R/ui.R

In crisprseekplus: crisprseekplus

#' cspUI
#'
#' Creates a shinyUI to be able to run crsiprseekplus interactively.
#'
#' @note \code{cspUI}
#' @return the panel for the UI;
#'
#' @examples
#'     x<-cspUI()
#'
#' @export
#'

cspUI <- function() {
addResourcePath(prefix = "www", directoryPath =
                system.file("extdata", "www", 
                package = "crisprseekplus"))
  
shinyUI(fluidPage(
shinyjs::useShinyjs(),
  
conditionalPanel(
condition <- "input.goButton > 0", uiOutput("loading")),
    uiOutput("logo"),
    titlePanel("CRISPRseekPlus"),
    br(),
    br(),
    br(),
    sidebarLayout(
    #File Upload
    sidebarPanel(
    radioButtons("chooseAction", "Choose which function you would like to do",
    choices = list("Off Target Analysis" = 1,
                "Compare 2 Sequences" = 2, "GUIDEseq" = 3), selected = "1"),
      
    conditionalPanel(
    condition <- "input.chooseAction == 1",
    paste("Off Target Analysis File Upload"),
    br(),
        fileInput("file1", label = "Choose Input File",
        accept=c('text/csv', 
                    'text/comma-separated-values,text/plain', 
                    '.csv')),
        fileInput("file2", label = "Choose Pattern File",
        accept=c('text/csv', 
                    'text/comma-separated-values,text/plain', 
                    '.csv')),
    conditionalPanel(
    condition <- "input.scoringmethod == 2",
        fileInput("mismatchActivityFile", label = "Choose Mismatch Activity File",
        accept=c('text/csv', 
                    'text/comma-separated-values,text/plain', 
                    '.csv')))),
    conditionalPanel(
    condition <- "input.chooseAction == 2",
        paste("Compare 2 Sequences File Upload"),
    br(),
        fileInput("file3", label = "Choose Input File 1",
        accept=c('text/csv', 
                    'text/comma-separated-values,text/plain', 
                    '.csv')),
        fileInput("file4", label = "Choose Input File 2",
        accept=c('text/csv', 
                    'text/comma-separated-values,text/plain', 
                    '.csv')),
    conditionalPanel(
    condition <- "input.scoringmethod == 2",
        fileInput("mismatchActivityFile", label = "Choose Mismatch Activity File",
        accept=c('text/csv', 
                    'text/comma-separated-values,text/plain', 
                    '.csv')))),
    conditionalPanel(
    condition <- "input.chooseAction == 3",
    paste("GUIDE-Seq File Upload"),
    br(),
        fileInput("file5", label = "Choose UMI File",
        accept=c('text/csv', 
                    'text/comma-separated-values,text/plain', 
                    '.csv')),
        fileInput("file6", label = "Choose Input Alignment File",
        accept=c('text/csv', 
                 'text/comma-separated-values,text/plain', 
                 '.csv')),
        fileInput("file7", label = "Choose Input gRNA File",
        accept=c('text/csv', 
                    'text/comma-separated-values,text/plain', 
                    '.csv'))),
    helpText(a(strong("Help Page"), 
            href=
            "http://crisprseeker.readthedocs.io/en/develop/index.html",
             TARGET="_blank")),
    helpText(a("What is Off Target Analysis?", 
            href=
            "http://crisprseeker.readthedocs.io/en/latest/quickstart.html#what-is-off-target-analysis",
            TARGET="_blank")),
    helpText(a("What is Compare 2 Sequences?", 
            href="http://crisprseeker.readthedocs.io/en/latest/quickstart.html#what-is-compare-2-sequences",
            TARGET="_blank")),
    helpText(a("What is GUIDEseq?", 
            href=
            "http://crisprseeker.readthedocs.io/en/latest/quickstart.html#what-is-guide-seq-analysis",
            TARGET="_blank")),
    helpText(a("How To Use the Interface", 
            href=
            "http://crisprseeker.readthedocs.io/en/develop/quickstart.html#using-the-interface",
            TARGET="_blank")),
    helpText(a("About Files", 
            href=
            "http://crisprseeker.readthedocs.io/en/develop/quickstart.html#about-files",
            TARGET="_blank")),
    br(),
    downloadButton("downloadData", "Download Output")
    ),#Sidebar Panel
    
    #Data Entry
mainPanel( 
tabsetPanel(
    tabPanel("Submissions Panel",
    fluidRow(
    column(4, 
            textInput("runNum", "Enter Run Name for Output File Title:", ""))),
    wellPanel(
    fluidRow(
    column(6, actionLink("mainPanel", "Main Options"))),
        conditionalPanel(
        condition <- "input.mainPanel%2 == 1",
    br(), br(),
    fluidRow(
        conditionalPanel(
        condition <- "input.chooseAction == 1 || input.chooseAction == 2",
    column(3,
        selectInput("fileFormat", "Format of input file",
        choices = list("fasta" =1, "fastq" =2, "bed" = 3),
        selected =1)),
        conditionalPanel(
        condtion <- "input.chooseAction == 2",
    column(3,
        selectInput("fileFormat2", "Format of input file",
        choices = list("fasta" =1, "fastq" =2, "bed" = 3),
        selected =1))),
        conditionalPanel(
        condtion <- "input.fileFormat == 3 || input.fileFormat2 == 3",
    column(3,
        radioButtons("fileHeader", "Does input file contain a header?",
        choices = list("Yes" = 1, "No" =2), selected = 2))),
        column(3,
            selectInput("gRNAexport", "Export potential gRNAs in which format?",
            choices = list("fasta" =1, "genbank" =2, "both" = 3,
            "none" = 4), selected =3)))),
    fluidRow(
    column(4,
        selectInput("organism", "Organism:",
        choices = list("hg19" = 1, "mm10" = 2,
        "ce6" = 3, "rn5" = 4,"dm3" = 5), selected = 1)),
    column(4,
        radioButtons("overwriteFile", "Overwrite the existing files in output directory?",
        choices = c("Yes" = 1, "No" = 2), selected = 1))),
        br(),
    fluidRow(
    conditionalPanel(
    condition <- ("input.chooseAction == 1"),
    column(4,
        textInput("chromSearch", "Chromosome to search:", value = "chrX")),
    column(4,
        radioButtons("annPaired1", "Annotate paired information?",
        choices = c("Yes" = 1, "No" = 2), selected = 1))),
    conditionalPanel(
    condition <- ("input.chooseAction == 2"),
    column(4,
        radioButtons("annPaired2", "Annotate paired information?",
        choices = c("Yes" = 1, "No" = 2), selected = 2))),
    conditionalPanel(
    condtion <- ("input.chooseAction == 3"),
    column(4,
        numericInput("umicol", "Index of column containing the umi/first 
        few bases of sequence R1 reads", value = 2)),
    column(4,
        radioButtons("umiheader", "Does input umi file contain a header line?",
        choices = list("Yes" = 1, "No" = 2),
        selected = 2)),
    column(4,
        numericInput("readID", "Index of umi file column containing the read identifier",
        value = 1))),
    conditionalPanel(
    condtion <- "input.chooseAction == 1",
    column(4,
        radioButtons("multicore", "Enable parallel processing?",
        choices = list("Yes" = 1, "No" = 2),
        selected = 2)))),
    conditionalPanel(
    condition<- "input.chooseAction == 1",
    fluidRow(
        textInput("chromExclude", "Set Chromosomes to Exclude",
        "chr17_ctg5_hap1, chr4_ctg9_hap1, chr6_apd_hap1,
        chr6_cox_hap2, chr6_dbb_hap3, chr6_mann_hap4"))))
    ), #FIRST WELL PANEL
                 
#################### GRNA PANEL #######################
    wellPanel(
    fluidRow(
    column(6, actionLink("gRNApanel", "gRNA Advanced Options"))),
    conditionalPanel(
    condition <- "input.gRNApanel%2 == 1",
    br(), 
    br(),
    fluidRow(
    conditionalPanel(
    condition <- ("input.chooseAction == 1"),
    column(4,
        radioButtons("radio1", "Find gRNAS with RE cut only?",
        choices = list("Yes" = 1, "No" = 2),
        selected = 1)),
    column(4,
        radioButtons("radio2", "Find  paired gRNAS only?",
        choices = list("Yes" = 1, "No" = 2),
        selected = 2))),
    conditionalPanel(
    condition <- ("input.chooseAction == 2"),
    column(4,
        radioButtons("radio3", "Find gRNAS with RE cut only?",
        choices = list("Yes" = 1, "No" = 2),
        selected = 2)),
    column(4,
        radioButtons("radio4", "Find  paired gRNAS only?",
        choices = list("Yes" = 1, "No" = 2),
        selected = 2))),
    column(4,
        numericInput("gRNASize", "Enter gRNA size", value = 20))),
    fluidRow(
    column(12,
        sliderInput("overlapgRNA", "Set overlap positions of gRNA and
        restriction enzyme cut site", 
        min = 0, max = 50, c(17, 18)))),
    fluidRow(
    conditionalPanel(
    condtion <- "input.chooseAction == 1 || input.chooseAction == 2",
    column(4,
        numericInput("baseBefore", "Number bases before gRNA for efficiency", value = 4)),
    column(4,
        numericInput("minGap", "Minimum distance between two oppositely oriented 
        gRNAs to be validly paired", value = 0)),
    column(4,
        numericInput("maxGap", "Maximum distance between two oppositely oriented 
        gRNAs to be validly paired", value = 20)))),
    fluidRow(
    conditionalPanel(
    condtion <- "input.chooseAction == 2",
    column(4,
        radioButtons("removeDetails", "Remove detailed gRNA information?",
        choices = list("Yes(both files)" = 1, "No(both files)" = 2,
        "Yes(file1)/No(file2)" = 3, "No(file1)/Yes(file2)" = 4),
        selected = 2)),
    column(4,
        radioButtons("findgRNA2", "Find gRNAs from input sequences?",
        choices = c("Yes (both inputs)" = 1, "No (both inputs)" = 2,
        "Yes(input1)/No(input 2)" = 3, "No(input1)/Yes(input2)" = 4),
        selected = 1)),
    column(4,
        checkboxGroupInput("searchDir", "Search direction",
        choices = list("Both" = "both", "1to2" = "1to2", "2to1" = "2to1"),
        selected = c("both", "1to2", "2to1")))),
    conditionalPanel(
    condition <- "input.chooseAction == 1",
    column(4,
        radioButtons("findgRNA1", "Find gRNAs from input sequences?",
        choices = c("Yes" = 1, "No" = 2), selected = 1)),
    column(4,
        radioButtons("usescore", "Use score to indicate gRNA efficacy?",
        choices = list("Yes" = 1, "No" = 2), selected = 1)),
    conditionalPanel(
    condition <- "input.usescore == 1",
    column(3, 
        radioButtons("efficacyFromIS", "Use input sequences 
        to calculate gRNA efficacy?",
        choices = list("Yes" = 1, "No" = 2), selected = 2))))),
    fluidRow(
    conditionalPanel(
    condtion <- "input.chooseAction == 1 || input.chooseAction == 2",
    column(4,
        textInput("gRNAname", "Enter a prefix used when assigning a
        name to found gRNAs", "gRNA"))),
    conditionalPanel(
    condition <- "input.chooseAction == 1",
    column(3,
        numericInput("upstreamSearch","Upstream offset from the bed 
        input starts for gRNA search", value = 0)),
    column(3,
        numericInput("downstreamSearch","Downstream offset from the bed 
        input ends for gRNA search",value = 0)))))
    ), ###gRNA Settings
      
#################### PAM PANEL #######################
    wellPanel(
    fluidRow(
    column(6, actionLink("PAMpanel", "PAM Advanced Options"))),
    conditionalPanel(
    condition <- "input.PAMpanel%2 == 1",
    br(), br(),
    fluidRow(
    column(4,
        numericInput("pamSize", "Set PAM length", value = 3)),
    column(4, 
        numericInput("PAMmismatch", "Number degenerative bases in the PAM",
        value = 2)),
    conditionalPanel(
    condition <- "input.chooseAction == 1 || input.chooseAction == 2",
    column(4,
        numericInput("baseAfter", "Number bases after PAM for efficiency", 
        value = 3)))),
    fluidRow(
    column(4,
        textInput("PAMSeq", "Enter PAM Sequence after gRNA", "NGG")),
    conditionalPanel(
    condition <- "input.chooseAction == 1 || input.chooseAction == 2",
    column(4,
        textInput("PAMpattern", "Enter PAM pattern for off target", "N[A|G]G$"))),
    conditionalPanel(
    condition <- "input.chooseAction == 3",
    column(4,
        textInput("PAMpattern", "Enter PAM pattern for off target",
        "(NAG|NGG|NGA)$"))))
    )), ###PAM Settings
     
#################### MORE ADVANCED PANEL #######################
    wellPanel(
    fluidRow(
    column(6, actionLink("advanced", "Other Advanced Options"))),
    conditionalPanel(
    condition <- "input.advanced%2 == 1",
    br(),
    conditionalPanel(
    condtion <- "input.chooseAction == 1 || input.chooseAction == 2",
    fluidRow(
    column(4,
        numericInput("temp", "Set temperature (celsius)", value = 37)),
    conditionalPanel(
    condition <- "input.chooseAction == 1",
    column(4,
        radioButtons("annExon", "Indicate whether off target is inside an exon?",
        choices = list("Yes" = 1, "No" = 2),
        selected = 1)),
    column(4,
        numericInput("REPatSize1", "Minimum RE Pattern Size", value = 4))),
    conditionalPanel(
    condition <- "input.chooseAction == 2",
    column(4,
        numericInput("REPatSize2", "Minimum RE Pattern Size", value = 6))))),
    conditionalPanel(
    condition <- "input.chooseAction == 3",
    fluidRow(
    column(4,
        numericInput("minR1", "Max mapped R1 bp length to be 
        considered for downstream analysis", value = 30)),
    column(4,
        numericInput("minR2", "Max mapped R2 bp length to be
        considered for downstream analysis",
        value = 30)),
    column(4,
        radioButtons("applyMinMapped", 
        "Apply min. mapped length requirements to both R1 and R2",
        choices = list("Yes" = 1, "No" = 2),
        selected = 2))),
    fluidRow(
    column(4,
        radioButtons("concordantStrand", 
        "R1 and R2 aligned to same strand or opposite strand?",
        choices = list("Opposite Strand" = 1, "Same Strand" = 2),
        selected = 1)),
    column(4,
        numericInput("maxPairedDistance",
        "Maximum bp distance between paired R1 and R2 reads",
        value = 1000)),
    column(4,
        numericInput("minMapQuality", "Minimum mapping quality of acceptable alignments",
        value = 30))),
    fluidRow(
    column(4,
        numericInput("distInterChrom", 
        "Distance value to assign to paired reads that are alighned to different
        chromosome", value = -1)),
    column(4,
        radioButtons("sameChrom", "Paired reads aligned to same chromosome?",
        choices = list("Yes" = 1, "No" = 2), selected = 1)),
    column(4,
        numericInput("minReads", "Minimum number of reads to be considered a peak",
        value = 20L))),
    fluidRow(
    column(4,
        numericInput("max.P", 
        "Maximum p-value to be considered as significant",
        value = 0.05)),
    column(4,
        selectInput("stat", "Statistical test choice",
        choices = list("poisson" = 1, "nbinom" = 2),
        selected = 1)),
    column(4,
        numericInput("distThreshold", 
        "Maximum gap allowed between plus and negative strand peak",
        value = 40))),
    fluidRow(
        radioButtons("adjustMethods", "Adjustment method for multiple comparisons",
        choices = list("None" = 1, "BH" = 2, "holm" = 3, "hochberg" =4,
        "hommel"= 5, "bonferroni" =6, "BY" = 7, "fdr" = 8),
        selected = 1, inline = TRUE))),
        br(),
        br(),
    conditionalPanel(
    condition <- "input.chooseAction == 1",
    fluidRow(
    column(4, 
        numericInput("minScore", "Minimum score of an off target to be included in the final output",
        value = 0)),
    column(4, 
        numericInput("top.N", "Top N off targets to be included in the final output",
        value = 1000)),
    column(4, 
        numericInput("topNscore", "Top N off target used to calculate the total off target score",
        value = 10))),
    fluidRow(
    column(3, 
        radioButtons("fetchSeq", "Fetch flank sequence of off target?",
        choices = list("Yes" = 1, "No" = 2), selected = 1)),
    conditionalPanel(
    condition <- "input.fetchSeq == 1",
    column(3,
        numericInput("up.stream", "Upstream offset from the off target start", 200)),
    column(3,
        numericInput("down.stream", "Downstream offset from the off target start", 
        200))))),
    fluidRow(
    conditionalPanel(
    condition <- "input.chooseAction == 2",
    column(3,
        numericInput("up.stream", "Upstream offset from the off target start", 0)),
    column(3,
        numericInput("down.stream", "Downstream offset from the off target start", 0))),
    conditionalPanel(
    condition <- "input.chooseAction == 3",
    column(3,
        numericInput("up.stream", "Upstream offset from the off target start", 50)),
    column(3,
        numericInput("down.stream", "Downstream offset from the off target start", 50)))),
    conditionalPanel(
    condition <- "input.chooseAction == 1 || input.chooseAction == 2",
    fluidRow(
        selectInput("scoringmethod", "Select method to use for offtarget cleavage rate
        estimation", choices = list("Hsu-Zhang" = 1, "CFDscore"= 2),
        selected = 1))),
    fluidRow(
    conditionalPanel(
    condition <- "input.scoringmethod == 1",
    column(8, 
    print(strong("Weights")), br(),
        tags$textarea(id="weight", rows = 2, cols = 100, 
        paste0("0, 0, 0.014, 0, 0, 0.395, 0.317, 0, 0.389, 0.079, 
               0.445, 0.508, 0.613,
               0.851, 0.732, 0.828, 0.615, 0.804, 0.685, 0.583"))))),
    conditionalPanel(
    condition <- "input.scoringmethod == 2",
    br(),
    paste("Please see side panel for Mismatch Activity File Upload"),
    br(), br(),
    fluidRow(
    column(6,
        numericInput("subPamPos1", "Start Position of Sub PAM", value = 22)),
    column(6,
        numericInput("subPamPos2", "End Position of Sub PAM", value = 23))),
        print("Sub PAM Activity Input:"),
        br(),
    column(3, numericInput("AA", "AA", value = 0)),
    column(3, numericInput("AC", "AC", value = 0)),
    column(3, numericInput("AG", "AG", value = 0.259259259)),
    column(3, numericInput("AT", "AT", value = 0)),
    column(3, numericInput("CA", "CA", value = 0)),
    column(3, numericInput("CC", "CC", value = 0)),
    column(3, numericInput("CG", "CG", value = 0.107142857)),
    column(3, numericInput("CT", "CT", value = 0)),
    column(3, numericInput("GA", "GA", value = 0.0694444440)),
    column(3, numericInput("GC", "GC", value = 0.022222222)),
    column(3, numericInput("GG", "GG", value = 1)),
    column(3, numericInput("GT", "GT", value = 0.016129032)),
    column(3, numericInput("TA", "TA", value = 0)),
    column(3, numericInput("TC", "TC", value = 0)),
    column(3, numericInput("TG", "TG", value = 0.038961039)),
    column(3, numericInput("TT", "TT", value = 0))),
    fluidRow(
    conditionalPanel(
    condition <- "input.chooseAction == 3",
    column(4,
        numericInput("window", "Window size to calculate coverage", value = 20)),
    column(4,
        numericInput("stepSize", "Step size to calculate coverage", value = 20)),
    column(4,
        numericInput("BGWindow", "Background Window Size", value = 5000)))),
    fluidRow(
    column(4,
        numericInput("mismatch", "Maximum mismatch:", min = 0, value = 3)))
    )#advanced settings
    ),
    fluidRow(
    column(4, actionButton("goButton", "Submit"))),
    br(),
    fluidRow(
    column(4, actionButton("resetFields", "Reset all fields to defaults"))),
    uiOutput('output1')),#Tab for Submission Panel
      
    tabPanel("Data Table",
    conditionalPanel(
    condition <- "input.chooseAction == 1",
    titlePanel("RE Cut Details")),
    
    conditionalPanel(
    condition <- "input.chooseAction == 2",
    titlePanel("Scores for 2 Input Sequences")),
    
    conditionalPanel(
    condition <- "input.chooseAction == 3",
    titlePanel("gRNA Peaks")),
        DT::dataTableOutput("tables")),#Tab for Data Table Panel
     
tabPanel("View Input Files",
    conditionalPanel(
    condition <- "input.chooseAction == 1",
        radioButtons("fileViewChoices", "Choose file to view",
        choices = list("Input File" = 1, "Pattern File" =2,
        "Mismatch Activity File" = 3), selected = 1),
                
    conditionalPanel(
    condition <- "input.fileViewChoices == 1",
    textOutput("fileInput1")),
  
    conditionalPanel(
    condition <- "input.fileViewChoices == 2",
        DT::dataTableOutput("fileInput2"))),
    conditionalPanel(
    condition <- "input.chooseAction == 2",
        radioButtons("fileViewChoices2", "Choose file to view",
        choices = list("Input File 1" = 1, "Input File 2" =2,
        "Mismatch Activity File" = 3), selected = 1),
    
    conditionalPanel(
    condition <- "input.fileViewChoices2 == 1",
    textOutput("fileInput3")),
    
    conditionalPanel(
    condition <- "input.fileViewChoices2 == 2",
    textOutput("fileInput4"))),
    
    conditionalPanel(
    condition <- "input.chooseAction == 3",
        radioButtons("fileViewChoices3", "Choose file to view",
        choices = list("UMI File" = 1, "Alignment File" = 2, 
        "gRNA File" = 3), selected =1),
        
    conditionalPanel(
    condition <- "input.fileViewChoices3 == 1",
        DT::dataTableOutput("fileInput5")),
    
    conditionalPanel(
    condition <- "input.fileViewChoices3 == 2",
    print("Alignment file too large to view")),
    
    conditionalPanel(
    condition <- "input.fileViewChoices3 == 3",
    textOutput("fileInput7")
    ))))#Tabset Panel
)#mainPanel
)#sidebarLayout
))}