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ui.R
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# Author: Tokhir Dadaev
# License: MIT + file LICENSE.txt
# About -------------------------------------------------------------------
# User interface file for shiny
# Define UI ---------------------------------------------------------------
shinyUI(
fluidPage(
shinyjs::useShinyjs(),
theme = shinytheme("united"),
#titlePanel("NGS v0.1", "NGS"),
titlePanel(title = div("NGS v0.1", img(src = "logoICR.png",
style = "float: right",
height = "40")), "NGS"),
# ~ sidebarPanel ------------------------------------------------------
sidebarPanel(width = 3,
checkboxGroupInput("data", "Data",
choices =
setNames(namesVCF, gsub("_", " ", namesVCF)),
selected = namesVCF[1]),
hr(),
conditionalPanel(
condition = "input.tabsetPanelMain == 'Panel'",
radioButtons("typePanel", "Select panel type:",
c("ICR curated" = "ICR",
"Wood R.D." = "DNA_repair_pathways_Woods",
"MutSigDB Hallmark" = "MutSigDB_hallmark")),
uiOutput("ui_genePanel"),
uiOutput("ui_gene")
),
conditionalPanel(
condition = "input.tabsetPanelMain == 'Variants'",
radioButtons("plotParallelVariantGrp", "Parallel plot group:",
c("SYMBOL", "IMPACT", "LoF", "REVEL", "CADD_PHRED"),
inline = TRUE),
radioButtons("andOr", "FilterOption", choices = c("AND", "OR"),
selected = "OR", inline = TRUE),
#MAF
sliderInput("ExAC_AF_NFE", "ExAC_AF_NFE *", min = 0, max = 1, value = 0.01),
h6("* Non-Finnish European Allele Frequency from ExAC"),
# ClinVar
selectInput("CLNSIG", "CLNSIG (ClinVar)", filterCol$CLNSIG,
#selected = filterCol$CLNSIG[11],
multiple = TRUE, selectize = TRUE),
# VEP
selectInput("Consequence", "Consequence", filterCol$Consequence,
#selected = filterCol$Consequence[1],
multiple = TRUE, selectize = TRUE),
checkboxGroupInput("IMPACT", "IMPACT", filterCol$IMPACT, inline = TRUE),
checkboxGroupInput("LoF", "LoF", filterCol$LoF, inline = TRUE),
checkboxGroupInput("SIFT", "SIFT", filterCol$SIFT, inline = TRUE),
checkboxGroupInput("PolyPhen", "PolyPhen", filterCol$PolyPhen,
inline = TRUE)
), # END input.tabsetPanelMain == 'Variants'
conditionalPanel(
condition = "input.tabsetPanelMain == 'Sample'",
radioButtons("plotParallelSampleGrp", "Parallel plot group:",
c("Mutation", "PrCa", "FH", "COD_PrCa", "AgeDiag",
"GleasonScore", "Gleason7",
"NCCN", "NICE",
"TStage", "NStage", "MStage",
"PSADiag"),
selected = "Mutation",
inline = TRUE),
checkboxGroupInput("samplePrCa", "Prostate cancer:",
c("0", "1", "NA"),
selected = c("0", "1", "NA"),
inline = TRUE),
checkboxGroupInput("sampleEthnicityOA", "Ethnicity OA:",
c("African", "Asian", "European", "Mixed_ethnic", "NA"),
selected = "European",
inline = TRUE),
checkboxGroupInput("sampleEthnicity", "Ethnicity Progeny:",
c("0", "1", "6", "7", "8", "NA"),
selected = "1",
inline = TRUE),
splitLayout(
checkboxGroupInput("sampleFH", "Family history:",
c("0", "1", "NA"), selected = c("0", "1", "NA"), inline = TRUE),
checkboxGroupInput("sampleCOD", "COD PrCa:",
c(0, 1, "NA"), selected = c(0, 1, "NA"), inline = TRUE)),
sliderInput("sampleAge", "AgeDiag:",
min = 0, max = 100, value = c(20, 100), step = 2.5),
sliderInput("sampleGleason", "Gleason:",
min = 0, max = 10, value = c(2, 10), step = 1),
sliderInput("samplePSADiag", "PSA at diagnosis:",
min = -1, max = 100, value = c(0, 100), step = 1),
checkboxGroupInput("sampleTStage", "TStage:",
c(1:4, "NA"), selected = c(1:4, "NA"), inline = TRUE),
splitLayout(
checkboxGroupInput("sampleNStage", "NStage:",
c(0, 1, "NA"), selected = c(0, 1, "NA"), inline = TRUE),
checkboxGroupInput("sampleMStage", "MStage:",
c(0, 1, "NA"), selected = c(0, 1, "NA"), inline = TRUE))
), # END "input.tabsetPanelMain == 'Sample'"
conditionalPanel(
condition = "input.tabsetPanelMain == 'Panel'",
sliderInput("qcMissVariant", "Variant missingness", min = 0, max = 0.5, value = 0.5),
sliderInput("qcMissSample", "Sample missingness", min = 0, max = 0.5, value = 0.5)
),
conditionalPanel(
condition = "input.tabsetPanelMain == 'Stats'",
checkboxGroupInput("cacoType", "Status:",
c("COD_PrCa", "FH",
"GleasonScore", "Gleason7",
"TStage", "NStage", "MStage", "PSADiag", "NCCN", "NICE"),
selected = c("NStage", "MStage"), inline = TRUE)
)
),#sidebarPanel
# ~ mainPanel---------------------------------------------------------
mainPanel(
tabsetPanel(
id = "tabsetPanelMain",
tabPanel("Panel",
h4("Panel"),
hr(),
plotOutput("geneOverlap"),
dataTableOutput("genes")),
tabPanel("Variants",
h4("Variants"),
hr(),
#tableOutput("testInput"),
splitLayout(
plotOutput("variantOverlap", width = "80%"),
plotOutput("variantSubsetOverlap", width = "80%")),
hr(), plotOutput("variantParallel"),
hr(), dataTableOutput("annot")),
tabPanel("Sample",
h4("Sample"),
hr(),
#tableOutput("testFH"),
splitLayout(
plotOutput("sampleOverlap"),
plotOutput("sampleSubsetOverlap")),
hr(), plotOutput("phenoParallel"),
hr(), plotOutput("phenoNA"),
dataTableOutput("pheno")
),
tabPanel("QC",
h4("QC"),
hr(),
tableOutput("testGT"),
#plotOutput("qcMissGT"),
plotOutput("qcMissGTperGene"),
hr(), dataTableOutput("gt")
),
tabPanel("Stats",
h4("Stats"),
hr(),
tabsetPanel(id = "stats", type = "pills",
tabPanel("Mutation count", hr(), dataTableOutput("mutCount")),
tabPanel("dNdScv", hr(),
dataTableOutput("dNdScv"),
h4("Input data for dNdScv"),
dataTableOutput("dNdScvInput")),
tabPanel("SKAT Gene", hr(),
dataTableOutput("geneSkat"),
hr(),
textOutput("geneSkatConsole")
),
tabPanel("Burden Gene", hr(), dataTableOutput("geneBurden")),
tabPanel("SKAT gene set", hr(),
dataTableOutput("allGenesSkat")),
tabPanel("Burden gene set", hr(), h3("to-do")))
),
tabPanel("Summary",
h4("Summary"),
hr(),
h3("to-do: some summary plots... ")),
# ~~ Help -------------------------------------------------------
tabPanel("Help",
h4("Help"),
hr(),
tabsetPanel(
tabPanel("About",
h4("About"),
hr(),
includeMarkdown("README.md")),
tabPanel("R Session Info",
h4("R Session Info"),
hr(),
includeMarkdown("Markdown/RSessionInfo.md")),
tabPanel("Raw data - VCFs",
h4("Raw data - VCFs"),
hr(),
img(src = "logoICR.png"),
hr(),
includeMarkdown("Markdown/ICR_Data.md")),
tabPanel("Theme",
hr("Theme"),
shinythemes::themeSelector()),
type = "pills")#tabsetPanel
)#tabPanel
)#tabsetPanel
)#mainPanel
)#fluidPage
)#shinyUI
# TESTING -----------------------------------------------------------------