create project with renv, add support for SVG

.gitignore

@@ -1,3 +1,4 @@
 
 .Rhistory
 rsconnect/shinyapps.io/goedhart/VolcaNoseR.dcf
+.Rproj.user

README.md

@@ -1,27 +1,23 @@
 # VolcaNoseR
-A Shiny App for making Volcano plots
-
+A Shiny App for making Volcano plots based on [VolcaNoseR](https://github.com/JoachimGoedhart/VolcaNoseR/)
 
 ### Running the App
 
-The web-tool runs from a shiny server, and can be accessed at:
-
-o [https://huygens.science.uva.nl/VolcaNoseR/](https://huygens.science.uva.nl/VolcaNoseR/)
-
-o [https://goedhart.shinyapps.io/VolcaNoseR/](https://goedhart.shinyapps.io/VolcaNoseR/), while bandwidth lasts
-
-Alternatively, the app can run from R/Rstudio and this is perhaps the best option for loading large files. See instructions below
+o [Check](https://fuzzylife.shinyapps.io/VolcaNoseR/), while bandwidth lasts
 
-#### Preparations
-Note that the app depends on several R packages that need to be installed (shiny, ggplot2, dplyr, magrittr, ggrepel, DT, shinycssloaders, RCurl, readxl). 
-
-Run this command in R/Rstudio to download and install all the packages (only needs to be done once):
+#### Server 
+o [Install](https://rstudio.com/products/shiny/download-server/ubuntu/)
+```
+sudo su - -c "R -e \"install.packages(c('ggplot2','dplyr','ggrepel','shinycssloaders','readxl','DT', 'RCurl','svglite')repos='https://cran.rstudio.com/')\""
 ```
-install.packages("shiny", "ggplot2", "dplyr", "magrittr", "ggrepel", "DT", "shinycssloaders", "RCurl", "readxl")
+o log monitor *example*
 ```
+tail -f /var/log/shiny-server/VolcaNoseR-shiny-*.log
+```
+
 o The first option is running it directly from Github. In the command line (in R or Rstudio) type:
 ```
-shiny::runGitHub('VolcaNoseR', 'JoachimGoedhart')
+shiny::runGitHub('VolcaNoseR', 'animesh')
 ```
 o The second option is download the app and to use it offline:
 

VolcaNoseR.Rproj

@@ -0,0 +1,16 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 12
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+QuitChildProcessesOnExit: Yes
+DisableExecuteRprofile: Yes

app.R

@@ -25,6 +25,7 @@ options(shiny.maxRequestSize=10*1024^2)
 #Load necessary packages
 
 library(shiny)
+library(svglite)
 library(ggplot2)
 library(magrittr)
 library(dplyr)
@@ -344,7 +345,7 @@ ui <- fluidPage(
  tabPanel("Plot",h3("Volcano Plot"
  ),
  downloadButton("downloadPlotPDF", "Download pdf-file"),
- # downloadButton("downloadPlotSVG", "Download svg-file"),
+ downloadButton("downloadPlotSVG", "Download svg-file"),
  downloadButton("downloadPlotPNG", "Download png-file"),
 
  actionButton("settings_copy", icon = icon("clone"),
@@ -1392,21 +1393,32 @@ output$hover_info <- renderUI({
 
  ######### DEFINE DOWNLOAD BUTTONS FOR ORDINARY PLOT ###########
 
- output$downloadPlotPDF <- downloadHandler(
- filename <- function() {
- paste("VolcaNoseR_", Sys.time(), ".pdf", sep = "")
- },
- content <- function(file) {
- pdf(file, width = input$plot_width/72, height = input$plot_height/72)
- plot(plot_data())
-
- dev.off()
- },
- contentType = "application/pdf" # MIME type of the image
- )
-
-
- output$downloadPlotPNG <- downloadHandler(
+output$downloadPlotPDF <- downloadHandler(
+ filename <- function() {
+ paste("VolcaNoseR_", Sys.time(), ".pdf", sep = "")
+ },
+ content <- function(file) {
+ pdf(file, width = input$plot_width/72, height = input$plot_height/72)
+ plot(plot_data())
+
+ dev.off()
+ },
+ contentType = "application/pdf" # MIME type of the image
+)
+
+
+output$downloadPlotSVG <- downloadHandler(
+ filename <- function() {
+ paste("VolcaNoseR_", Sys.Date(), ".svg", sep = "")
+ },
+ content <- function(file) {
+ ggplot2::ggsave(file=file,plot=plot_data())
+ },
+ contentType = "application/svg" # MIME type of the image
+)
+
+
+output$downloadPlotPNG <- downloadHandler(
  filename <- function() {
  paste("VolcaNoseR_", Sys.time(), ".png", sep = "")
  },

rsconnect/shinyapps.io/fuzzylife/VolcanoseR.dcf

@@ -0,0 +1,12 @@
+name: VolcanoseR
+title: VolcanoseR
+username:
+account: fuzzylife
+server: shinyapps.io
+hostUrl: https://api.shinyapps.io/v1
+appId: 3388466
+bundleId: 3975914
+url: https://fuzzylife.shinyapps.io/VolcaNoseR/
+when: 1607704032.45113
+asMultiple: FALSE
+asStatic: FALSE