 Genome Browser
+Version: 0.7.0.9000
 Authors@R: 
-    person(given = "First",
-           family = "Last",
+    person(given = "Elliot",
+           family = "Hershberg",
            role = c("aut", "cre"),
-           email = "[email protected]",
-           comment = c(ORCID = "YOUR-ORCID-ID"))
-Description: What the package does (one paragraph).
+           email = "[email protected]",
+           comment = c(ORCID = "https://orcid.org/0000-0003-2068-3366"))
+Description: Provides an R interface to the JBrowse 2 genome browser.
+    Enables embedding a JB2 genome browser in a Shiny app or RMarkdown
+    document. The browser can also be launced from an interactive R console.
+    The browser can be loaded with a variety of common genomics data types,
+    and can be used with a custom theme.
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true

LICENSE

@@ -1,2 +1,2 @@
 YEAR: 2021
-COPYRIGHT HOLDER: RBrowse authors
+COPYRIGHT HOLDER: jBrowseR authors

LICENSE.md

@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2021 RBrowse authors
+Copyright (c) 2021 JBrowseR authors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

NAMESPACE

@@ -1,12 +1,12 @@
 # Generated by roxygen2: do not edit by hand
 
 export("%>%")
-export(RBrowse)
-export(RBrowseOutput)
+export(JBrowseR)
+export(JBrowseROutput)
 export(assembly)
 export(default_session)
 export(json_config)
-export(renderRBrowse)
+export(renderJBrowseR)
 export(theme)
 export(track_alignments)
 export(track_feature)

R/RBrowse.R → R/JBrowseR.R

@@ -11,49 +11,49 @@
 #'
 #' @import htmlwidgets
 #' @export
-RBrowse <- function(view, ..., width = NULL, height = NULL, elementId = NULL) {
+JBrowseR <- function(view, ..., width = NULL, height = NULL, elementId = NULL) {
 
   # describe a React component to send to the browser for rendering.
   component <- reactR::component(view, list(...))
 
   # create widget
   htmlwidgets::createWidget(
-    name = "RBrowse",
+    name = "JBrowseR",
     reactR::reactMarkup(component),
     width = width,
     height = height,
-    package = "RBrowse",
+    package = "JBrowseR",
     elementId = elementId
   )
 }
 
-#' Shiny bindings for RBrowse
+#' Shiny bindings for JBrowseR
 #'
-#' Output and render functions for using RBrowse within Shiny
+#' Output and render functions for using JBrowseR within Shiny
 #' applications and interactive Rmd documents.
 #'
 #' @param outputId output variable to read from
 #' @param width Must be a valid CSS unit or a number, which will be coerced to a string and have \code{'px'} appended.
 #' @param height Must be a valid CSS unit or a number, which will be coerced to a string and have \code{'px'} appended.
-#' @param expr An expression that generates a RBrowse
+#' @param expr An expression that generates a JBrowseR
 #' @param env The environment in which to evaluate \code{expr}.
 #' @param quoted Is \code{expr} a quoted expression (with \code{quote()})? This
 #'   is useful if you want to save an expression in a variable.
 #'
-#' @name RBrowse-shiny
+#' @name JBrowseR-shiny
 #'
 #' @export
-RBrowseOutput <- function(outputId, width = "100%", height = "400px") {
-  htmlwidgets::shinyWidgetOutput(outputId, "RBrowse", width, height, package = "RBrowse")
+JBrowseROutput <- function(outputId, width = "100%", height = "400px") {
+  htmlwidgets::shinyWidgetOutput(outputId, "JBrowseR", width, height, package = "JBrowseR")
 }
 
-#' @rdname RBrowse-shiny
+#' @rdname JBrowseR-shiny
 #' @export
-renderRBrowse <- function(expr, env = parent.frame(), quoted = FALSE) {
+renderJBrowseR <- function(expr, env = parent.frame(), quoted = FALSE) {
   if (!quoted) {
     expr <- substitute(expr)
   } # force quoted
-  htmlwidgets::shinyRenderWidget(expr, RBrowseOutput, env, quoted = TRUE)
+  htmlwidgets::shinyRenderWidget(expr, JBrowseROutput, env, quoted = TRUE)
 }
 
 #' Called by HTMLWidgets to produce the widget's root element.
@@ -63,8 +63,8 @@ renderRBrowse <- function(expr, env = parent.frame(), quoted = FALSE) {
 #' @param class htmltools class
 #' @param ... Additional arguments passed on
 #'
-#' @rdname RBrowse-shiny
-RBrowse_html <- function(id, style, class, ...) {
+#' @rdname JBrowseR-shiny
+JBrowseR_html <- function(id, style, class, ...) {
   htmltools::tagList(
     # Necessary for RStudio viewer version < 1.2
     reactR::html_dependency_corejs(),

R/assembly.R

@@ -38,7 +38,7 @@
 #'   name aliases. For more info see
 #'   \url{https://jbrowse.org/jb2/docs/config_guide#configuring-reference-name-aliasing}
 #'
-#' @return a string of RBrowse assembly configuration
+#' @return a string of JBrowseR assembly configuration
 #' @export
 #'
 #' @examples

README.Rmd

@@ -16,7 +16,7 @@ knitr::opts_chunk$set(
 # JBrowseR <img src='man/figures/logo.png' align="right" height="136" />
 
 <!-- badges: start -->
-[![R-CMD-check](https://github.com/elliothershberg/RBrowse/workflows/R-CMD-check/badge.svg)](https://github.com/elliothershberg/RBrowse/actions)
+[![R-CMD-check](https://github.com/elliothershberg/JBrowseR/workflows/R-CMD-check/badge.svg)](https://github.com/elliothershberg/JBrowseR/actions)
 <!-- badges: end -->
 
 JBrowseR is an R package that provides a simple and clean interface to [JBrowse 2](https://jbrowse.org/jb2/) for R users.
@@ -30,25 +30,25 @@ With this functionality, you can deploy a first-class genome browser with your d
 
 ## Installation
 
-You can **soon** install the released version of RBrowse from [CRAN](https://CRAN.R-project.org) with:
+You can **soon** install the released version of JBrowseR from [CRAN](https://CRAN.R-project.org) with:
 
 ``` r
-install.packages("RBrowse")
+install.packages("JBrowseR")
 ```
 
 And the development version from [GitHub](https://github.com/) with:
 
 ``` r
 # install.packages("devtools")
-devtools::install_github("elliothershberg/RBrowse")
+devtools::install_github("elliothershberg/JBrowseR")
 ```
 ## Example
 
 This line of code can be a used to launch a genome browser from your R console:
 
 ```{r example, eval=FALSE}
-library(RBrowse)
-RBrowse("ViewHg19",
+library(JBrowseR)
+JBrowseR("ViewHg19",
         location = "10:29,838,737..29,838,819")
 ```
 

README.md

@@ -5,7 +5,7 @@
 
 <!-- badges: start -->
 
-[![R-CMD-check](https://github.com/elliothershberg/RBrowse/workflows/R-CMD-check/badge.svg)](https://github.com/elliothershberg/RBrowse/actions)
+[![R-CMD-check](https://github.com/elliothershberg/JBrowseR/workflows/R-CMD-check/badge.svg)](https://github.com/elliothershberg/JBrowseR/actions)
 <!-- badges: end -->
 
 JBrowseR is an R package that provides a simple and clean interface to
@@ -23,18 +23,18 @@ with your data in just a few lines of R code!
 
 ## Installation
 
-You can **soon** install the released version of RBrowse from
+You can **soon** install the released version of JBrowseR from
 [CRAN](https://CRAN.R-project.org) with:
 
 ``` r
-install.packages("RBrowse")
+install.packages("JBrowseR")
 ```
 
 And the development version from [GitHub](https://github.com/) with:
 
 ``` r
 # install.packages("devtools")
-devtools::install_github("elliothershberg/RBrowse")
+devtools::install_github("elliothershberg/JBrowseR")
 ```
 
 ## Example
@@ -43,8 +43,8 @@ This line of code can be a used to launch a genome browser from your R
 console:
 
 ``` r
-library(RBrowse)
-RBrowse("ViewHg19",
+library(JBrowseR)
+JBrowseR("ViewHg19",
         location = "10:29,838,737..29,838,819")
 ```
 

_pkgdown.yml

@@ -1 +1 @@
-url: https://elliothershberg.github.io/RBrowse
+url: https://elliothershberg.github.io/JBrowseR

app.R

@@ -1,11 +1,11 @@
 library(shiny)
-library(RBrowse)
+library(JBrowseR)
 
-ui <- fluidPage(titlePanel("RBrowse Example"),
-                RBrowseOutput('widgetOutput'))
+ui <- fluidPage(titlePanel("JBrowseR Example"),
+                JBrowseROutput('widgetOutput'))
 
 server <- function(input, output, session) {
-  output$widgetOutput <- renderRBrowse(RBrowse("ViewHg19",
+  output$widgetOutput <- renderJBrowseR(JBrowseR("ViewHg19",
                                                location = "10:29,838,737..29,838,819"))
 }
 

custom_app.R

@@ -1,9 +1,9 @@
 library(shiny)
-library(RBrowse)
+library(JBrowseR)
 
 ui <- fluidPage(
   titlePanel("JBrowseR Example"),
-  RBrowseOutput("widgetOutput")
+  JBrowseROutput("widgetOutput")
 )
 
 server <- function(input, output, session) {
@@ -51,8 +51,8 @@ server <- function(input, output, session) {
   # create a custom color palette theme for the browser
   theme <- theme("#311b92", "#0097a7", "#f57c00", "#d50000")
 
-  output$widgetOutput <- renderRBrowse(
-    RBrowse("View",
+  output$widgetOutput <- renderJBrowseR(
+    JBrowseR("View",
       assembly = assembly,
       tracks = tracks,
       location = "10:31,419,497..33,370,375",

json_app.R

@@ -1,16 +1,16 @@
 library(shiny)
-library(RBrowse)
+library(JBrowseR)
 
 ui <- fluidPage(
   titlePanel("JSON JBrowseR Example"),
-  RBrowseOutput("widgetOutput")
+  JBrowseROutput("widgetOutput")
 )
 
 server <- function(input, output, session) {
   config <- json_config("./config.json")
 
-  output$widgetOutput <- renderRBrowse(
-    RBrowse("JsonView",
+  output$widgetOutput <- renderJBrowseR(
+    JBrowseR("JsonView",
             config = config,
             location = "10:29,838,737..29,838,819"
     )

srcjs/RBrowse.jsx → srcjs/JBrowseR.jsx

@@ -4,4 +4,4 @@ import ViewHg19 from "./components/ViewHg19";
 import View from "./components/View"
 import JsonView from "./components/JsonView"
 
-reactWidget("RBrowse", "output", { ViewHg38, ViewHg19, View, JsonView });
+reactWidget("JBrowseR", "output", { ViewHg38, ViewHg19, View, JsonView });

tests/testthat.R

@@ -1,4 +1,4 @@
 library(testthat)
-library(RBrowse)
+library(JBrowseR)
 
-test_check("RBrowse")
+test_check("JBrowseR")

webpack.config.js

@@ -3,10 +3,10 @@ var CompressionPlugin = require("compression-webpack-plugin");
 
 module.exports = {
     mode: 'production',
-    entry: ['@babel/polyfill', path.join(__dirname, 'srcjs', 'RBrowse.jsx')],
+    entry: ['@babel/polyfill', path.join(__dirname, 'srcjs', 'JBrowseR.jsx')],
     output: {
         path: path.join(__dirname, 'inst/htmlwidgets'),
-        filename: 'RBrowse.js'
+        filename: 'JBrowseR.js'
     },
     module: {
         rules: [