added MDS

server.R

@@ -10,6 +10,8 @@ suppressPackageStartupMessages({
   library(car)
   library(plotly)
   library(openxlsx)
+  library(ggplot2)
+  library(ggrepel)
 })
 
 options(stringsAsFactors = FALSE)
@@ -849,6 +851,29 @@ shinyServer(function(input, output) {
     plotOutput('runPCA', width = paste(input$width,"%",sep = ""), 
                height = input$height, click = "plot_click")
   })
+  output$plotMDS <- renderUI({
+    plotOutput('runMDS', width = paste(input$width,"%",sep = ""), 
+               height = input$height)
+  })
+  output$runMDS <- renderPlot({
+    if (!input$displayMDS)  return(NULL)
+    dat2 <- getgenind()
+
+    obj <- genind2genpop(dat2)
+    dst <- dist.genpop(obj, method = 1)
+    # hc <- hclust(dst)
+    # plot(as.dendrogram(hc), horiz=T, xlab = "", sub = "", main = "Nei's distance between populations")
+
+    MDS <- cmdscale(dst)
+    MDS <- data.frame(ax1 = MDS[, 1], ax2 = MDS[, 2], pop = rownames(MDS))
+    # plot(MDS, xlab = "MDS Axis 1", ylab = "MDS Axis 2", pch = 16, col = dat2@pop)
+    p <- ggplot(MDS, aes(x=ax1, y=ax2, color = pop, label = pop)) +
+      geom_point() +
+      geom_text_repel() + 
+      labs( x = "MDS Axis 1", y = "MDS Axis 2", title = "MDS based on Nei's distance")  +
+      theme_minimal()
+    plot(p)
+  })
 
   # DL principal components
   output$dlPCAeigen <- downloadHandler(

ui.R

@@ -298,9 +298,13 @@ shinyUI(
                     downloadButton('dlFstMatXL', 'Download as Excel (.xlsx)')
                   ),
 
-                  tags$hr(),
+                  tags$hr()
 
-                  h4("Principal Component Analysis"),
+                ),
+                tabPanel(
+                  "PCA - MDS",
+
+                  h4("Principal Component Analysis (PCA)"),
 
                   checkboxInput(
                     'displayPCA',
@@ -333,7 +337,20 @@ shinyUI(
 
                   ),
 
-                  tags$hr()
+                  tags$hr(),
+
+                  h4("Multidimensional Scaling (MDS) based on Nei's distance"),
+
+                  checkboxInput(
+                    'displayMDS',
+                    "Compute Nei's genetic distance between populations and run MDS",
+                    FALSE
+                  ),
+                  conditionalPanel(
+
+                    condition = "input.displayMDS == true",
+                    uiOutput('plotMDS')
+                  )
 
                 ),
                 tabPanel(
@@ -465,6 +482,7 @@ shinyUI(
                h3("Updates"),
 
                tags$ul(
+                 tags$li("1.4.0 (09/02/2021) – STRAF can now perform an MDS. All results can be downloaded as Excel files. Minor bug fixes in file conversion."), 
                  tags$li("1.3.3 (03/02/2021) – Minor bug fixes in file conversion and PIC computation. Improved graphics."), 
                  tags$li("1.3.0 (01/02/2021) – STRAF can convert files to the Genepop and Familias formats. A File conversion tab has been added."), 
                  tags$li("1.2.2 (09/01/2021) – STRAF has moved to an AWS server (without any changes in the License)."),