Nothing
inst/shinyApp/ui.R
In TVTB: TVTB: The VCF Tool Box
# This is the user-interface definition of a Shiny web application.
# You can find out more about building applications with Shiny here:
#
# http://shiny.rstudio.com
#
library(shiny)
shinyUI(navbarPage(
theme = "bootstrap.css",
title = "tSVE",
id = "tSVE",
navbarMenu(
title = "Input",
tabPanel(
title = "Phenotypes",
# Phenotype options ----
wellPanel(
h4("Phenotypes"),
hr(),
fluidRow(
column(
width = 2,
p(strong("Phenotype file")),
actionButton(
"selectPheno", "Browse",
icon = icon("file"), width = '100%')
),
column(
width = 6,
strong("File"),
br(),
uiOutput("phenoFile"),
# Wrap long file names
tags$head(tags$style(
"#phenoFile{
display:block;
word-wrap:break-word;
}"
))
),
column(
width = 4,
strong("Summary"), br(),
htmlOutput("phenoFileSummary")
)
),
fluidRow(
column(
width = 2,
br(),
actionButton(
"demoPheno", "Sample file",
icon = icon("file-text"), width = '100%')
)
)
),
fluidRow(
column(
width = 12,
tags$h4("Notes"),
"The phenotype file must be formatted as follows:",
tags$ul(
tags$li(
"Fields separator must be 'white space', the default",
tags$a(
href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/read.table.html",
tags$code("read.table")
),
"field separator."
),
tags$li(
"First row must be phenotype names."
),
tags$li(
"First column must be samples identifiers matching those in",
"the VCF file(s)."
)
)
)
)
),
tabPanel(
title = "Genomic ranges",
# GRanges options ----
wellPanel(
h4("Genomic ranges"),
hr(),
fluidRow(
column(
width = 2,
selectInput(
"grangesInputMode", "Input type",
choices = list(
"BED file" = "bed",
"UCSC browser" = "ucsc",
"EnsDb package" = "EnsDb"
),
selected = "bed",
width = '100%')
),
column(
width = 4, offset = 6,
strong("Summary"),
htmlOutput("rangesSummary")
)
),
fluidRow(
conditionalPanel(
condition = "input.grangesInputMode == 'bed'",
fluidRow(
column(
width = 2,
br(),
actionButton(
"selectBed", "Browse",
icon = icon("file"), width = '100%')
),
column(
width = 6,
strong("File"), br(),
uiOutput("bedFile")
),
# Wrap long file names
tags$head(tags$style(
"#bedFile{
display:block;
scanVcfHeader word-wrap:break-word;
}"
))
),
fluidRow(
column(
width = 2,
br(),
actionButton(
"demoBed", "Sample file",
icon = icon("file-text"), width = '100%')
)
)
),
conditionalPanel(
condition = "input.grangesInputMode == 'ucsc'",
column(
width = 8,
textInput(
"ucscRanges", "UCSC-type genomic ranges",
value = "",
placeholder = paste(
"chr21:33,031,597-33,041,570",
"chr2:2,031,597-2,041,570",
"...",
sep = " ; "),
width = "100%")
),
column(
width = 2,
br(),
actionButton(
"demoUCSC", "Sample input",
icon = icon("font"), width = '100%')
)
),
conditionalPanel(
condition = "input.grangesInputMode == 'EnsDb'",
column(
width = 2,
selectInput(
"ensDb.type", "Type",
choices = list("Gene name" = "Genename"),
selected = "Genename")
),
column(
width = 1,
selectInput(
"ensDb.condition", "Condition",
choices = c("=", "!=", "like", "in"),
selected = "=")
),
column(
2,
textInput(
"ensDb.value", "Value",
value = "",
placeholder = "SLC24A5,IL17A,...")
),
column(
width = 2,
actionButton(
"demoEnsDb", "Sample input",
icon = icon("font"), width = '100%')
),
column(
width = 4, offset = 1,
strong("Note"),
p(
"For the ", code("like"), "filter,",
"use ", code("%"), "as wildcard."
)
),
tabsetPanel(
id = "ensDb.resultTab",
selected = "Genes",
tabPanel(
title = 'Genes',
DT::dataTableOutput("ensDb.Genes")
)#, # TODO
# tabPanel('Transcripts',
# dataTableOutput("Transcripts")
# ),
# tabPanel('Exons',
# dataTableOutput("Exons")
# )
)
)
)
)
),
tabPanel(
title = "Variants",
# VCF options ----
wellPanel(
h4("VCF file(s)"),
hr(),
fluidRow(
column(
width = 2,
selectInput(
"vcfInputMode", "VCF input type",
choices = list(
"Single VCF" = "SingleVcf",
"One per chromosome" = "OnePerChr"
),
selected = "OnePerChr",
width = '100%')
),
conditionalPanel(
condition = "input.vcfInputMode == 'SingleVcf'",
column(
width = 2,
br(),
actionButton(
"selectVcf", "Browse",
icon = icon("file"), width = '100%')
),
column(
width = 2,
br(),
actionButton(
"demoVcf", "Sample file",
icon = icon("file-text"), width = '100%')
),
column(
width = 4, offset = 2,
strong("Summary"),
br(),
textOutput("selectedVcf"),
# Wrap long file names
tags$head(tags$style(
"#selectedVcf{
display:block;
word-wrap:break-word;
}"
))
)
),
conditionalPanel(
condition = "input.vcfInputMode == 'OnePerChr'",
column(
width = 6,
textInput(
"vcfFolder", "Folder of VCF files",
value = system.file("extdata", package = "TVTB"),
width = '100%',
placeholder = "/path/to/VCF/folder")
),
column(
width = 4,
strong("Summary"),
htmlOutput("vcfFolderSummary")
)
)
),
fluidRow(
conditionalPanel(
condition = "input.vcfInputMode == 'OnePerChr'",
fluidRow(
column(
width = 6, offset = 2,
textInput(
"vcfPattern",
paste(
"Pattern of VCF files",
"(%s : chromosome placeholder)"
),
value = "^chr%s\\..*\\.vcf\\.gz$",
width = '100%',
placeholder = "^chr%s_.*\\.vcf\\.gz$")
)
)
)
)
),
wellPanel(
h4("VCF scan parameters"),
hr(),
fluidRow(
# ScanVcfParam ----
# INFO fields (except VEP) ----
column(
width = 8,
fluidRow(
column(
width = 12,
selectInput(
"vcfInfoKeys", "INFO fields",
choices = character(),
multiple = TRUE)
)
),
fluidRow(
column(
width = 2,
actionButton(
"tickAllInfo", "Select all",
icon = icon("check-square-o"))
),
column(
width = 2,
actionButton(
"untickAllInfo", "Deselect all",
icon = icon("square-o"))
),
column(
width = 7, offset = 1,
strong("Note:"),
"VEP field implicitely required"
)
)
),
# VEP prediction INFO field ----
column(
width = 2,
textInput(
"vepKey", "VEP field (INFO)",
value = get("vepKey", .tSVE),
placeholder = 'CSQ, ANN, ...')
),
# FORMAT fields ----
column(
width = 2,
selectInput(
"vcfFormatKeys", "FORMAT fields",
choices = character(),
multiple = TRUE),
strong("Note:"), "\"GT\" implicitely required"
)
)
),
wellPanel(
fluidRow(
# VCF import button! ----
column(
width = 2,
checkboxInput(
"autodetectGTimport", "Autodetect genotypes",
value = get("autodetectGTimport", .tSVE)
)
),
column(
width = 2, offset = 3,
br(),
actionButton(
"importVariants", "Import variants",
icon = icon("open", lib = "glyphicon")
)
),
column(
width = 4, offset = 1,
strong("Summary"),
htmlOutput("vcfSummary")
)
)
),
hr(),
fluidRow(
column(
width = 6,
h4("Content of folder"),
hr(),
DT::dataTableOutput("vcfContent")
),
column(
width = 6,
h4("VCF file(s) matching pattern"),
hr(),
DT::dataTableOutput("vcfFiles")
)
)
),
tabPanel(
title = "Annotations",
# Genome annotation package ----
wellPanel(
h4("Annotations"),
hr(),
fluidRow(
column(
width = 3,
selectInput(
"annotationPackage",
"Select installed EnsDb package",
choices = as.list(.EnsDbPacks),
width = '100%')
),
column(
3,
strong("EnsDb annotation"),
htmlOutput("ensembl_organism"),
htmlOutput("ensembl_version"),
htmlOutput("ensembl_genome")
),
column(
width = 6,
strong("Note"),
p(
"Only",
tags$code("EnsDb"),
"annotation packages supported for starters.",
"Ideally, ",
tags$code("TxDb"),
"and",
tags$code("OrganismDb"),
"packages supported soon.")
)
)
)
)
),
# Calculate frequencies ----
tabPanel(
title = "Frequencies", icon = icon("calculator "),
uiOutput("TVTBparamWarning"),
wellPanel(
fluidRow(
column(
width = 2,
strong("Latest changes:")
),
column(
width = 10,
uiOutput("latestFrequenciesCalculated")
)
)
),
wellPanel(
fluidRow(
h4("Overall frequencies"), hr(),
column(
width = 1, offset = 1,
actionButton(
"addOverallFrequencies", "Add",
icon = icon("plus")
)
),
column(
width = 1,
actionButton(
"removeOverallFrequencies", "Remove",
icon = icon("minus")
)
)
)
),
wellPanel(
fluidRow(
h4("Frequencies in phenotype levels"), hr(),
column(
width = 2,
selectInput(
"phenoAddFrequencies",
"Phenotype",
choices = character()
)
),
column(
width = 2, offset = 1,
actionButton(
"tickAllPhenoLevelsFreq",
"Select all",
icon = icon("check-square-o"),
width = "100%"
), br(),
actionButton(
"untickAllPhenoLevelsFreq",
"Deselect all",
icon = icon("square-o"),
width = "100%"
)
),
column(
width = 2, offset = 1,
br(),
actionButton(
"buttonFrequencies", "Refresh",
icon = icon("refresh"), width = "100%"
)
)
),
fluidRow(
column(
width = 12,
checkboxGroupInput(
"phenoLevelFreqCheckboxes", "Phenotype levels",
choices = c(), inline = TRUE
)
)
)
)
),
# VCF filter Rules ----
tabPanel(
title = "Filters", icon = icon("filter"),
wellPanel(
h4("Add filter"),
fluidRow(
column(
width = 1,
br(),
actionButton(
"addNewFilter", "Add filter",
icon = icon("plus")
)
),
column(
width = 1,
selectInput(
"newFilterClass", "Type",
choices = list(
"fixed" = "VcfFixedRules",
"info" = "VcfInfoRules",
"VEP" = "VcfVepRules"
),
selected = "VcfFixedRules"
)
),
column(
width = 1,
br(),
checkboxInput(
"newFilterActive", "Active?",
value = TRUE
)
),
column(
width = 7,
textInput(
"newFilterExpression", "Expression",
placeholder = paste(
"grepl(\"pass\", tolower(FILTER))",
"ALT + HET > 0",
"IMPACT %in% c(\"HIGH\", \"MODERATE\")",
sep = " - or - "
)
)
),
column(
width = 2,
br(),
actionButton(
"demoFilter", "Sample input",
icon = icon("font"), width = '100%')
)
),
fluidRow(
column(
width = 12,
uiOutput("vcfFilterTest")
)
),
fluidRow(
br(),
p(strong("Notes:")),
tags$ul(
tags$li(
"Filters are tested against variants to ensure the",
"validity of filters. Therefore, variants must be",
"loaded", em("before"), "filters can be created."
),
tags$li(
"Currently, filters are not re-tested if variants are",
"updated. If variants are refreshed, users should",
"ensure filters remain valid, or remove filters",
"manually."
),
tags$li(
"Users may ignore auto-correction of quotes in the",
strong("Expression"), "field. The application",
"automatically substitutes",
"curly quotes (single and double) by their",
"corresponding regular quotes (",
em("i.e."), code("\""), "and", code("'"), ")"
)
)
)
),
wellPanel(
fluidRow(
column(
width = 4, offset = 1,
strong("Summary"), br(),
uiOutput("filtersSummary")
),
column(
width = 2,
actionButton(
"filterVariants", "Apply filters",
icon = icon("filter"), width = "100%"
)
),
column(
width = 4,
strong("Summary"), br(),
uiOutput("filteredVcfSummary")
)
)
),
wellPanel(
fluidRow(
column(
width = 1,
strong("Class")
),
column(
width = 1,
strong("Active?")
),
column(
width = 8,
strong("Expression")
)
),
br(),
uiOutput("vcfFilterControls")
),
wellPanel(
fluidRow(
column(
width = 12,
verbatimTextOutput("vcfRules")
)
)
)
),
tabPanel(
title = "Views", icon = icon("picture-o"),
tabsetPanel(
id = "tabset.views",
# Genomic ranges view ----
tabPanel(
title = "Genomic ranges",
fluidRow(
column(
width = 12,
DT::dataTableOutput("rangesTableView")
)
)
),
# Variants view ----
tabPanel(
title = "Variants",
fluidRow(
column(
width = 12,
wellPanel(
uiOutput("vcfCols")
)
)
),
fluidRow(
column(
width = 12,
DT::dataTableOutput("vcfRowRangesView")
)
)
),
# Variants INFO view ----
tabPanel(
title = "INFO",
fluidRow(
column(
width = 12,
wellPanel(
uiOutput("vcfInfoCols"),
br(),
p(strong("Notes:")),
tags$ul(
tags$li(
"Fields that contain more than one value",
"(", tags$em("e.g."), "confidence intervals)",
"may not display properly."
)
)
)
)
),
fluidRow(
column(
width = 12,
DT::dataTableOutput("vcfInfoView")
)
)
),
# VEP predictions view ----
tabPanel(
title = "VEP",
fluidRow(
column(
width = 12,
wellPanel(
uiOutput("vepCols")
)
)
),
fluidRow(
column(
width = 12,
DT::dataTableOutput("vcfVepView")
)
)
),
# Phenotypes view ----
tabPanel(
title = "Phenotypes",
fluidRow(
column(
width = 12,
"This panel displays phenotype information attached to",
"the imported VCF object.",
wellPanel(
uiOutput("phenoCols")
)
)
),
fluidRow(
column(
width = 12,
DT::dataTableOutput("phenotypesView")
)
)
),
# Genotypes view ----
tabPanel(
title = "Genotypes",
tabsetPanel(
tabPanel(
title = "Matrix",
fluidRow(
wellPanel(
column(
width = 6,
uiOutput("genoNumRows")
),
column(
width = 6,
uiOutput("genoFirstRow")
)
)
),
fluidRow(
wellPanel(
column(
width = 6,
uiOutput("genoNumCols")
),
column(
width = 6,
uiOutput("genoFirstCol")
)
)
),
fluidRow(
column(
width = 12,
tableOutput("genotypesSample")
)
)
),
tabPanel(
title = "Heatmap",
p(
"Click the button after loading variants",
"to generate/update the figure",
actionButton(
"doGenoHeatmap", "Go!",
icon = icon("time")
)
),
fluidRow(
column(
width = 12,
plotOutput(
"heatmapGenotype",
height = get("genoHeatmap.height", .tSVE)
)
)
),
p(
"Notes",
tags$ul(
tags$li(
"This may take some time to plot.",
em(
"(~15s for 218 variants & 5844",
"samples)"
)
),
tags$li(
"Only genotypes codes found in the data",
"are listed in the legend, irrespective",
"of those defined in the",
tags$strong("Advanced settings"), "."
)
)
)
),
tabPanel(
title = "Info",
shiny::h4("Encoding"),
uiOutput("genotypeEncoding")
)
)
)
)
),
navbarMenu(
title = "Settings", icon = icon("wrench"),
# Advanced settings ----
tabPanel(
title = "Advanced",
wellPanel(
h4("Genotypes"),
hr(),
fluidRow(
column(
width = 1,
br(),
actionButton(
"genotypeAutofill", "Autofill", icon("magic")
)
),
column(
width = 3,
selectInput(
"refGenotypes", "Reference homozygote genotype(s)",
choices = c(get("refGT", .tSVE), get("hetGT", .tSVE), get("altGT", .tSVE)),
selected = get("refGT", .tSVE),
multiple = TRUE
)
),
column(
width = 4,
selectInput(
"hetGenotypes", "Heterozygote genotype(s)",
choices = c(get("refGT", .tSVE), get("hetGT", .tSVE), get("altGT", .tSVE)),
selected = get("hetGT", .tSVE),
multiple = TRUE
)
),
column(
width = 4,
selectInput(
"altGenotypes", "Alternate homozygote genotype(s)",
choices = c(get("refGT", .tSVE), get("hetGT", .tSVE), get("altGT", .tSVE)),
selected = get("altGT", .tSVE),
multiple = TRUE
)
)
),
fluidRow(
column(
width = 1,
textInput(
"refSuffix", "Suffix",
value = get("refSuffix", .tSVE),
placeholder = get("refSuffix", .tSVE)
)
),
column(
width = 1, offset = 3,
textInput(
"hetSuffix", "Suffix",
value = get("hetSuffix", .tSVE),
placeholder = get("hetSuffix", .tSVE)
)
),
column(
width = 1, offset = 3,
textInput(
"altSuffix", "Suffix",
value = get("altSuffix", .tSVE),
placeholder = get("altSuffix", .tSVE)
)
)
),
fluidRow(
column(
width = 12,
tags$strong("Notes:"), br(),
tags$ul(
tags$li(
"The",tags$strong("choices"),"of genotypes are updated when",
"new variants are imported."
),
tags$li(
"The",tags$strong("selected"),"genotypes may be automatically",
"updated immediately after import using the",
tags$strong("Autodetect genotypes"), "checkbox in the",
tags$strong("Input"), "panel, or manually after import using",
"the", tags$strong("Autofill"), "button in this panel."
),
tags$li(
"Selected genotypes are not allowed to overlap.",
"Selecting a genotype removes it from the choices",
"available in the other widgets. As a consequence, genotypes",
"must first be unselected from a widget before it can be",
"selected in another one."
)
)
)
)
),
wellPanel(
h4("INFO suffixes"),
hr(),
fluidRow(
column(
width = 3,
textInput(
"aafSuffix", "ALT allele freq.",
value = get("aafSuffix", .tSVE),
placeholder = get("aafSuffix", .tSVE)
)
),
column(
width = 3,
textInput(
"mafSuffix", "Minor allele freq.",
value = get("mafSuffix", .tSVE),
placeholder = get("mafSuffix", .tSVE)
)
)
)
),
wellPanel(
h4("VCF file(s)"),
hr(),
fluidRow(
column(
width = 2,
numericInput(
"yieldSize", "VCF yield size (100-100^3)",
min = 100, max = 100E3,
value = 4E3,
step = 1E3
)
)
)
)
),
tabPanel(
title = "Parallel",
wellPanel(
h4("Parallel settings"),
hr(),
fluidRow(
column(
width = 3,
numericInput(
"bpCores", "Cores",
value = .PS[["default.bpCores"]],
min = 1, max = .PS[["default.bpCores"]], step = 1)
),
column(
width = 3,
selectInput(
"bpConfig", "Cluster configuration",
choices = structure(
as.list(.PS[["choices.bpClass"]]),
names = gsub(
"Param", "", .PS[["choices.bpClass"]])),
selected = .PS[["default.bpClass"]])
),
conditionalPanel(
condition = "input.bpConfig != 'SerialParam'",
column(
width = 3,
selectInput(
"bpType", "Cluster type",
choices = structure(
as.list(.PS[["choices.bpType"]]),
names = gsub(
"Param", "", .PS[["choices.bpType"]])),
selected = .PS[["default.bpType"]])
)
)
) # fluidRow
), # wellPanel
wellPanel(
fluidRow(
column(
width = 12,
h1("Platforms tested"),
DT::dataTableOutput("parallelReport")
)
)
),
tags$h4(
"Notes",
tags$ul(
tags$li(
"Report"
), br(),
tags$ul(
tags$li(
tags$strong("Hang:"),
"Application hangs while CPUs work infinitely at full capacity."
)
)
)
)
)
),
# Session settings view ----
tabPanel(
title = "Session",
tabsetPanel(
id = "tabset.session",
tabPanel(
title = "Session info",
verbatimTextOutput("sessionInfo")
),
tabPanel(
title = "TVTB settings",
verbatimTextOutput("TVTBsettings")
),
tabPanel(
title = "General settings",
verbatimTextOutput("generalSettings")
),
tabPanel(
title = "Advanced settings",
verbatimTextOutput("advancedSettings")
),
tabPanel(
title = "ExpandedVCF",
"This panel displays the structure of the imported",
tags$code("ExpandedVCF"), "object:",
verbatimTextOutput("ExpandedVCF"),
"and the attached", tags$code("metadata"), ":",
verbatimTextOutput("vcfMetadata")
),
tabPanel(
title = "VEP",
verbatimTextOutput("vepStructure")
),
tabPanel(
title = "Errors",
verbatimTextOutput("Errors")
)
)
)
))
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# This is the user-interface definition of a Shiny web application.
# You can find out more about building applications with Shiny here:
#
# http://shiny.rstudio.com
#
library(shiny)
shinyUI(navbarPage(
theme = "bootstrap.css",
title = "tSVE",
id = "tSVE",
navbarMenu(
title = "Input",
tabPanel(
title = "Phenotypes",
# Phenotype options ----
wellPanel(
h4("Phenotypes"),
hr(),
fluidRow(
column(
width = 2,
p(strong("Phenotype file")),
actionButton(
"selectPheno", "Browse",
icon = icon("file"), width = '100%')
),
column(
width = 6,
strong("File"),
br(),
uiOutput("phenoFile"),
# Wrap long file names
tags$head(tags$style(
"#phenoFile{
display:block;
word-wrap:break-word;
}"
))
),
column(
width = 4,
strong("Summary"), br(),
htmlOutput("phenoFileSummary")
)
),
fluidRow(
column(
width = 2,
br(),
actionButton(
"demoPheno", "Sample file",
icon = icon("file-text"), width = '100%')
)
)
),
fluidRow(
column(
width = 12,
tags$h4("Notes"),
"The phenotype file must be formatted as follows:",
tags$ul(
tags$li(
"Fields separator must be 'white space', the default",
tags$a(
href="http://stat.ethz.ch/R-manual/R-devel/library/utils/html/read.table.html",
tags$code("read.table")
),
"field separator."
),
tags$li(
"First row must be phenotype names."
),
tags$li(
"First column must be samples identifiers matching those in",
"the VCF file(s)."
)
)
)
)
),
tabPanel(
title = "Genomic ranges",
# GRanges options ----
wellPanel(
h4("Genomic ranges"),
hr(),
fluidRow(
column(
width = 2,
selectInput(
"grangesInputMode", "Input type",
choices = list(
"BED file" = "bed",
"UCSC browser" = "ucsc",
"EnsDb package" = "EnsDb"
),
selected = "bed",
width = '100%')
),
column(
width = 4, offset = 6,
strong("Summary"),
htmlOutput("rangesSummary")
)
),
fluidRow(
conditionalPanel(
condition = "input.grangesInputMode == 'bed'",
fluidRow(
column(
width = 2,
br(),
actionButton(
"selectBed", "Browse",
icon = icon("file"), width = '100%')
),
column(
width = 6,
strong("File"), br(),
uiOutput("bedFile")
),
# Wrap long file names
tags$head(tags$style(
"#bedFile{
display:block;
scanVcfHeader word-wrap:break-word;
}"
))
),
fluidRow(
column(
width = 2,
br(),
actionButton(
"demoBed", "Sample file",
icon = icon("file-text"), width = '100%')
)
)
),
conditionalPanel(
condition = "input.grangesInputMode == 'ucsc'",
column(
width = 8,
textInput(
"ucscRanges", "UCSC-type genomic ranges",
value = "",
placeholder = paste(
"chr21:33,031,597-33,041,570",
"chr2:2,031,597-2,041,570",
"...",
sep = " ; "),
width = "100%")
),
column(
width = 2,
br(),
actionButton(
"demoUCSC", "Sample input",
icon = icon("font"), width = '100%')
)
),
conditionalPanel(
condition = "input.grangesInputMode == 'EnsDb'",
column(
width = 2,
selectInput(
"ensDb.type", "Type",
choices = list("Gene name" = "Genename"),
selected = "Genename")
),
column(
width = 1,
selectInput(
"ensDb.condition", "Condition",
choices = c("=", "!=", "like", "in"),
selected = "=")
),
column(
2,
textInput(
"ensDb.value", "Value",
value = "",
placeholder = "SLC24A5,IL17A,...")
),
column(
width = 2,
actionButton(
"demoEnsDb", "Sample input",
icon = icon("font"), width = '100%')
),
column(
width = 4, offset = 1,
strong("Note"),
p(
"For the ", code("like"), "filter,",
"use ", code("%"), "as wildcard."
)
),
tabsetPanel(
id = "ensDb.resultTab",
selected = "Genes",
tabPanel(
title = 'Genes',
DT::dataTableOutput("ensDb.Genes")
)#, # TODO
# tabPanel('Transcripts',
# dataTableOutput("Transcripts")
# ),
# tabPanel('Exons',
# dataTableOutput("Exons")
# )
)
)
)
)
),
tabPanel(
title = "Variants",
# VCF options ----
wellPanel(
h4("VCF file(s)"),
hr(),
fluidRow(
column(
width = 2,
selectInput(
"vcfInputMode", "VCF input type",
choices = list(
"Single VCF" = "SingleVcf",
"One per chromosome" = "OnePerChr"
),
selected = "OnePerChr",
width = '100%')
),
conditionalPanel(
condition = "input.vcfInputMode == 'SingleVcf'",
column(
width = 2,
br(),
actionButton(
"selectVcf", "Browse",
icon = icon("file"), width = '100%')
),
column(
width = 2,
br(),
actionButton(
"demoVcf", "Sample file",
icon = icon("file-text"), width = '100%')
),
column(
width = 4, offset = 2,
strong("Summary"),
br(),
textOutput("selectedVcf"),
# Wrap long file names
tags$head(tags$style(
"#selectedVcf{
display:block;
word-wrap:break-word;
}"
))
)
),
conditionalPanel(
condition = "input.vcfInputMode == 'OnePerChr'",
column(
width = 6,
textInput(
"vcfFolder", "Folder of VCF files",
value = system.file("extdata", package = "TVTB"),
width = '100%',
placeholder = "/path/to/VCF/folder")
),
column(
width = 4,
strong("Summary"),
htmlOutput("vcfFolderSummary")
)
)
),
fluidRow(
conditionalPanel(
condition = "input.vcfInputMode == 'OnePerChr'",
fluidRow(
column(
width = 6, offset = 2,
textInput(
"vcfPattern",
paste(
"Pattern of VCF files",
"(%s : chromosome placeholder)"
),
value = "^chr%s\\..*\\.vcf\\.gz$",
width = '100%',
placeholder = "^chr%s_.*\\.vcf\\.gz$")
)
)
)
)
),
wellPanel(
h4("VCF scan parameters"),
hr(),
fluidRow(
# ScanVcfParam ----
# INFO fields (except VEP) ----
column(
width = 8,
fluidRow(
column(
width = 12,
selectInput(
"vcfInfoKeys", "INFO fields",
choices = character(),
multiple = TRUE)
)
),
fluidRow(
column(
width = 2,
actionButton(
"tickAllInfo", "Select all",
icon = icon("check-square-o"))
),
column(
width = 2,
actionButton(
"untickAllInfo", "Deselect all",
icon = icon("square-o"))
),
column(
width = 7, offset = 1,
strong("Note:"),
"VEP field implicitely required"
)
)
),
# VEP prediction INFO field ----
column(
width = 2,
textInput(
"vepKey", "VEP field (INFO)",
value = get("vepKey", .tSVE),
placeholder = 'CSQ, ANN, ...')
),
# FORMAT fields ----
column(
width = 2,
selectInput(
"vcfFormatKeys", "FORMAT fields",
choices = character(),
multiple = TRUE),
strong("Note:"), "\"GT\" implicitely required"
)
)
),
wellPanel(
fluidRow(
# VCF import button! ----
column(
width = 2,
checkboxInput(
"autodetectGTimport", "Autodetect genotypes",
value = get("autodetectGTimport", .tSVE)
)
),
column(
width = 2, offset = 3,
br(),
actionButton(
"importVariants", "Import variants",
icon = icon("open", lib = "glyphicon")
)
),
column(
width = 4, offset = 1,
strong("Summary"),
htmlOutput("vcfSummary")
)
)
),
hr(),
fluidRow(
column(
width = 6,
h4("Content of folder"),
hr(),
DT::dataTableOutput("vcfContent")
),
column(
width = 6,
h4("VCF file(s) matching pattern"),
hr(),
DT::dataTableOutput("vcfFiles")
)
)
),
tabPanel(
title = "Annotations",
# Genome annotation package ----
wellPanel(
h4("Annotations"),
hr(),
fluidRow(
column(
width = 3,
selectInput(
"annotationPackage",
"Select installed EnsDb package",
choices = as.list(.EnsDbPacks),
width = '100%')
),
column(
3,
strong("EnsDb annotation"),
htmlOutput("ensembl_organism"),
htmlOutput("ensembl_version"),
htmlOutput("ensembl_genome")
),
column(
width = 6,
strong("Note"),
p(
"Only",
tags$code("EnsDb"),
"annotation packages supported for starters.",
"Ideally, ",
tags$code("TxDb"),
"and",
tags$code("OrganismDb"),
"packages supported soon.")
)
)
)
)
),
# Calculate frequencies ----
tabPanel(
title = "Frequencies", icon = icon("calculator "),
uiOutput("TVTBparamWarning"),
wellPanel(
fluidRow(
column(
width = 2,
strong("Latest changes:")
),
column(
width = 10,
uiOutput("latestFrequenciesCalculated")
)
)
),
wellPanel(
fluidRow(
h4("Overall frequencies"), hr(),
column(
width = 1, offset = 1,
actionButton(
"addOverallFrequencies", "Add",
icon = icon("plus")
)
),
column(
width = 1,
actionButton(
"removeOverallFrequencies", "Remove",
icon = icon("minus")
)
)
)
),
wellPanel(
fluidRow(
h4("Frequencies in phenotype levels"), hr(),
column(
width = 2,
selectInput(
"phenoAddFrequencies",
"Phenotype",
choices = character()
)
),
column(
width = 2, offset = 1,
actionButton(
"tickAllPhenoLevelsFreq",
"Select all",
icon = icon("check-square-o"),
width = "100%"
), br(),
actionButton(
"untickAllPhenoLevelsFreq",
"Deselect all",
icon = icon("square-o"),
width = "100%"
)
),
column(
width = 2, offset = 1,
br(),
actionButton(
"buttonFrequencies", "Refresh",
icon = icon("refresh"), width = "100%"
)
)
),
fluidRow(
column(
width = 12,
checkboxGroupInput(
"phenoLevelFreqCheckboxes", "Phenotype levels",
choices = c(), inline = TRUE
)
)
)
)
),
# VCF filter Rules ----
tabPanel(
title = "Filters", icon = icon("filter"),
wellPanel(
h4("Add filter"),
fluidRow(
column(
width = 1,
br(),
actionButton(
"addNewFilter", "Add filter",
icon = icon("plus")
)
),
column(
width = 1,
selectInput(
"newFilterClass", "Type",
choices = list(
"fixed" = "VcfFixedRules",
"info" = "VcfInfoRules",
"VEP" = "VcfVepRules"
),
selected = "VcfFixedRules"
)
),
column(
width = 1,
br(),
checkboxInput(
"newFilterActive", "Active?",
value = TRUE
)
),
column(
width = 7,
textInput(
"newFilterExpression", "Expression",
placeholder = paste(
"grepl(\"pass\", tolower(FILTER))",
"ALT + HET > 0",
"IMPACT %in% c(\"HIGH\", \"MODERATE\")",
sep = " - or - "
)
)
),
column(
width = 2,
br(),
actionButton(
"demoFilter", "Sample input",
icon = icon("font"), width = '100%')
)
),
fluidRow(
column(
width = 12,
uiOutput("vcfFilterTest")
)
),
fluidRow(
br(),
p(strong("Notes:")),
tags$ul(
tags$li(
"Filters are tested against variants to ensure the",
"validity of filters. Therefore, variants must be",
"loaded", em("before"), "filters can be created."
),
tags$li(
"Currently, filters are not re-tested if variants are",
"updated. If variants are refreshed, users should",
"ensure filters remain valid, or remove filters",
"manually."
),
tags$li(
"Users may ignore auto-correction of quotes in the",
strong("Expression"), "field. The application",
"automatically substitutes",
"curly quotes (single and double) by their",
"corresponding regular quotes (",
em("i.e."), code("\""), "and", code("'"), ")"
)
)
)
),
wellPanel(
fluidRow(
column(
width = 4, offset = 1,
strong("Summary"), br(),
uiOutput("filtersSummary")
),
column(
width = 2,
actionButton(
"filterVariants", "Apply filters",
icon = icon("filter"), width = "100%"
)
),
column(
width = 4,
strong("Summary"), br(),
uiOutput("filteredVcfSummary")
)
)
),
wellPanel(
fluidRow(
column(
width = 1,
strong("Class")
),
column(
width = 1,
strong("Active?")
),
column(
width = 8,
strong("Expression")
)
),
br(),
uiOutput("vcfFilterControls")
),
wellPanel(
fluidRow(
column(
width = 12,
verbatimTextOutput("vcfRules")
)
)
)
),
tabPanel(
title = "Views", icon = icon("picture-o"),
tabsetPanel(
id = "tabset.views",
# Genomic ranges view ----
tabPanel(
title = "Genomic ranges",
fluidRow(
column(
width = 12,
DT::dataTableOutput("rangesTableView")
)
)
),
# Variants view ----
tabPanel(
title = "Variants",
fluidRow(
column(
width = 12,
wellPanel(
uiOutput("vcfCols")
)
)
),
fluidRow(
column(
width = 12,
DT::dataTableOutput("vcfRowRangesView")
)
)
),
# Variants INFO view ----
tabPanel(
title = "INFO",
fluidRow(
column(
width = 12,
wellPanel(
uiOutput("vcfInfoCols"),
br(),
p(strong("Notes:")),
tags$ul(
tags$li(
"Fields that contain more than one value",
"(", tags$em("e.g."), "confidence intervals)",
"may not display properly."
)
)
)
)
),
fluidRow(
column(
width = 12,
DT::dataTableOutput("vcfInfoView")
)
)
),
# VEP predictions view ----
tabPanel(
title = "VEP",
fluidRow(
column(
width = 12,
wellPanel(
uiOutput("vepCols")
)
)
),
fluidRow(
column(
width = 12,
DT::dataTableOutput("vcfVepView")
)
)
),
# Phenotypes view ----
tabPanel(
title = "Phenotypes",
fluidRow(
column(
width = 12,
"This panel displays phenotype information attached to",
"the imported VCF object.",
wellPanel(
uiOutput("phenoCols")
)
)
),
fluidRow(
column(
width = 12,
DT::dataTableOutput("phenotypesView")
)
)
),
# Genotypes view ----
tabPanel(
title = "Genotypes",
tabsetPanel(
tabPanel(
title = "Matrix",
fluidRow(
wellPanel(
column(
width = 6,
uiOutput("genoNumRows")
),
column(
width = 6,
uiOutput("genoFirstRow")
)
)
),
fluidRow(
wellPanel(
column(
width = 6,
uiOutput("genoNumCols")
),
column(
width = 6,
uiOutput("genoFirstCol")
)
)
),
fluidRow(
column(
width = 12,
tableOutput("genotypesSample")
)
)
),
tabPanel(
title = "Heatmap",
p(
"Click the button after loading variants",
"to generate/update the figure",
actionButton(
"doGenoHeatmap", "Go!",
icon = icon("time")
)
),
fluidRow(
column(
width = 12,
plotOutput(
"heatmapGenotype",
height = get("genoHeatmap.height", .tSVE)
)
)
),
p(
"Notes",
tags$ul(
tags$li(
"This may take some time to plot.",
em(
"(~15s for 218 variants & 5844",
"samples)"
)
),
tags$li(
"Only genotypes codes found in the data",
"are listed in the legend, irrespective",
"of those defined in the",
tags$strong("Advanced settings"), "."
)
)
)
),
tabPanel(
title = "Info",
shiny::h4("Encoding"),
uiOutput("genotypeEncoding")
)
)
)
)
),
navbarMenu(
title = "Settings", icon = icon("wrench"),
# Advanced settings ----
tabPanel(
title = "Advanced",
wellPanel(
h4("Genotypes"),
hr(),
fluidRow(
column(
width = 1,
br(),
actionButton(
"genotypeAutofill", "Autofill", icon("magic")
)
),
column(
width = 3,
selectInput(
"refGenotypes", "Reference homozygote genotype(s)",
choices = c(get("refGT", .tSVE), get("hetGT", .tSVE), get("altGT", .tSVE)),
selected = get("refGT", .tSVE),
multiple = TRUE
)
),
column(
width = 4,
selectInput(
"hetGenotypes", "Heterozygote genotype(s)",
choices = c(get("refGT", .tSVE), get("hetGT", .tSVE), get("altGT", .tSVE)),
selected = get("hetGT", .tSVE),
multiple = TRUE
)
),
column(
width = 4,
selectInput(
"altGenotypes", "Alternate homozygote genotype(s)",
choices = c(get("refGT", .tSVE), get("hetGT", .tSVE), get("altGT", .tSVE)),
selected = get("altGT", .tSVE),
multiple = TRUE
)
)
),
fluidRow(
column(
width = 1,
textInput(
"refSuffix", "Suffix",
value = get("refSuffix", .tSVE),
placeholder = get("refSuffix", .tSVE)
)
),
column(
width = 1, offset = 3,
textInput(
"hetSuffix", "Suffix",
value = get("hetSuffix", .tSVE),
placeholder = get("hetSuffix", .tSVE)
)
),
column(
width = 1, offset = 3,
textInput(
"altSuffix", "Suffix",
value = get("altSuffix", .tSVE),
placeholder = get("altSuffix", .tSVE)
)
)
),
fluidRow(
column(
width = 12,
tags$strong("Notes:"), br(),
tags$ul(
tags$li(
"The",tags$strong("choices"),"of genotypes are updated when",
"new variants are imported."
),
tags$li(
"The",tags$strong("selected"),"genotypes may be automatically",
"updated immediately after import using the",
tags$strong("Autodetect genotypes"), "checkbox in the",
tags$strong("Input"), "panel, or manually after import using",
"the", tags$strong("Autofill"), "button in this panel."
),
tags$li(
"Selected genotypes are not allowed to overlap.",
"Selecting a genotype removes it from the choices",
"available in the other widgets. As a consequence, genotypes",
"must first be unselected from a widget before it can be",
"selected in another one."
)
)
)
)
),
wellPanel(
h4("INFO suffixes"),
hr(),
fluidRow(
column(
width = 3,
textInput(
"aafSuffix", "ALT allele freq.",
value = get("aafSuffix", .tSVE),
placeholder = get("aafSuffix", .tSVE)
)
),
column(
width = 3,
textInput(
"mafSuffix", "Minor allele freq.",
value = get("mafSuffix", .tSVE),
placeholder = get("mafSuffix", .tSVE)
)
)
)
),
wellPanel(
h4("VCF file(s)"),
hr(),
fluidRow(
column(
width = 2,
numericInput(
"yieldSize", "VCF yield size (100-100^3)",
min = 100, max = 100E3,
value = 4E3,
step = 1E3
)
)
)
)
),
tabPanel(
title = "Parallel",
wellPanel(
h4("Parallel settings"),
hr(),
fluidRow(
column(
width = 3,
numericInput(
"bpCores", "Cores",
value = .PS[["default.bpCores"]],
min = 1, max = .PS[["default.bpCores"]], step = 1)
),
column(
width = 3,
selectInput(
"bpConfig", "Cluster configuration",
choices = structure(
as.list(.PS[["choices.bpClass"]]),
names = gsub(
"Param", "", .PS[["choices.bpClass"]])),
selected = .PS[["default.bpClass"]])
),
conditionalPanel(
condition = "input.bpConfig != 'SerialParam'",
column(
width = 3,
selectInput(
"bpType", "Cluster type",
choices = structure(
as.list(.PS[["choices.bpType"]]),
names = gsub(
"Param", "", .PS[["choices.bpType"]])),
selected = .PS[["default.bpType"]])
)
)
) # fluidRow
), # wellPanel
wellPanel(
fluidRow(
column(
width = 12,
h1("Platforms tested"),
DT::dataTableOutput("parallelReport")
)
)
),
tags$h4(
"Notes",
tags$ul(
tags$li(
"Report"
), br(),
tags$ul(
tags$li(
tags$strong("Hang:"),
"Application hangs while CPUs work infinitely at full capacity."
)
)
)
)
)
),
# Session settings view ----
tabPanel(
title = "Session",
tabsetPanel(
id = "tabset.session",
tabPanel(
title = "Session info",
verbatimTextOutput("sessionInfo")
),
tabPanel(
title = "TVTB settings",
verbatimTextOutput("TVTBsettings")
),
tabPanel(
title = "General settings",
verbatimTextOutput("generalSettings")
),
tabPanel(
title = "Advanced settings",
verbatimTextOutput("advancedSettings")
),
tabPanel(
title = "ExpandedVCF",
"This panel displays the structure of the imported",
tags$code("ExpandedVCF"), "object:",
verbatimTextOutput("ExpandedVCF"),
"and the attached", tags$code("metadata"), ":",
verbatimTextOutput("vcfMetadata")
),
tabPanel(
title = "VEP",
verbatimTextOutput("vepStructure")
),
tabPanel(
title = "Errors",
verbatimTextOutput("Errors")
)
)
)
))
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