updtaes

server.R

-
 # Shiny app allowing: plot and parameters for microbial growth dataset
-# Severine Martini, Marc Garel, Christian Tamburini
+# Marc Garel, Severine Martini, Christian Tamburini
 ### October 2017
 
 
@@ -19,38 +18,24 @@ shinyServer(function(input, output) {
     do<-reactiveValues(data=dd)
     
     output$plot <- renderPlot({
-   #   plot(dd$H,dd$A, pch=19, xlab="Time(h)", ylab="DO600nm")
-  #    lines(dd$H,SSlogis(summary(fit)$parameters[1,1],summary(fit)$parameters[2,1],summary(fit)$parameters[3,1]))
-  #    crssce=data.frame(dd$H,dd$A)
-  #    SSlogis(dd$H,asym,xmid,scal)
-  #   coef=getInitial(dd$A~SSlogis(dd$H,asym,xmid,scal),data=crssce)
-  #    lines(dd$H,SSlogis(dd$H,coef[1],coef[2],coef[3]),lwd=1.5,col="blue")
-  #    grid(col="grey")
       
       
       ##############
       x=rep(dd[,1],ncol(dd)-1)
       y=unlist(dd[,2:ncol(dd)])
       crssce=data.frame(y,x)
-      w0=seq(0,90)
-      #modlog2=nls(x ~ SSlogis(y,Asym,xmid,scal),crssce)
-      modlog=nls(y ~ SSlogis(x,Asym,xmid,scal),crssce)
+      # limit axes extended
+      maxx=max(x,na.rm=T)+(max(x,na.rm=T)/4)
+      maxy=max(y,na.rm=T)+(max(y,na.rm=T)/4)
+      w0=seq(0,maxx)
+      # modlog2=nls(x ~ SSlogis(y,Asym,xmid,scal),crssce)
+      # modlog=nls(y ~ SSlogis(x,Asym,xmid,scal),crssce)
       coef=getInitial(y~SSlogis(x,asym,xmid,scal),data=cbind.data.frame(x,y))
       mu=1/coef[3]
+      # output plot
       plot(x,y)
-      points(x,y,xlim=c(0,90),ylim=c(0,1.1),xlab="temps(h)",ylab="DO600nm",las=1,pch=22,bg=1)
+      points(x,y,xlim=c(0,maxx),ylim=c(0,maxy),xlab="temps(h)",ylab="DO600nm",las=1,pch=22,bg=1)
       lines(w0,SSlogis(w0,coef[1],coef[2],coef[3]),lwd=1.5)
-      # ou, ce qui revient au même
-      
-      #x=dd[,1]
-      #y=dd[]
-      #coef=getInitial(y~SSlogis(x,asym,xmid,scal),data=cbind.data.frame(x,y))
-      #mu=1/coef[3]
-      #plot(x,y)
-      #points(x,y,xlim=c(0,90),ylim=c(0,1.1),xlab="temps(h)",ylab="DO600nm",las=1,pch=22,bg=1)
-      #lines(w0,SSlogis(w0,coef[1],coef[2],coef[3]),lwd=1.5)
-      
-      ###############
 
       observeEvent(input$clicks, {print(as.numeric(do$data))})
      

ui.R

-#
-#
-
+# Shiny app allowing: plot and parameters for microbial growth dataset
+# Marc Garel, Severine Martini,  Christian Tamburini
+### October 2017
 library(shiny)
 
 
 shinyUI(fluidPage(
-  headerPanel("Welcome on a growth curve app"),
+  headerPanel("Application of a logistic model on microbial datasets"),
 # load dataset
 titlePanel("Upload file"),
   sidebarLayout(