From f987815e50f8c5f327de6acdb0289df039121fd3 Mon Sep 17 00:00:00 2001
From: agouy <contact@agouy.com>
Date: Wed, 3 Feb 2021 00:37:27 +0100
Subject: [PATCH] 1.3.3

---
 server.R | 33 +++++++++++++++++++++------------
 ui.R     | 13 ++++++++++---
 2 files changed, 31 insertions(+), 15 deletions(-)

diff --git a/server.R b/server.R
index c013a17..62e1299 100644
--- a/server.R
+++ b/server.R
@@ -8,6 +8,7 @@ suppressPackageStartupMessages({
   library(hierfstat)
   library(DT)
   library(car)
+  library(plotly)
 })
 
 shinyServer(function(input, output) {
@@ -514,7 +515,7 @@ shinyServer(function(input, output) {
   })
   
   # plot in the reactive UI
-  output$plotIndices <-  renderPlot({
+  output$plotIndices <-  renderPlotly({
     
     if(is.null(input$selectPop2)) return(NULL)
     else taB <- reacIndices()[[input$selectPop2]]
@@ -525,21 +526,29 @@ shinyServer(function(input, output) {
     if(is.null(input$plotIndicesFOR)) return(NULL)
     
     par(mar=rep(input$margin,4))
-    barplot(
-      dat[,input$plotIndicesFOR],
-      names.arg = dat[,"locus"],
-      horiz = TRUE,
-      las = 1,
-      col = transp(input$barplotcolor, input$transparency),
-      border = as.numeric(input$borderbarplot),
-      cex.axis = input$cexaxis,
-      cex.names = input$cexaxis,
-      xlab = input$plotIndicesFOR
+    library(plotly)
+    
+    fig <- plot_ly(
+      x = dat[, input$plotIndicesFOR],
+      y = dat[, "locus"],
+      name = "bp_for",
+      type = "bar",
+      text = paste0(
+        "Locus: ", dat[, "locus"],
+        "\nValue: ", round(dat[, input$plotIndicesFOR], 4)
+      ),
+      hoverinfo = 'text',
+      marker = list(color = transp(input$barplotcolor, input$transparency))
+    ) %>% layout(
+      xaxis = list(title = input$plotIndicesFOR, zeroline = FALSE),
+      yaxis = list(title = "Locus")
     )
+    
+    (fig)
   })
   
   output$plotFOR <- renderUI({
-    plotOutput('plotIndices', width=paste(input$width,"%",sep=""),
+    plotlyOutput('plotIndices', width=paste(input$width,"%",sep=""),
                height=input$height)
   })
   
diff --git a/ui.R b/ui.R
index 36ddfe6..889bd7e 100644
--- a/ui.R
+++ b/ui.R
@@ -11,7 +11,7 @@ shinyUI(
 
   navbarPage(
 
-    "STRAF 1.3.2: STR Analysis for Forensics",
+    "STRAF 1.3.3: STR Analysis for Forensics",
     
     ##### ANALYSIS TAB ----------------------------------------------------------
     tabPanel(
@@ -20,6 +20,12 @@ shinyUI(
         theme = "bootstrap.css",
         tags$head(includeHTML(("./www/googleanalytics.html"))),
         tags$head(tags$style(type="text/css", ".container-fluid {max-width: 1200px}")),
+        tags$head(tags$style('body {font-family: Arial;}')),
+        tags$head(tags$style('table {font-family: Arial;}')),
+        tags$head(tags$style('h1 {font-family: Arial;}')),
+        tags$head(tags$style('h2 {font-family: Arial;}')),
+        tags$head(tags$style('h3 {font-family: Arial;}')),
+        tags$head(tags$style('h4 {font-family: Arial;}')),
         
         sidebarLayout(
           
@@ -60,8 +66,8 @@ shinyUI(
               condition="input.hidegraph",
               
               p("Barplot color"),
-              colourInput("barplotcolor", NULL, "#AEA79F", showColour = "background"),
-              checkboxInput("borderbarplot", "Bar border", TRUE),
+              colourInput("barplotcolor", NULL, "#36648B", showColour = "background"),
+              checkboxInput("borderbarplot", "Bar border", FALSE),
               sliderInput("transparency", "Tranparency", 0, 1, 0.8, ticks = FALSE),
               sliderInput("width", "Plot width", 40, 100, 100, ticks = FALSE, post = "%"),
               sliderInput("height", "Plot height", 300, 800, 500, ticks = FALSE, post = "px"),
@@ -450,6 +456,7 @@ shinyUI(
                h3("Updates"),
                
                tags$ul(
+                 tags$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)."), 
                  tags$li("1.1.2 (03/10/2020) – Preparation for integration to Tercen; few minor updates"),