Bug fix: plot can be exported

Plots can be exported as png or pdf files

about.html

@@ -6,32 +6,44 @@
 
 
 <h3>About PlotsOfData</h3>
-<p>The PlotsOfData Shiny app plots the data and statistics to enable the comparison of (experimental) conditions. The philosophy of the approach is that plotting the raw data (instead of a summary) improves transparency and interpretation (see also <a href="http://thenode.biologists.com/leaving-bar-five-steps/">this blog</a>). To further facilitate the comparison, summary statistics (mean, median, boxplot) and inferential statistics (confidence intervals) can be added. The user has full control over the visibility of the raw data and statistics by adjustment of the transparency (alpha).</p>
-<p>Bootstrapping is used to calculate the (asymmetric) 95% CI of medians. More information in <a href="http://thenode.biologists.com/a-better-bar/education/">this blog</a> </p>
+<p>The PlotsOfData Shiny app plots the data and statistics to enable the comparison of (experimental) conditions. The philosophy of the approach is that plotting the raw data (instead of a summary) improves transparency and interpretation. To further facilitate the comparison, summary statistics (mean, median, boxplot, violinplot) and inferential statistics (confidence intervals) can be added. The user has full control over the visibility of the raw data and statistics by adjustment of the transparency (alpha). More details about the PlotsOfData app can be found in our <a href="https://doi.org/10.1101/426767">publication</a>.</br> </p>
 
-<p>The data can be supplied in spreadsheet/long format (e.g. by copy-pasting from excel) or in tidy format. For more information on the conversion of spreadsheet data to tidy data see <a href="http://thenode.biologists.com/converting-excellent-spreadsheets-tidy-data/education/">this blog</a>.</p>
 
+<h4>Source</h4>
+<p>PlotsOfData is created and maintained by Joachim Goedhart (<a href="https://twitter.com/joachimgoedhart">@joachimgoedhart</a>) and Marten Postma</br>
+
+Source code is available at <a href="https://github.com/JoachimGoedhart/PlotsOfData">github/JoachimGoedhart</a>
+</br>
+Please cite our work if you use the app: "PlotsOfData - a web app for visualizing data together with its summaries" - doi: <a href="https://doi.org/10.1101/426767">10.1101/426767</a>
+</br>
+
+</p>
 
-<p>The plot can be saved as a PDF file, which can be opened and edited with Adobe Illustrator to allow for fine adjustments of the lay-out.</p>
 
 <h4>Credits</h4>
 
-<p>PlotsOfData is inspired on <a href="http://shiny.chemgrid.org/boxplotr/">BoxPlotR</a>. See <a href="https://www.nature.com/articles/nmeth.2813">this link</a>
-  for background information on boxplots.</br>
+<p>PlotsOfData is inspired by <a href="http://shiny.chemgrid.org/boxplotr/">BoxPlotR</a></br>
 
 The code for the shiny app is partially derived from <a href="https://github.com/gertstulp/ggplotgui">ggplotGUI</a>
  by <a href="https://www.gertstulp.com">Gert Stulp</a></br>
-The colorblind safe palletes were developed by <a href="https://personal.sron.nl/~pault/">Paul Tol</a>.</p>
-
-<p>PlotsOfData is created and maintained by Joachim Goedhart (<a href="https://twitter.com/joachimgoedhart">@joachimgoedhart</a>) and Marten Postma
+The colorblind safe palettes were developed by <a href="https://personal.sron.nl/~pault/">Paul Tol</a>.</p>
 
 
-</p>
 
- </br>
-
 
+<h4>Further reading</h4>
+<p>Some aspects of the app are explained in <a href="http://thenode.biologists.com/author/joachimg/">blogs at The Node</a>:
+</br>
+<a href="http://thenode.biologists.com/leaving-bar-five-steps/">Leaving the bar</a> (On plotting the actual data rather than summaries)
+</br>
+<a href="http://thenode.biologists.com/a-better-bar/education/">A better bar</a> (Explains the calculation of 95% CI for the median)
+</br>
+<a href="http://thenode.biologists.com/converting-excellent-spreadsheets-tidy-data/education/">Converting excellent spreadsheets to tidy data</a> (An introduction to tidy data)
+</br>
+<a href="http://thenode.biologists.com/p-value-parroting/research/">Prevent p-value parroting</a> (Why not every graph needs a p-value)
+</br>
 
+</p>
 
 
 </html>

app.R

@@ -491,22 +491,35 @@ height <- reactive ({ input$plot_height })
 
 output$downloadPlotPDF <- downloadHandler(
   filename <- function() {
-    paste("ComparisonPlot_", Sys.time(), ".pdf", sep = "")
+    paste("PlotsOfData_", Sys.time(), ".pdf", sep = "")
+#    paste("PlotsOfData.pdf")
   },
   content <- function(file) {
-    ggsave(file, width = input$plot_width/72,
-           height = input$plot_height/72, dpi="retina")
+    pdf(file, width = input$myWidth/72, height = input$myHeight/72)
+    ## ---------------
+    plot(plotdata())
+    ## ---------------
+    dev.off()
+    # ggsave(file, width = input$plot_width/72,
+    #        height = input$plot_height/72, dpi="retina")
   },
   contentType = "application/pdf" # MIME type of the image
 )
 
 output$downloadPlotPNG <- downloadHandler(
   filename <- function() {
-    paste("ComparisonPlot_", Sys.time(), ".png", sep = "")
+    paste("PlotsOfData_", Sys.time(), ".png", sep = "")
   },
   content <- function(file) {
-    ggsave(file, width = input$plot_width/72,
-           height = input$plot_height/72)
+    png(file, width = input$plot_width*4, height = input$plot_height*4, res=300)
+    ## ---------------
+    plot(plotdata())
+    ## ---------------
+    dev.off()
+
+
+    # ggsave(file, width = input$plot_width/72,
+    #        height = input$plot_height/72)
   },
   contentType = "application/png" # MIME type of the image
 )
@@ -518,7 +531,7 @@ output$downloadPlotPNG <- downloadHandler(
 ######## PREPARE PLOT FOR DISPLAY ##########
  ###########################################
 
-output$coolplot <- renderPlot(width = width, height = height, {
+plotdata <- reactive({
 
 
 ####### Read the order from the ordered dataframe #############  
@@ -689,9 +702,20 @@ output$coolplot <- renderPlot(width = width, height = height, {
    }
 
     ### Output the plot ######
-    p
+    return(p)
 
-  }) #close output$coolplot
+  }) #close plotdata
+
+
+
+ ########################################
+##### Make actual plot ############
+
+output$coolplot <- renderPlot(width = width, height = height, {
+  plot(plotdata())
+}
+)
+##########################################
 
 
 ###########################################

rsconnect/shinyapps.io/goedhart/PlotsOfData.dcf

@@ -5,9 +5,9 @@ account: goedhart
 server: shinyapps.io
 hostUrl: https://api.shinyapps.io/v1
 appId: 458873
-bundleId: 1604090
+bundleId: 1609765
 url: https://goedhart.shinyapps.io/PlotsOfData/
-when: 1537871761.02692
+when: 1538074556.99123
 asMultiple: FALSE
 asStatic: FALSE
-ignoredFiles: .RData|.Rapp.history|ComparisonPlot_example1.png
+ignoredFiles: .Rapp.history