CRISPRbeers.R

# PACKAGE INSTALLATION FUNCTION
# helper function to install package if not already installed
usePackage <- function(p) {
  if (!is.element(p, installed.packages()[,1]))
    install.packages(p, dep = TRUE)
  require(p, character.only = TRUE)
}


# LOADING LIBRARIES
usePackage('shiny') 
usePackage('shinythemes') 
usePackage('tidyverse') 

#######################################################################################
# ENTER YOUR WORKING DIRECTORY CONTAINING THE CRISPR BEERS DATABASE HERE: 
#

setwd("~/CRISPRbeers/App")

#
#######################################################################################

CRISPRbeers <- as.data.frame(read.csv("BEERS_database.csv"))

colnames(CRISPRbeers)[28] = 'increased_product_purity'
colnames(CRISPRbeers)[29] = 'increased_on_target'
colnames(CRISPRbeers)[31] = 'Reduced_DNA_off_targets'
colnames(CRISPRbeers)[32] = 'Reduced_RNA_off_targets'

sort(CRISPRbeers$MAX, decreasing = TRUE)

b64 <- base64enc::dataURI(file="BEpos1.png", mime="image/png")


### UI ####
ui <- fluidPage(
  theme = shinytheme("united"),
  
  tags$style('.container-fluid {
                             background-color: #F0F8FF;
              }'),
  fluidRow(
    column(2,
  img(src=b64)),
  column(5,offset = 5,
  titlePanel(
    h1(p("CRISPR Base Editor Exchange Repository", style = "color:purple", align = "center"))
  )
  )
  ),
  hr(),

  


  
  sidebarLayout(
    sidebarPanel(tags$style(".well {background-color:#FFFFDB;}"),

                 checkboxGroupInput(inputId = "A",
                                    label = "Single Effector:",
                                    choices = unique(CRISPRbeers$single_effector),
                                    inline = TRUE),
                
                 
                 checkboxGroupInput(inputId = "B_",
                             label = "Editing Class:",
                             choices = unique(CRISPRbeers$editing_class),
                             inline = T),
                
                 
                 checkboxGroupInput(inputId = "B",
                                    label = "Endonuclease:",
                                    choices = unique(CRISPRbeers$endonuclease),
                                    inline= T),
                 
                 checkboxGroupInput(inputId = "C",
                                    label = "PAM Requirement:",
                                    choices = unique(CRISPRbeers$PAM_requirement),
                                    inline = TRUE),
                 
                 checkboxGroupInput(inputId = "D",
                                    label = "Reduced DNA Off-Targets:",
                                    choices = unique(CRISPRbeers$Reduced_DNA_off_targets),
                                    inline = TRUE),
                 
                 checkboxGroupInput(inputId = "E",
                                    label = "Reduced RNA Off-Targets:",
                                    choices = unique(CRISPRbeers$Reduced_RNA_off_targets),
                                    inline = TRUE),
                 
                 
                 checkboxGroupInput(inputId = "F_",
                                    label = "Increased Product Purity:",
                                    choices = unique(CRISPRbeers$increased_product_purity),
                                    inline = TRUE),
                 
                 checkboxGroupInput(inputId = "G",
                                    label = "Increased on Target:",
                                    choices = unique(CRISPRbeers$increased_on_target),
                                    inline = TRUE),
                 # selectizeInput(inputId = "mode","View Mode",choices=c("mode 1","mode 2"),selected= "mode 1"),
                 uiOutput("modeUI1"),
                 uiOutput("sortby"),
                 #img(src="BEpos.png",style="width:100%;height:auto")
                 
                 
    ),

    mainPanel(
      dataTableOutput("DataTable"),
      h4("This repository of CRISPR Base Editors can be used to prioritise effector enzymes to be used to target your sequence of interest. This database 
contains base editors which been manually curated, and experimentally derived servers for some specific editors can be found elsewhere.
")
    )
  )
)



### Server ####
server <- function(input, output,session) {
  
  r<-reactiveValues(cols=NULL,sortCol=NULL,asc=FALSE)
  
  
  df<-reactive({
    single_effector_sel <- if (is.null(input$A)) unique(as.vector(CRISPRbeers$single_effector)) else input$A
    endonuclease_sel <- if (is.null(input$B)) unique(as.vector(CRISPRbeers$endonuclease)) else input$B
    editing_class_sel <- if (is.null(input$B_)) unique(as.vector(CRISPRbeers$editing_class)) else input$B_
    PAM_requirement_sel <- if (is.null(input$C)) unique(as.vector(CRISPRbeers$PAM_requirement)) else input$C
    Reduced_DNA_off_targets_sel <- if (is.null(input$D)) unique(as.vector(CRISPRbeers$Reduced_DNA_off_targets)) else input$D
    Reduced_RNA_off_targets_sel <- if (is.null(input$E)) unique(as.vector(CRISPRbeers$Reduced_RNA_off_targets)) else input$E
    increased_product_purity_sel <- if (is.null(input$F_)) unique(as.vector(CRISPRbeers$increased_product_purity)) else input$F_
    increased_on_target_sel <- if (is.null(input$G)) unique(as.vector(CRISPRbeers$increased_on_target)) else input$G
    
    A = dplyr::filter(CRISPRbeers, single_effector %in% single_effector_sel,
                      endonuclease %in% endonuclease_sel,
                      editing_class %in% editing_class_sel,
                      PAM_requirement %in% PAM_requirement_sel,
                      Reduced_DNA_off_targets %in% Reduced_DNA_off_targets_sel,
                      Reduced_RNA_off_targets %in% Reduced_RNA_off_targets_sel,
                      increased_product_purity %in% increased_product_purity_sel,
                      increased_on_target %in% increased_on_target_sel)
    
    A <- A[,c(2,3,5,33:58)]
    names(A)<-c("base_editor","PMID","MAX",as.character(-6:-1),as.character(1:20))
    
    if(!is.null(r$cols)){
      A<-A[,c("base_editor","PMID","MAX",r$cols)]
    }
    
    if(!is.null(r$sortCol)){
      A<-A%>%
        arrange(... = if(!r$asc){A[,r$sortCol]}else{desc(A[,r$sortCol])}
        )
      
    }
    
    A
  })
  
  output$DataTable <- renderDataTable({
    df()
  },options = list(scrollX = TRUE))
  
  observe(
  print(r$asc)
  )
  output$sortby<-renderUI({tagList(
    selectizeInput("sortCol","Column to sort by",choices=names(df()),selected=r$sortCol,multiple=F),
    checkboxInput("asc","Descending",value = r$asc)
  )})
  
  observeEvent(input$sortCol,{
    r$sortCol<-input$sortCol
  })
  
  observeEvent(input$asc,{
    r$asc<-input$asc
  })
  
  # output$modeUI<-renderUI({
  #   if(input$mode=="mode 2"){
  #     vars<-names(CRISPRbeers)[33:58]
  #     selectizeInput(inputId = "cols","Editing Window to Display",choices=vars,multiple = TRUE)
  #   }
  # })
  
  observeEvent(input$cols,{
    r$cols<-input$cols
  })
  
  output$modeUI1<-renderUI({
      sliderInput("slideCol","Editing Window to Display:",min = -6,max = 20,step = 1,value = c(4,9))
  })
  
  observeEvent(input$slideCol,{
    k<-as.character(input$slideCol[1]:input$slideCol[2])
    k<-k[k!="0"]
    r$cols<-k
    print(k)
    if(!input$sortCol%in%c("base_editor","PMID","MAX",input$slideCol)){
      r$sortCol<-as.character(min(as.integer(k)))
      # updateSelectizeInput(inputId = "sortCol",selected = min(input$slideCol),session=session)
    }
  })
  
  # observeEvent(input$mode,{
  #   updateSelectizeInput(session = session,inputId = "cols",selected = NULL)
  # })
  
  
}
shinyApp(ui, server)