Population Genetics: Shiny app at http://www.statistics.calpoly.edu/shiny

#SP_Render.txt

Population Genetics Shiny App
 
Base R code created by Helen Hilton
Shiny app files created by Helen Hilton

Cal Poly Statistics Dept Shiny Series 
http://statistics.calpoly.edu/shiny

DESCRIPTION

Title: Population Genetics
Author: Helen Hilton
AuthorUrl: https://www.linkedin.com/in/helen-hilton-39aba269
License: MIT
DisplayMode: Normal
Tags: Population genetics
Type: Shiny

LICENSE

The MIT License (MIT)
 
Copyright (c) 2018 Helen Hilton
 
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
 
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
 
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.

server.R

shinyServer(function(input, output) {
  
  output$start1 <- renderUI ({
    if(input$button3==1 || is.null(input$button3)) st1 <<- NULL
    isolate(if(input$node==1 && values$shouldShow2) st1 <<- input$start)
    if(values$shouldShow2 | values$shouldShow3){
    if(input$node==1) #withMathJax(helpText('$$A^1$$'))
    paste("Starting %A^1: ", st1)
   # expression(paste("Starting","%A"^"1"))
    
    }
  })
  
  output$start2 <- renderText ({
    if(input$button3==1 || is.null(input$button3)) st2 <<- NULL
    if(values$shouldShow3) {
      isolate(if(input$node2==1) st2 <<- input$start)
      if(input$node2==0) {""}
      else if(input$node==1) {
        paste("Starting %A^1: ", st2)}
    }
  })
  
  output$gen1 <- renderText ({
    if(input$button3==1 || is.null(input$button3)) g1 <<- NULL
    if(values$shouldShow2 | values$shouldShow3){
      isolate(if(input$node==1 && values$shouldShow2) g1 <<- input$gen)
      if(input$node==0) {""}
      else if(input$node==1) {
        paste("Number of Generations:", g1)}
    }
  })
  
  output$gen2 <- renderText ({
    if(input$button3==1 || is.null(input$button3)) g2 <<- NULL
    if(values$shouldShow3){
      isolate(if(input$node2==1) g2 <<- input$gen)
      if(input$node2==0) {""}
      else if(input$node2==1 && !is.null(input$node2)) {
        paste("Number of Generations:", g2)}
    }
  })
  
  output$pop1 <- renderText ({
    if(input$button3==1 || is.null(input$button3)) p1 <<- NULL
    if(values$shouldShow2 | values$shouldShow3){
      isolate(if(input$node==1 & values$shouldShow2) p1 <<- input$pop)
      if(input$node==0) {""}
      else if(input$node>=1) {
        paste("Population Size: ", p1)}
    }
  })
  
  output$pop2 <- renderText ({
    if(input$button3==1) p2 <<- NULL
    if(values$shouldShow3){
      isolate(if(input$node2==1) p2 <<- input$pop)
      if(input$node2==0) {""}
      else if(input$node2==1 && !is.null(input$node2)) {
        paste("Population Size: ", p2)}
    }
  })
  
  output$AA1 <- renderText ({
    if(input$button3==1 || is.null(input$button3)) A1 <<- NULL
    if(values$shouldShow2 | values$shouldShow3){
      isolate(if(input$node==1 & values$shouldShow2) A1 <<- input$AA)
      if(input$node==0) {""}
      else if(input$node>=1) {
        #withMathJax(helpText('A/A'))
        paste("A^1/A^1 Fitness %:", A1)
        #expression(paste("A"^"1"))
      }
    }
  })
  
  
  output$AA2 <- renderText ({
    if(input$button3==1 || is.null(input$button3)) A2 <<- NULL
    if(values$shouldShow3){
      isolate(if(input$node2==1) A2 <<- input$AA)
      if(input$node2==0) {""}
      else if(input$node2==1 && !is.null(input$node2)) {
        paste("A^1/A^1 Fitness %:", A2)}
    }
  })
  
  output$AB1 <- renderText ({
    if(input$button3==1 || is.null(input$button3)) AB_1 <<- NULL
    if(values$shouldShow2 | values$shouldShow3) {
      isolate(if(input$node==1 & values$shouldShow2) AB_1 <<- input$AB)
      if(input$node==0) {""}
      else if(input$node>=1) {
#         tags$div(
#           HTML(paste("A", tags$sup(1), sep = "")), 
#           HTML(paste("A", tags$sup(2), sep = "")),
#           HTML(paste("Fitness %"))
#         )
        paste("A^1/A^2 Fitness %:", AB_1)
      }
    }
  })
  
  output$AB2 <- renderText ({
    if(input$button3==1 || is.null(input$button3)) AB_2 <<- NULL
    if(values$shouldShow3){
      isolate(if(input$node2==1 && !is.null(input$node2)) AB_2 <<- input$AB)
      if(input$node2==0) {""}
      else if(input$node2==1) {
        paste("A^1/A^2 Fitness %:", AB_2)}
    }
  })
  
  output$BB1 <- renderText ({
    if(input$button3==1 || is.null(input$button3)) B1 <<- NULL
    if(values$shouldShow2 | values$shouldShow3){
      isolate(if(input$node==1 & values$shouldShow2) B1 <<- input$BB)
      if(input$node==0) {""}
      else if(input$node>=1) {
        paste("A^2/A^2 Fitness %:", B1)}
    }
  })
  
  
  output$BB2 <- renderText ({
    if(input$button3==1 || is.null(input$button3)) B2 <<- NULL
    if(values$shouldShow3){
      isolate(if(input$node2==1 && !is.null(input$node2)) B2 <<- input$BB)
      if(input$node2==0 || is.null(input$node2)) {""}
      else if(input$node2==1) {
        paste("A^2/A^2 Fitness %:", B2)}
    }
  })
  
  output$Population1 <- renderImage({
    if(values$shouldShow2 | values$shouldShow3)
      
      return(list(
        src="www/population_logo_red.png", contentType="image/png", alt="Population", align='left')) 
    
    
    
    
  }, deleteFile=FALSE) 
  
  output$Population2 <- renderImage({
    if(values$shouldShow3)
      if(input$node2==1) {
        return(list(
          src="www/population_logo_blue.png", contentType="image/png", alt="Population", align='left')) 
      }
    
    
    
  }, deleteFile=FALSE)
  
  
  output$distPlot <- renderPlot({
    
    
    if(input$node==1) {
      sim1 <<- matrix(nrow=g1,ncol=1000)
      sim1[1,] <<- st1
    }
    
    if(input$node2==1) {
      sim2 <<- matrix(nrow=g2,ncol=1000)
      sim2[1,] <<- st2
    }
    
    #labelsY=parse(text=paste("%","A", "^1", sep=""))
    #labelsY=parse(text=paste("A","^1",sep=""))
    title=expression(paste("%A"^"1"," in Population"))
    p <- ggplot()+
      xlab("Generation")+ylab(expression(paste("%A"^"1")))+labs(title=title)+
      ylim(0,100)
    
    
    input$drawpop
    withProgress(message='Generating Simulations',value=0.1, {
      Sys.sleep(0.25) #newcode
    isolate({
      j <<- 1
      for(k in 1:input$drawmorepops){
        incProgress(0.25, detail="Generating Populations")
        for(i in 2:g1) {
          
          allele1 <- (runif(p1)<sim1[i-1,j]/100)
          allele2 <- (runif(p1)<sim1[i-1,j]/100)
          
          ######FOR SURVIVAL %
          if(A1!=100) {
            aa <- (allele1==1 & allele2==1)
            minus.a <- round(sum(aa)*2*(1-(A1/100)))
          } 
          else {
            minus.a <- 0
          }
          if(B1!=100){
            bb <- (allele1==0 & allele2==0)
            minus.b <- round(sum(bb)*2*(1-(B1/100)))
          }
          else {
            minus.b <- 0
          }
          if(AB_1!=100) {
            ab <- ((allele1==1 & allele2==0) | (allele1==0 & allele2==1))
            minus.ab <- round(sum(ab)*(1-(AB_1/100)))
          }
          else {
            minus.ab <- 0
          }
          
          sim1[i,j] <<- ((sum(allele1+allele2)-minus.a-minus.ab)/((p1*2)-minus.a-minus.b-2*minus.ab))*100
        }
        if(input$node2==1) {
          for(i in 2:g2) {
            allele3 <- (runif(p2)<sim2[i-1,j]/100)
            allele4 <- (runif(p2)<sim2[i-1,j]/100)
            if(A2!=100) {
              aa <- (allele3==1 & allele4==1)
              minus.a <- round(sum(aa)*2*(1-(A2/100)))
            } 
            else {
              minus.a <- 0
            }
            if(B2!=100){
              bb <- (allele3==0 & allele4==0)
              minus.b <- round(sum(bb)*2*(1-(B2/100)))
            }
            else {
              minus.b <- 0
            }
            if(AB_2!=100) {
              ab <- ((allele3==1 & allele4==0) | (allele3==0 & allele4==1))
              minus.ab <- round(sum(ab)*(1-(AB_2/100)))
            }
            else {
              minus.ab <- 0
            }
            sim2[i,j] <<- ((sum(allele3+allele4)-minus.a-minus.ab)/((p2*2)-minus.a-minus.b-2*minus.ab))*100
          }
        }
        
        j <<- j+1
      }
    }) #isolate
    incProgress(0.5, detail="Generating Plot")
    y_sim1 <<- melt(sim1[,1:j])
    if(input$node2==1) y_sim2 <<- melt(sim2[,1:j])
    p <- p+geom_line(data = y_sim1, aes(x = Var1, y = value, group = Var2, colour="pop1"))
    if(input$node2==0) {p <- p+  scale_colour_manual(name="Population", values=c(pop1="red"),
                                                     labels=c("Population 1"))}
    if(input$node2==1) {
      p<- p+geom_line(data = y_sim2, aes(x=Var1, y=value, group=Var2, colour="pop2"))+
        scale_colour_manual(name="Population",
                            values=c(pop1="red", pop2="blue"),
                            labels=c("Population 1", "Population 2"))
    }
    print(p)
    })
  }) #renderPlot
  ####TO CLEAR POPULATIONS
  values <- reactiveValues(shouldShow = FALSE)
  values <- reactiveValues(shouldShow2 = FALSE)
  values <- reactiveValues(shouldShow3 = FALSE)
  
  observe({
    if (input$begin == 0) return()
    values$shouldShow = TRUE
    values$shouldShow2 = FALSE
    values$shouldShow3 = FALSE
  })
  
  observe({
    if(is.null(input$node) || input$node==0)
      return()
    values$shouldShow = FALSE
    values$shouldShow2 = TRUE
    values$shouldShow3 = TRUE
  })
  
  observe({
    if (is.null(input$node2) || input$node2 == 0)
      return()
    values$shouldShow2 = FALSE
  })
  
  observe({
    if(is.null(input$button3) || input$button3==1) {
      values$shouldShow=FALSE
      values$shouldShow2=FALSE
      values$shouldShow3=FALSE
    }
  })
  
  
  output$uiButton1 <- renderUI({
    if(values$shouldShow)
      actionButton("node", "Make Population 1")
  })
  
  output$uiButton2 <- renderUI({
    if (values$shouldShow2)
      actionButton("node2","Make Population 2")
  })
  
  output$uiButton3 <- renderUI({
    if(values$shouldShow3)
      actionButton("button3", "Clear Populations")
  })
  
})

styles.css

.shiny-progress {
  top: 50% !important;
  left: 50% !important;
  margin-top: -100px !important;
  margin-left: -250px !important;
}

ui.r

library(ggplot2)
library(reshape2)
shinyUI(navbarPage(
  "Population Genetics",
  
  tabPanel("Make Your Population",
  tags$head(tags$link(rel = "icon", type = "image/x-icon", href =
       "https://webresource.its.calpoly.edu/cpwebtemplate/5.0.1/common/images_html/favicon.ico")),
           
  fluidRow(
    column(4,
      numericInput("start", tags$div( 
        HTML(paste("Starting %")),
        HTML(paste("A", tags$sup(1), sep = ""))
         ), 50),
      numericInput("gen", "Number of Generations", 100),
      numericInput("pop", "Starting Population", 100),
      numericInput("AA", 
                   #withMathJax(helpText('$$A^1$$')),
                   tags$div(
                     HTML(paste("A", tags$sup(1), sep = "")), 
                     HTML(paste("A", tags$sup(1), sep = "")),
                     HTML(paste("Fitness %"))
                   ), 
                   100),
      numericInput("AB", 
                   tags$div(
                     HTML(paste("A", tags$sup(1), sep = "")), 
                     HTML(paste("A", tags$sup(2), sep = "")),
                     HTML(paste("Fitness %"))
                   )
                   , 100),
      numericInput("BB", 
                   tags$div(
                     HTML(paste("A", tags$sup(2), sep = "")), 
                     HTML(paste("A", tags$sup(2), sep = "")),
                     HTML(paste("Fitness %"))
                   ), 100),
      actionButton("begin","Click To Begin"),
      uiOutput("uiButton1"),
      uiOutput("uiButton2"),
      uiOutput("uiButton3"),
      br(), br(), br(), br(), 
      
      div("Shiny app by", a(href="https://www.linkedin.com/in/helen-hilton-39aba269",target="_blank", 
                            "Helen Hilton"),align="left", style = "font-size: 8pt"),
      
      div("Base R code by", a(href="https://www.linkedin.com/in/helen-hilton-39aba269/",target="_blank", 
                              "Helen Hilton"),align="left", style = "font-size: 8pt"),
      
      div("Shiny source files:", a(href="https://gist.github.com/calpolystat/f9dd35b71dc3e73b845160018ecacea2",
                                   target="_blank","GitHub Gist"),align="left", style = "font-size: 8pt"),
      
      div(a(href="http://www.statistics.calpoly.edu/shiny",target="_blank", 
            "Cal Poly Statistics Dept Shiny Series"),align="left", style = "font-size: 8pt")
      
    ),
    
    column(4,
           absolutePanel(
             top=125, bottom=0, left=320, right=0, fixed=TRUE,
             #              h3("Population 1"),
             imageOutput("Population1")
             
           )
    ),
    
    column(4,
           absolutePanel(
             top=425, bottom=0, left=320, right=0, fixed=TRUE,
             #              h3("Population 2"),
             imageOutput("Population2")
             
           )
    ),
    
    column(4,
           absolutePanel(  #Prints information for Population #1
             top=170, bottom=0, left=670, right=0, fixed=TRUE,
             tags$style(type="text/css",
                        ".shiny-output-error { visibility: hidden; }",
                        ".shiny-output-error:before { visibility: hidden; }"),
             uiOutput("start1"),
             textOutput("gen1"),
             textOutput("pop1"),
              textOutput("AA1"),
              textOutput("AB1"),
              textOutput("BB1")
           ), #absolutePanel
           absolutePanel(  #Prints information for Population #2
             top=470, bottom=0, left=670, right=0, fixed=TRUE,
              textOutput("start2"),
              textOutput("gen2"),
              textOutput("pop2"),
              textOutput("AA2"),
              textOutput("AB2"),
              textOutput("BB2")
           )
           
    ) #column
    
    
  ) #fluidRow
), #tabPanel

tabPanel("Simulation",
         sidebarLayout(
                  
           sidebarPanel(
             
             numericInput("drawmorepops", "Number of Simulations", 1),
             actionButton("drawpop", "Simulate"),
             br(), br(), br(), br(), 
             
             div("Shiny app by", a(href="https://www.linkedin.com/in/helen-hilton-39aba269/",target="_blank", 
                                   "Helen Hilton"),align="right", style = "font-size: 8pt"),
             
             div("Base R code by", a(href="https://www.linkedin.com/in/helen-hilton-39aba269/",target="_blank", 
                                     "Helen Hilton"),align="right", style = "font-size: 8pt"),
             
             div("Shiny source files:", a(href="https://gist.github.com/calpolystat/f9dd35b71dc3e73b845160018ecacea2",
                                          target="_blank","GitHub Gist"),align="right", style = "font-size: 8pt"),
             
             div(a(href="http://www.statistics.calpoly.edu/shiny",target="_blank", 
                   "Cal Poly Statistics Dept Shiny Series"),align="right", style = "font-size: 8pt")
             
           ),#sidebarPanel  
           mainPanel( 
             plotOutput("distPlot")
           )#mainPanel
         )#sidebarLayout
         
) #tabPanel
) #navbarPage
) #shinyUI