Dowload wizard files added and Dil slider update

dev/app.R

@@ -636,7 +636,7 @@ server <- function(input, output, session) {
                        "Narrower dilution ranges decrease the CIs of rel. potency, and increase the CIs of upper and lower asymptote ratios, ands Hill's slope ratios",
 
               ),
-              tabPanel("Histograms",
+              tabPanel("Plots",
                 h4("Histograms of parameters"),
                 plotOutput("linerangeCIs"),
                 plotOutput("ratioSlope"),
@@ -658,10 +658,10 @@ server <- function(input, output, session) {
               tabPanel(
                 "Report",
                 h4("Settings for report"),
-                useShinyjs(),
+                #useShinyjs(),
-                actionButton("btn2", "Download PDF report", icon = icon("download")),
+                #actionButton("btn2", "Download PDF report", icon = icon("download")),
-                downloadButton("downloadWizardReport", label = "Download report", class = "butt"),
+                downloadButton("downloadWizardData", label = "Download model and plots", class = "butt"),
-                tags$style(type = "text/css", "#downloadWizardReport {background-color: #4FCBD9; color: black;font-family: Courier New}"),
+                tags$style(type = "text/css", "#downloadWizardData {background-color: #4FCBD9; color: black;font-family: Courier New}"),
                 # textInput("Author", "Author", value = ""),
                 # textInput("RepIdentifier", "Report name", value = ""),
                 # textInput("NoP", "Product name", value = ""),
@@ -2235,15 +2235,17 @@ server <- function(input, output, session) {
     ratioDF <- data.frame(WS_name = URMcoefsDF[,1], slopeRatio = slopeRatio, LasRatio = LasRatio, UasRatio = UasRatio)
     
     RMcoefsDF <- t(matrix(unlist(RMcoefsL),nrow=6))
-    
+    colnames(RMcoefsDF) <- c("WS name", "lower asymptote","Hill's slope","upper asymptote","log(EC50 ref)","logEC50 difference")
     Dat$URMcoefsDF <- URMcoefsDF
+    Dat$ModU <- URMcoefsDF
     Dat$RestrM <- RMcoefsDF
+    Dat$ModR <- RMcoefsDF
     
     CalcPotDF <-  t(matrix(unlist(potEstL),nrow=3))
     colnames(CalcPotDF) <- c("rel_potency","lower_CI","upper_CI")
     Dat$CalcPot <- CalcPotDF
     # 
-    #### sigmoid plots ----
+    #### Wizard sigmoid plots ----
     
     Slope <- as.numeric(URMcoefsDF[1,3])
     if (Slope > 0) {
@@ -2484,12 +2486,15 @@ server <- function(input, output, session) {
    if (!is.null(p2)) {
      #p2 <- Dat$p2
      p_dil <- p2 +
-       annotate("pointrange", x = dils2, y = rep(min_y, length(dils2)), xmin = min(dils2), xmax = max(dils2),colour = "red" ,linetype = 3) +
+       geom_vline(xintercept = dils2, col = "red", linetype = 2, alpha=0.5) +
+       annotate("pointrange", x = dils2, y = rep(min_y, length(dils2)), xmin = min(dils2), xmax = max(dils2),
+                colour = "red" ,linetype = 3, shape=24) +
        annotate("text", x = dils2, y = rep(min_y + (max_y - min_y) * 0.05, length(dils2)), label = as.character(round(dils2, 3)),colour = "red") +
        annotate("text",
          x = dils2[-1] + (max(dils2) - min(dils2)) * 0.05,
          y = rep(min_y + (max_y - min_y) * 0.1, length(dils2[-1])),
          label = as.character(round(dilfactors[-1], 3)),colour = "red") 
+     
        # geom_line(
        #   data = as.data.frame(pl_df), aes(x = dils2, y = SAMPLE50), color = "grey15", linetype = 2,
        #   inherit.aes = F
@@ -2498,23 +2503,6 @@ server <- function(input, output, session) {
        #   data = as.data.frame(pl_df), aes(x = dils2, y = SAMPLE200), color = "grey15", linetype = 2,
        #   inherit.aes = F
        # ) +
-       # geom_vline(xintercept = c(Xbend50, Xbend200), col = "grey15", linetype = 2) +
-       # { if (input$scenario == "scenario 6") {
-       #     annotate("pointrange",
-       #       x = optdils2, y = rep(min_y + (max_y - min_y) * 0.2, length(optdils2)),
-       #       xmin = min(optdils2), xmax = max(optdils2), color = "seagreen"
-       #     )
-       #   }
-       # } +
-       # {
-       #   if (input$scenario == "scenario 6") {
-       #     annotate("text",
-       #       x = optdils2, y = rep(min_y + (max_y - min_y) * 0.25, length(optdils2)),
-       #       label = as.character(round(optdils2, 3)), color = "seagreen"
-       #     )
-       #   }
-       # } +
-      
     
        # annotate("text",
        #   x = optdils[1], y = (max_y + min_y) * 0.5,
@@ -2525,6 +2513,7 @@ server <- function(input, output, session) {
           print(p_dil)
        })
      
+       Dat$DilPlot <- p_dil
       } # if (!is.null(p2))
     } # if !is.null Dat$Mws
 
@@ -2892,30 +2881,53 @@ server <- function(input, output, session) {
     
     #### download Wizard report ----
     
-    output$downloadWizardReport <- downloadHandler(
+    output$downloadWizardData <- downloadHandler(
-      filename = paste0("Report_Meta", Dat$nameRep, ".pdf"),
+      
+      filename = paste0("CompiledData", Dat$nameRep, ".zip"),
       content = function(file) {
+        fs <- c()
         tpdr <- tempdir()
-        tempReport <- file.path(tpdr, "Doc_BioassayLinReport.Rmd")
+        filename = paste0("CompiledData", Dat$nameRep, ".zip")
-        file.copy("Doc_BioassayLinReport.Rmd", tempReport, overwrite = TRUE)
+        #tempReport <- file.path(tpdr, "Doc_BioassayLinReport.Rmd")
+        #file.copy("Doc_BioassayLinReport.Rmd", tempReport, overwrite = TRUE)
         
-        tempReportc <- file.path(tpdr, "logov2.png")
+        #tempReportc <- file.path(tpdr, "logov2.png")
-        file.copy("logov2.png", tempReportc, overwrite = TRUE)
+        #file.copy("logov2.png", tempReportc, overwrite = TRUE)
         
-        rmarkdown::render(tempReport,
+        # rmarkdown::render(tempReport,
-                          output_file = file,
+        #                   output_file = file,
-                          params = list(
+        #                   params = list(
-                            FileName = Dat$FileName,
+        #                     FileName = Dat$FileName,
-                            author = Dat$Author,
+        #                     author = Dat$Author,
-                            NoP = Dat$NoP,
+        #                     NoP = Dat$NoP,
-                            Assay = Dat$Assay,
+        #                     Assay = Dat$Assay,
-                            REP = REP,
+        #                     REP = REP,
-                            REPlin = REPlin,
+        #                     REPlin = REPlin,
-                            coeffsLin = Dat$coeffs_UN
+        #                     coeffsLin = Dat$coeffs_UN
-                          ),
+        #                   ),
-                          envir = new.env(parent = globalenv())
+        #                   envir = new.env(parent = globalenv())
-        )
+        # )
-      }
+     #browser()   
+        fileOutModU=paste(paste0(tpdr, sep='/', 'unrModelFits'), sep='','.csv')
+        fs=c(fs, fileOutModU)
+        ModU <- Dat$ModU
+        write.csv(ModU, fileOutModU, row.names = F)
+        
+        fileOutModR=paste(paste0(tpdr, sep='/', 'restrModelFits'), sep='','.csv')
+        fs=c(fs, fileOutModR)
+        ModR <- Dat$ModR
+        write.csv(ModR, fileOutModR, row.names = F)
+        
+        DilPlot <- Dat$DilPlot
+        fileOutDilPlot =paste(paste0(tpdr, sep='/', 'SigmoidDilutionsPlot'), sep='','.png')
+        fs=c(fs, fileOutDilPlot)
+        png(fileOutDilPlot, width=600, height=400)
+        print(DilPlot)
+        dev.off()
+    #browser()    
+        zip::zipr(zipfile=file, files=fs, include_directories = F)
+        
+      }, contentType = "application/zip"
     )
 }