inst/shiny-dir/ui.R
In Manuelaio/uncoverappLib: Interactive graphical application for clinical assessment of sequence coverage at the base-pair level
#' @title unCOVERApp user interface
#'
#' @description This function allows you to open graphical interface.
#' @param agree visualization.
#' @keywords app
#' @export
#' @examples
#' uncoverappLib.run()
require(shiny)
require(shinyWidgets)
require(shinyBS)
require(shinyjs)
require(markdown)
require(DT)
#options(repos = BiocInstaller::biocinstallRepos())
#getOption("repos")
#require(data.table)
#require(dplyr)
require(Gviz)
require(Homo.sapiens)
require(OrganismDbi)
require(stringr)
require(condformat)
require(shinyjs)
require(shinycssloaders)
require(bedr)
require(Rsamtools)
require(TxDb.Hsapiens.UCSC.hg19.knownGene)
require(TxDb.Hsapiens.UCSC.hg38.knownGene)
#require(BSgenome.Hsapiens.UCSC.hg19)
#require(BSgenome.Hsapiens.UCSC.hg38)
require(EnsDb.Hsapiens.v75)
require(EnsDb.Hsapiens.v86)
require(org.Hs.eg.db)
options("browser" = "xdg-open")
first.file <- system.file(
"extdata",
"intro.md",
package = "uncoverappLib"
)
second.file <- system.file(
"extdata",
"script.js",
package = "uncoverappLib"
)
third.file <- system.file(
"extdata",
"CONTACTS.md",
package = "uncoverappLib"
)
intro_processing <- system.file(
"extdata",
"prep_input.md",
package = "uncoverappLib"
)
mdStyle <- "margin-left: 30px; margin-right: 30px"
intro <- function() {
tabPanel("home",
shiny::includeMarkdown(first.file),
#includeMarkdown(file.path(".","intro.md")),
style=mdStyle
)
}
preprocess <- function() {
shiny::tabPanel("Processing and Statistical Summary",
shiny::includeMarkdown(intro_processing),
#shiny::includeMarkdown(file.path(".", "prep_input.md")),
h1(strong("Prepare your input file")),
fluidPage(
sidebarLayout(
sidebarPanel(
shiny::selectInput("Genome",
label = "Reference Genome",
choices = c("hg19",
"hg38"),
selected = "UCSC genome"),
hr(),
shinyWidgets::pickerInput("notation",
label = "Chromosome Notation",
choices = c("chr", "number"),
options = list(`actions-box` = TRUE),
multiple =FALSE),
shinyWidgets::pickerInput("MAPQ",
label = "minum Mapping Quality (MAPQ)",
choices = c(1:1000),
options = list(`actions-box` = TRUE), multiple =FALSE),
shinyWidgets::pickerInput("base_qual",
label = "minimum Base Quality",
choices = c(1:1000),
options = list(`actions-box` = TRUE), multiple =FALSE),
hr(),
fileInput(inputId = "gene1",
label = "Load input file",
accept = c("text/csv",
".zip",
".gz",
".bed",
"text/comma-separated-values,text/plain",
".csv")),
helpText("Choose the type of your input file"),
radioButtons("type_file", "type of file",
choices = c("List of genes name" = "gene_name",
"Target Bed "= "target_bed"),
selected = "gene_name"),
br(),
br(),
fileInput(inputId = "bam_list",
label = "Load a bam.list file: one bam paths
in one row",
accept = c("text/csv",
".zip",
".gz",
".bed",
"text/comma-separated-values,text/plain",
".list")),
hr(),
hr(),
downloadButton("summary", "Statistical_Summary", class = "btn-primary",
style='color: #fff; background-color: #27ae60;
border-color: #fff;
padding: 15px 14px 15px 14px;
margin: 15px 5px 5px 5px; ')
),
shiny::mainPanel(
tabsetPanel(
tabPanel(title= "input for uncoverapp",
shinycssloaders::withSpinner(
dataTableOutput("input1"))
)
) )
)))
}
myHome <- function() {
tabPanel("Coverage Analysis",
h1(strong("Interactive web-application to visualize and
annotate low-coverage positions in clinical sequencing")),
#titlePanel("Coverage sequencing Explorer"),
helpText(em("Note:Select input options",
span("Upload your input bed
file with columns: chromosome, start, end, coverage
by sample and nucleotide count", style = "color:blue"))),
shinyjs::useShinyjs(),
includeScript(second.file),
sidebarPanel(
selectInput("UCSC_Genome",
label = "Reference Genome",
choices = c("hg19",
"hg38"),
selected = "UCSC genome"),
hr(),
textInput(inputId = "Gene_name",
label= "Gene name"),
#actionButton("button1",label= "Apply"),
shinyBS::bsButton("button1",label= "Apply", icon = icon("power-off"),
style = "success", size = "extra-small"),
shinyjs::hidden(p(id = "text1", "Running.....")),
#actionButton("remove",label= "Refresh"),
shinyBS::bsButton("remove",label= "Refresh", icon = icon("power-off"),
style = "success", size = "extra-small"),
helpText(em("write gene name and push apply button")),
hr(),
textInput(inputId ="Chromosome",
label = "Chromosome"),
#shinyWidgets::pickerInput("Chromosome",
# label = "Chromosome",
# choices = c("chr1", "chr2","chr3", "chr4","chr5",
# "chr6","chr7","chr8","chr9","chr10",
# "chr11","chr12","chr13","chr14","chr15",
# "chr16","chr17",
# "chr18","chr19", "chr20", "chr21",
# "chr22", "chrX", "chrY","chrM",
# names("file1")),
# options = list(`actions-box` = TRUE),
# multiple =FALSE),
hr(),
shinyWidgets::pickerInput("coverage_co",
label = "Coverage threshold",
choices = c(1:1000, "all",names("file1")),
options = list(`actions-box` = TRUE), multiple =FALSE),
helpText(em("Select minimum value as coverage threshold")),
hr(),
textInput(inputId = "Sample",
label= "Sample"),
helpText(em("Select name of sample for coverage analysis as reported
in bam list input.
Example:example_POLG.bam")),
hr(),
splitLayout(cellWidths = c("30%", "70%"),
textInput(inputId = "transcript_id",
label= "Transcript number"),
textInput(inputId = "id_t",
label= "Transcript ID")),
helpText(em("Retrieve your favourite transcript number from UCSC exons")),
hr(),
shinyWidgets::pickerInput("exon_number",
label= "exon number",
choices = c(1:150),
options = list(`actions-box` = TRUE), multiple =FALSE),
#actionButton("button5",label= "Make exon"),
shinyBS::bsButton("button5",label= "Make exon",
icon = icon("power-off"), style = "success",
size = "extra-small"),
shinyjs::hidden(p(id = "text1", "Running.....")),
#actionButton("remove5",label= "Refresh"),
shinyBS::bsButton("remove5",label= "Refresh",
icon = icon("power-off"), style = "default",
size = "extra-small"),
helpText(em("zooming one exon")),
hr(),
hr(),
textInput(inputId = "Start_genomicPosition",
label = "START genomic position"),
textInput(inputId = "end_genomicPosition",
label = "END genomic position"),
helpText(em("change genomic interval for zooming")),
hr(),
hr(),
textInput(inputId = "query_Database",
label= "Region coordinates"),
helpText(em("write to expand dbNSFP-annotated genomic positions.
For example 2:166845670-166930180")),
hr(),
hr(),
downloadButton("downloadData", "Download", class = "btn-primary",
style='padding:4px; font-size:120%'),
hr(),
hr(),
shiny::tags$button(
id = 'close',
type = "button",
class = "btn action-button",
style='color: white; background-color: #dd4b39;
padding:4px; font-size:120%',
onclick = "setTimeout(function(){window.close();},500);",
# close browser
"Close App")),
mainPanel(
fileInput(inputId = "file1",
label = "Select input file",
accept = c("text/csv",
".bedGraph",
".bedGraph.gz",
".zip",
".gz",
".bed",
"text/comma-separated-values,text/plain",
".csv")),
checkboxInput("header", "Header", TRUE),
shinyBS::bsButton("pileup",
label= "load input file",
icon = icon("file"), style = "info",
size = "default"),
#shinyBS::bsButton("example_data",
# label= "load example dataset",
# icon = icon("file"), style = "info",
# size = "extra-small"),
#helpText(em("load example dataset with
# base coverage counts of POLG gene")),
hr(),
tabsetPanel(
tabPanel("bed file", shinycssloaders::withSpinner(
DT::dataTableOutput("text"))),
tabPanel("UCSC gene",
DT::dataTableOutput("ccg")),
tabPanel("UCSC exons",
helpText(em("Extract protein coding positions from
UCSC")), DT::dataTableOutput("exon_pos")),
tabPanel("Low-coverage positions",
DT::dataTableOutput("text_cv")),
tabPanel("Gene coverage", shinycssloaders::withSpinner(
plotOutput("all_gene")),
DT::dataTableOutput('df.l')),
tabPanel("Exon coverage", helpText(em("This is a Gviz function
and it plots exon with ideogram, genome coordinates,
coverage information, Ensembl and UCSC gene annotation.The
annotation for the databases are directly fetched from Ensemb and
all tracks will be plotted in a 3' -> 5' direction.")),
plotOutput("ens",
dblclick = "plot1_dblclick",
brush = brushOpts( id = "plot1_brush",
resetOnNew = TRUE)),
DT::dataTableOutput("tabExon")),
tabPanel("Zoom to sequence",
helpText(em("choose a few genomic intervals")),
plotOutput("sequence")),
tabPanel("Annotations on low-coverage positions",
helpText(em("dbSNP-annotation collects all
consequences found in VEP-defined
canonical transcripts")),
shinycssloaders::withSpinner(
condformat::condformatOutput("uncover_position"))),
id = "tabSet"
),
hr(),
fluidRow(
column(12,DT::dataTableOutput("x4"))
)
)
)
}
myTab1 <- function() {
tabPanel("Calculate AF by allele frequency app",
# Application title
titlePanel("Maximum credible population allele frequency"),
##### Bootstrap method for page costruction
fluidPage(
fluidRow(
##### Sidebar
column(8,wellPanel(radioButtons("inh",
"Inheritance:",
choices = list("monoallelic",
"biallelic"),
selected = "monoallelic"),
numericInput("prev","Prevalence = 1 in ...
(people)",
min = 1,max = 1e8,value = 500),
options = NULL),
br(),
sliderInput("hetA","Allelic heterogeneity:",
min = 0, max = 1,value = 0.1),
sliderInput("hetG",
"Genetic heterogeneity:",
min = 0, max = 1,value = 1),
br(),
sliderInput("pen", "Penetrance:",
min = 0, max = 1, value = 0.5))),
br(),
column(8,
h3("Maximum credible population AF:"),
h2(textOutput("maxAF"),align="center",style = "color:blue")),
column(8,
h3("Uncover position",
helpText(em("Low-coverage positions excluding sites
annotated as variants with AF> maxAF
(default maxAF value: 5%)"),align="center",
style="color:blue"),
style = "font-size: 100%; width: 100%",
shinycssloaders::withSpinner(
condformat::condformatOutput("uncoverPosition")))),
br(),
br(),
downloadButton("download_maxAF", "Download_maxAF",
class = "btn-primary",
style='padding:4px; font-size:80%',
helpText("download low coverage
position dbSNFP-annotation filtered by
maximum allele frequency",
class = "btn-primary",
style='padding:4px; font-size:60%'))
#)
))}
myTab2 <- function() {
tabPanel("Binomial distribution",
titlePanel("Binomial distribution "),
fluidRow(
column(4,(numericInput("p",
"Allele Fraction",
min = 0,
max = 1,
value = 0.05)),
helpText(em("the expected fraction of variant reads
(probability of success)",
align="center",
style="color:gray")),
hr(),
numericInput("num_all",
"Variant reads",
min=0,
max=100000,
value=10),
helpText(em("the minimum number of variant reads required
by the user to support variant evidence,
(number of successes)"),align="center",
style="color:gray"),
hr(),
textInput(inputId = "start_gp",
label = "Genomic position"),
#textInput(inputId = "end_gp",
# label = "END genomic position"),
helpText(em("Specify a genomic position of interest gene
in which calculating the
binomial distribution"))),
column(4,
h2("consideration:"),
h3(htmlOutput("ci"))),
column(4,
h2("Binomial Distribution", plotOutput("bd"))),
column(10, h2("Cumulative distribution function"),
h3(plotOutput("pbinom"))))
)}
myabout <- function() {
tabPanel("contacts",
includeMarkdown(third.file),
style=mdStyle
)
}
ui <- shinyUI(navbarPage("uncoverApp",
intro(),
preprocess(),
myHome(),
myTab1(),
myTab2(),
myabout()
))
Manuelaio/uncoverappLib documentation built on Feb. 16, 2023, 12:52 a.m.
R Package Documentation
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#' @title unCOVERApp user interface
#'
#' @description This function allows you to open graphical interface.
#' @param agree visualization.
#' @keywords app
#' @export
#' @examples
#' uncoverappLib.run()
require(shiny)
require(shinyWidgets)
require(shinyBS)
require(shinyjs)
require(markdown)
require(DT)
#options(repos = BiocInstaller::biocinstallRepos())
#getOption("repos")
#require(data.table)
#require(dplyr)
require(Gviz)
require(Homo.sapiens)
require(OrganismDbi)
require(stringr)
require(condformat)
require(shinyjs)
require(shinycssloaders)
require(bedr)
require(Rsamtools)
require(TxDb.Hsapiens.UCSC.hg19.knownGene)
require(TxDb.Hsapiens.UCSC.hg38.knownGene)
#require(BSgenome.Hsapiens.UCSC.hg19)
#require(BSgenome.Hsapiens.UCSC.hg38)
require(EnsDb.Hsapiens.v75)
require(EnsDb.Hsapiens.v86)
require(org.Hs.eg.db)
options("browser" = "xdg-open")
first.file <- system.file(
"extdata",
"intro.md",
package = "uncoverappLib"
)
second.file <- system.file(
"extdata",
"script.js",
package = "uncoverappLib"
)
third.file <- system.file(
"extdata",
"CONTACTS.md",
package = "uncoverappLib"
)
intro_processing <- system.file(
"extdata",
"prep_input.md",
package = "uncoverappLib"
)
mdStyle <- "margin-left: 30px; margin-right: 30px"
intro <- function() {
tabPanel("home",
shiny::includeMarkdown(first.file),
#includeMarkdown(file.path(".","intro.md")),
style=mdStyle
)
}
preprocess <- function() {
shiny::tabPanel("Processing and Statistical Summary",
shiny::includeMarkdown(intro_processing),
#shiny::includeMarkdown(file.path(".", "prep_input.md")),
h1(strong("Prepare your input file")),
fluidPage(
sidebarLayout(
sidebarPanel(
shiny::selectInput("Genome",
label = "Reference Genome",
choices = c("hg19",
"hg38"),
selected = "UCSC genome"),
hr(),
shinyWidgets::pickerInput("notation",
label = "Chromosome Notation",
choices = c("chr", "number"),
options = list(`actions-box` = TRUE),
multiple =FALSE),
shinyWidgets::pickerInput("MAPQ",
label = "minum Mapping Quality (MAPQ)",
choices = c(1:1000),
options = list(`actions-box` = TRUE), multiple =FALSE),
shinyWidgets::pickerInput("base_qual",
label = "minimum Base Quality",
choices = c(1:1000),
options = list(`actions-box` = TRUE), multiple =FALSE),
hr(),
fileInput(inputId = "gene1",
label = "Load input file",
accept = c("text/csv",
".zip",
".gz",
".bed",
"text/comma-separated-values,text/plain",
".csv")),
helpText("Choose the type of your input file"),
radioButtons("type_file", "type of file",
choices = c("List of genes name" = "gene_name",
"Target Bed "= "target_bed"),
selected = "gene_name"),
br(),
br(),
fileInput(inputId = "bam_list",
label = "Load a bam.list file: one bam paths
in one row",
accept = c("text/csv",
".zip",
".gz",
".bed",
"text/comma-separated-values,text/plain",
".list")),
hr(),
hr(),
downloadButton("summary", "Statistical_Summary", class = "btn-primary",
style='color: #fff; background-color: #27ae60;
border-color: #fff;
padding: 15px 14px 15px 14px;
margin: 15px 5px 5px 5px; ')
),
shiny::mainPanel(
tabsetPanel(
tabPanel(title= "input for uncoverapp",
shinycssloaders::withSpinner(
dataTableOutput("input1"))
)
) )
)))
}
myHome <- function() {
tabPanel("Coverage Analysis",
h1(strong("Interactive web-application to visualize and
annotate low-coverage positions in clinical sequencing")),
#titlePanel("Coverage sequencing Explorer"),
helpText(em("Note:Select input options",
span("Upload your input bed
file with columns: chromosome, start, end, coverage
by sample and nucleotide count", style = "color:blue"))),
shinyjs::useShinyjs(),
includeScript(second.file),
sidebarPanel(
selectInput("UCSC_Genome",
label = "Reference Genome",
choices = c("hg19",
"hg38"),
selected = "UCSC genome"),
hr(),
textInput(inputId = "Gene_name",
label= "Gene name"),
#actionButton("button1",label= "Apply"),
shinyBS::bsButton("button1",label= "Apply", icon = icon("power-off"),
style = "success", size = "extra-small"),
shinyjs::hidden(p(id = "text1", "Running.....")),
#actionButton("remove",label= "Refresh"),
shinyBS::bsButton("remove",label= "Refresh", icon = icon("power-off"),
style = "success", size = "extra-small"),
helpText(em("write gene name and push apply button")),
hr(),
textInput(inputId ="Chromosome",
label = "Chromosome"),
#shinyWidgets::pickerInput("Chromosome",
# label = "Chromosome",
# choices = c("chr1", "chr2","chr3", "chr4","chr5",
# "chr6","chr7","chr8","chr9","chr10",
# "chr11","chr12","chr13","chr14","chr15",
# "chr16","chr17",
# "chr18","chr19", "chr20", "chr21",
# "chr22", "chrX", "chrY","chrM",
# names("file1")),
# options = list(`actions-box` = TRUE),
# multiple =FALSE),
hr(),
shinyWidgets::pickerInput("coverage_co",
label = "Coverage threshold",
choices = c(1:1000, "all",names("file1")),
options = list(`actions-box` = TRUE), multiple =FALSE),
helpText(em("Select minimum value as coverage threshold")),
hr(),
textInput(inputId = "Sample",
label= "Sample"),
helpText(em("Select name of sample for coverage analysis as reported
in bam list input.
Example:example_POLG.bam")),
hr(),
splitLayout(cellWidths = c("30%", "70%"),
textInput(inputId = "transcript_id",
label= "Transcript number"),
textInput(inputId = "id_t",
label= "Transcript ID")),
helpText(em("Retrieve your favourite transcript number from UCSC exons")),
hr(),
shinyWidgets::pickerInput("exon_number",
label= "exon number",
choices = c(1:150),
options = list(`actions-box` = TRUE), multiple =FALSE),
#actionButton("button5",label= "Make exon"),
shinyBS::bsButton("button5",label= "Make exon",
icon = icon("power-off"), style = "success",
size = "extra-small"),
shinyjs::hidden(p(id = "text1", "Running.....")),
#actionButton("remove5",label= "Refresh"),
shinyBS::bsButton("remove5",label= "Refresh",
icon = icon("power-off"), style = "default",
size = "extra-small"),
helpText(em("zooming one exon")),
hr(),
hr(),
textInput(inputId = "Start_genomicPosition",
label = "START genomic position"),
textInput(inputId = "end_genomicPosition",
label = "END genomic position"),
helpText(em("change genomic interval for zooming")),
hr(),
hr(),
textInput(inputId = "query_Database",
label= "Region coordinates"),
helpText(em("write to expand dbNSFP-annotated genomic positions.
For example 2:166845670-166930180")),
hr(),
hr(),
downloadButton("downloadData", "Download", class = "btn-primary",
style='padding:4px; font-size:120%'),
hr(),
hr(),
shiny::tags$button(
id = 'close',
type = "button",
class = "btn action-button",
style='color: white; background-color: #dd4b39;
padding:4px; font-size:120%',
onclick = "setTimeout(function(){window.close();},500);",
# close browser
"Close App")),
mainPanel(
fileInput(inputId = "file1",
label = "Select input file",
accept = c("text/csv",
".bedGraph",
".bedGraph.gz",
".zip",
".gz",
".bed",
"text/comma-separated-values,text/plain",
".csv")),
checkboxInput("header", "Header", TRUE),
shinyBS::bsButton("pileup",
label= "load input file",
icon = icon("file"), style = "info",
size = "default"),
#shinyBS::bsButton("example_data",
# label= "load example dataset",
# icon = icon("file"), style = "info",
# size = "extra-small"),
#helpText(em("load example dataset with
# base coverage counts of POLG gene")),
hr(),
tabsetPanel(
tabPanel("bed file", shinycssloaders::withSpinner(
DT::dataTableOutput("text"))),
tabPanel("UCSC gene",
DT::dataTableOutput("ccg")),
tabPanel("UCSC exons",
helpText(em("Extract protein coding positions from
UCSC")), DT::dataTableOutput("exon_pos")),
tabPanel("Low-coverage positions",
DT::dataTableOutput("text_cv")),
tabPanel("Gene coverage", shinycssloaders::withSpinner(
plotOutput("all_gene")),
DT::dataTableOutput('df.l')),
tabPanel("Exon coverage", helpText(em("This is a Gviz function
and it plots exon with ideogram, genome coordinates,
coverage information, Ensembl and UCSC gene annotation.The
annotation for the databases are directly fetched from Ensemb and
all tracks will be plotted in a 3' -> 5' direction.")),
plotOutput("ens",
dblclick = "plot1_dblclick",
brush = brushOpts( id = "plot1_brush",
resetOnNew = TRUE)),
DT::dataTableOutput("tabExon")),
tabPanel("Zoom to sequence",
helpText(em("choose a few genomic intervals")),
plotOutput("sequence")),
tabPanel("Annotations on low-coverage positions",
helpText(em("dbSNP-annotation collects all
consequences found in VEP-defined
canonical transcripts")),
shinycssloaders::withSpinner(
condformat::condformatOutput("uncover_position"))),
id = "tabSet"
),
hr(),
fluidRow(
column(12,DT::dataTableOutput("x4"))
)
)
)
}
myTab1 <- function() {
tabPanel("Calculate AF by allele frequency app",
# Application title
titlePanel("Maximum credible population allele frequency"),
##### Bootstrap method for page costruction
fluidPage(
fluidRow(
##### Sidebar
column(8,wellPanel(radioButtons("inh",
"Inheritance:",
choices = list("monoallelic",
"biallelic"),
selected = "monoallelic"),
numericInput("prev","Prevalence = 1 in ...
(people)",
min = 1,max = 1e8,value = 500),
options = NULL),
br(),
sliderInput("hetA","Allelic heterogeneity:",
min = 0, max = 1,value = 0.1),
sliderInput("hetG",
"Genetic heterogeneity:",
min = 0, max = 1,value = 1),
br(),
sliderInput("pen", "Penetrance:",
min = 0, max = 1, value = 0.5))),
br(),
column(8,
h3("Maximum credible population AF:"),
h2(textOutput("maxAF"),align="center",style = "color:blue")),
column(8,
h3("Uncover position",
helpText(em("Low-coverage positions excluding sites
annotated as variants with AF> maxAF
(default maxAF value: 5%)"),align="center",
style="color:blue"),
style = "font-size: 100%; width: 100%",
shinycssloaders::withSpinner(
condformat::condformatOutput("uncoverPosition")))),
br(),
br(),
downloadButton("download_maxAF", "Download_maxAF",
class = "btn-primary",
style='padding:4px; font-size:80%',
helpText("download low coverage
position dbSNFP-annotation filtered by
maximum allele frequency",
class = "btn-primary",
style='padding:4px; font-size:60%'))
#)
))}
myTab2 <- function() {
tabPanel("Binomial distribution",
titlePanel("Binomial distribution "),
fluidRow(
column(4,(numericInput("p",
"Allele Fraction",
min = 0,
max = 1,
value = 0.05)),
helpText(em("the expected fraction of variant reads
(probability of success)",
align="center",
style="color:gray")),
hr(),
numericInput("num_all",
"Variant reads",
min=0,
max=100000,
value=10),
helpText(em("the minimum number of variant reads required
by the user to support variant evidence,
(number of successes)"),align="center",
style="color:gray"),
hr(),
textInput(inputId = "start_gp",
label = "Genomic position"),
#textInput(inputId = "end_gp",
# label = "END genomic position"),
helpText(em("Specify a genomic position of interest gene
in which calculating the
binomial distribution"))),
column(4,
h2("consideration:"),
h3(htmlOutput("ci"))),
column(4,
h2("Binomial Distribution", plotOutput("bd"))),
column(10, h2("Cumulative distribution function"),
h3(plotOutput("pbinom"))))
)}
myabout <- function() {
tabPanel("contacts",
includeMarkdown(third.file),
style=mdStyle
)
}
ui <- shinyUI(navbarPage("uncoverApp",
intro(),
preprocess(),
myHome(),
myTab1(),
myTab2(),
myabout()
))
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