R/ui.R
In UMMS-Biocore/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
))}
UMMS-Biocore/crisprseekplus documentation built on May 9, 2019, 5:20 p.m.
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#' 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
))}
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