Nothing
inst/shiny-dir/ui.R
In 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",
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 a txt file with gene(s) list: one gene
in one row",
accept = c("text/csv",
".zip",
".gz",
".bed",
"text/comma-separated-values,text/plain",
".csv")),
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"))),
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 number of sample for coverage analysis.
Example:1")),
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()
))
Try the uncoverappLib package in your browser
Any scripts or data that you put into this service are public.
uncoverappLib documentation built on Nov. 8, 2020, 5:07 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
#' @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",
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 a txt file with gene(s) list: one gene
in one row",
accept = c("text/csv",
".zip",
".gz",
".bed",
"text/comma-separated-values,text/plain",
".csv")),
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"))),
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 number of sample for coverage analysis.
Example:1")),
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()
))
Try the uncoverappLib package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.