R/shinyUI.R
In cayek/BenchmarkingR:
#' data viewer
#'
#'
#' TODO
#'
#' @return TODO
#'
#' @examples
#' TODO
#
#' @export
bench.dataviewer <- function(bench.proj) {
data = bench.proj$dataset()
shiny::shinyApp(
ui = shiny::fluidPage(
shiny::titlePanel('Data set'),
shiny::sidebarLayout(
shiny::sidebarPanel(
shiny::selectInput("select", label = shiny::h3("Select data set"),
choices = data$name,
selected = 1)
),
shiny::mainPanel(
shiny::tableOutput(outputId="data.info")
)
),
shiny::hr(),
shiny::headerPanel('snmf'),
shiny::sidebarPanel(
shiny::numericInput('K', 'ancestral population number', 2, step = 1, min = 1),
shiny::actionButton("snmf", label = "run sNMF")
),
shiny::mainPanel(
shiny::plotOutput('snmf.plot')
),
shiny::hr(),
shiny::headerPanel('PCA'),
shiny::sidebarPanel(
shiny::actionButton("pca", label = "run prcomp"),
shiny::selectInput('pca.x', 'X Variable', c("PC1", "PC2","PC3")),
shiny::selectInput('pca.y', 'Y Variable', c("PC1", "PC2","PC3"))
),
shiny::mainPanel(
shiny::plotOutput('pca.plot')
)
),
server = function(input, output,session) {
#data.name = input$select
output$data.info <- shiny::renderTable({ dplyr::select( dplyr::filter(data, name==input$select), name, description )})
# snmf
shiny::observeEvent(input$snmf, {
t = bench.snmf(bench.proj, input$select,K = input$K, again = TRUE)
})
output$snmf.plot <- shiny::renderPlot({
# Take a dependency on input$snmf
input$snmf
data.exploration = bench.getdata.exploration(bench.proj, input$select)
if(!is.null(data.exploration$snmf)){
# barplot(t(data.exploration$snmf$Q))
K = ncol(data.exploration$snmf$Q)
toplot = data.frame(data.exploration$snmf$Q)
names(toplot) = 1:K
toplot = dplyr::add_rownames(toplot)
toplot = tidyr::gather(toplot, "cluster", "coef", 2:(K+1))
ggplot2::ggplot(toplot, ggplot2::aes(x=rowname, y = coef, color = cluster, fill =cluster)) +
ggplot2::geom_bar(stat="identity") + ggplot2::xlab("Indiv")
}
})
# PCA
observeEvent(input$pca, {
t = bench.pca(bench.proj, input$select, again = TRUE)
})
output$pca.plot <- renderPlot({
# Take a dependency on input$snmf
input$pca
data.exploration = bench.getdata.exploration(bench.proj, input$select)
if(!is.null(data.exploration$pca)){
ggplot2::ggplot(data.frame(data.exploration$pca$x), ggplot2::aes(x = PC1, y = PC2)) +
ggplot2::geom_point()
}
})
},
options = list(height = 1250)
)
}
#' result viewer
#'
#'
#' TODO
#'
#' @return TODO
#'
#' @examples
#' TODO
#
#' @export
bench.resultviewer <- function(bench.proj) {
data = bench.proj$dataset()
methods = bench.proj$methods()
shiny::shinyApp(
ui = shiny::fluidPage(
shiny::titlePanel('Result'),
shiny::sidebarLayout(
shiny::sidebarPanel(
shiny::selectInput("data", label = shiny::h3("Select data set"),
choices = data$name,
selected = 1),
shiny::selectInput("method", label = shiny::h3("Select methods"),
choices = methods$name,
selected = 1)
),
shiny::mainPanel(
shiny::tableOutput(outputId="data.info")
)
),
shiny::hr(),
shiny::headerPanel('Result'),
shiny::sidebarPanel(
shiny::textInput("parameter", label = "Parameter", value = "parameter = list()"),
shiny::actionButton("run", label = "run"),
shiny::hr(),
shiny::selectInput('plot', 'Plot', c("histogram of pvalue", "manhattan plot","size effect"))
),
shiny::mainPanel(
shiny::plotOutput('result.plot')
)
),
server = function(input, output,session) {
#data.name = input$select
output$data.info <- shiny::renderTable({ dplyr::filter(bench.proj$summary(), data==input$data, method==input$method ) })
# plot result
shiny::observeEvent(input$run, {
eval(parse(text = input$parameter))
bench.run(bench.proj, data.name = input$data, method.name = input$method, again = TRUE,parameter = parameter)
#data.name = input$select
output$data.info <- shiny::renderTable({ dplyr::filter(bench.proj$summary(), data==input$data, method==input$method ) })
})
output$result.plot <- shiny::renderPlot({
# Take a dependency on input$snmf
input$run
plots = bench.plotres(bench.proj, data.name = input$data, method.name = input$method)
if(input$plot=="histogram of pvalue") {
plots$mplot
} else if(input$plot=="manhattan plot") {
plots$histpvalue
} else if(input$plot=="size effect") {
plots$b
}
})
},
options = list(height = 860)
)
}
#' result viewer
#'
#'
#' TODO
#'
#' @return TODO
#'
#' @examples
#' TODO
#
#' @export
bench.adddataviewer <- function(bench.proj) {
shiny::shinyApp(
ui = shiny::fluidPage(
shiny::headerPanel('Add/Remove Data Set'),
shiny::sidebarPanel(
shiny::h2("Add Data Set"),
shiny::fileInput("file.geno", label = "Genotype"),
shiny::fileInput("file.env", label = "Environmental Variable"),
shiny::fileInput("file.outlier", label = "Outlier"),
shiny::hr(),
shiny::h3("Remove Data Set"),
shiny::selectInput('plot', 'Plot', c("histogram of pvalue", "manhattan plot","size effect"))
),
shiny::mainPanel(
shiny::plotOutput('result.plot')
)
),
server = function(input, output,session) {
NULL
}
)
}
#' Comparaison viewer
#'
#'
#' TODO
#'
#' @return TODO
#'
#' @examples
#' TODO
#
#' @export
bench.comparaisonviewer <- function(bench.proj) {
methods = bench.proj$methods()
shiny::shinyApp(
ui = shiny::fluidPage(
shiny::headerPanel('Comparaison'),
shiny::sidebarPanel(
uiOutput("data"),
uiOutput("methods"),
shiny::hr(),
shiny::selectInput('plot', 'Plot', c("fdr", "power","fdr power", "F1 score", "correlation")),
shiny::sliderInput("fdr_lim", label = shiny::h3("Threshold"), min = 0,
max = 1.0, value = c(0.0, 0.25))
),
shiny::mainPanel(
shiny::plotOutput('comp.plot')
)
),
server = function(input, output,session) {
# select data
output$data <- renderUI({
data = bench.proj$dataset()
shiny::selectInput("data", label = shiny::h3("Select data set"), choices =
data$name)
})
# select method
output$methods <- renderUI({
sum = bench.proj$summary()
m = dplyr::filter(sum, data == input$data)$method
if(length(m) == 0) {
shiny::helpText("No run for this dataset")
} else {
shiny::checkboxGroupInput("methods", label = shiny::h3("Methods"), choices = m, selected = input$methods)
}
})
# comparaison plots
output$comp.plot <- shiny::renderPlot({
plots=bench.plotfdr_power(bench.proj, input$data, input$methods, input$fdr_lim)
if(input$plot=="fdr") {
plots$fdr
} else if(input$plot=="power") {
plots$power
} else if(input$plot=="fdr power") {
plots$fdr.power
} else if(input$plot=="F1 score") {
plots$f1.score
} else if(input$plot=="correlation") {
plots = bench.heatmap(bench.proj, input$data, input$methods)
plots$cor
}
})
},
options = list(height = 750)
)
}
#' run sampler viewer
#'
#'
#' TODO
#'
#' @return TODO
#'
#' @examples
#' TODO
#
#' @export
bench.samplerviewer <- function(bench.proj) {
sampler = bench.proj$sampler()
shiny::shinyApp(
ui = shiny::fluidPage(
shiny::headerPanel('Sampler'),
shiny::sidebarPanel(
shiny::selectInput("sampler", label = shiny::h3("Select sampler"),
choices = sampler$name,
selected = 1),
shiny::hr(),
uiOutput("param"),
shiny::actionButton("run", label = "run"),
shiny::hr(),
uiOutput("dataSelector"),
shiny::actionButton("remove", label = "remove")
),
shiny::mainPanel(
shiny::h3("Sampler"),
shiny::tableOutput(outputId="sampler.info"),
shiny::hr(),
shiny::h3("Dateset"),
shiny::tableOutput(outputId="data.info")
)
),
server = function(input, output,session) {
output$sampler.info <- shiny::renderTable({dplyr::select( dplyr::filter(sampler, name == input$sampler), name, description) })
output$param <- renderUI({
shiny::textInput("parameter", label = shiny::h3("Parameter"), value =
dplyr::select( dplyr::filter(sampler, name == input$sampler), default_parameter)[1])
})
shiny::observeEvent(input$run, {
eval(parse(text = input$parameter))
bench.runsampler(bench.proj, sampler.name = input$sampler, repetition = 1, parameter = parameter)
# data update
output$data.info <- shiny::renderTable({
data = bench.proj$dataset()
data[grep(input$sampler,data$name),c(1,2)]
})
output$dataSelector <- renderUI({
data = bench.proj$dataset()
names = data[grep(input$sampler,data$name),1]
shiny::selectInput("dataset", label = shiny::h3("Select dataset"),
choices = names,
selected = 1)
})
})
# data update
output$data.info <- shiny::renderTable({
data = bench.proj$dataset()
data[grep(input$sampler,data$name),c(1,2)]
})
output$dataSelector <- renderUI({
data = bench.proj$dataset()
names = data[grep(input$sampler,data$name),1]
shiny::selectInput("dataset", label = shiny::h3("Select dataset"),
choices = names,
selected = 1)
})
shiny::observeEvent(input$remove, {
bench.removedataset(bench.proj, input$dataset)
# data update
output$data.info <- shiny::renderTable({
data = bench.proj$dataset()
data[grep(input$sampler,data$name),c(1,2)]
})
output$dataSelector <- renderUI({
data = bench.proj$dataset()
names = data[grep(input$sampler,data$name),1]
shiny::selectInput("dataset", label = shiny::h3("Select dataset"),
choices = names,
selected = 1)
})
})
},
options = list(height = 750)
)
}
cayek/BenchmarkingR documentation built on May 13, 2019, 1:20 p.m.
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#' data viewer
#'
#'
#' TODO
#'
#' @return TODO
#'
#' @examples
#' TODO
#
#' @export
bench.dataviewer <- function(bench.proj) {
data = bench.proj$dataset()
shiny::shinyApp(
ui = shiny::fluidPage(
shiny::titlePanel('Data set'),
shiny::sidebarLayout(
shiny::sidebarPanel(
shiny::selectInput("select", label = shiny::h3("Select data set"),
choices = data$name,
selected = 1)
),
shiny::mainPanel(
shiny::tableOutput(outputId="data.info")
)
),
shiny::hr(),
shiny::headerPanel('snmf'),
shiny::sidebarPanel(
shiny::numericInput('K', 'ancestral population number', 2, step = 1, min = 1),
shiny::actionButton("snmf", label = "run sNMF")
),
shiny::mainPanel(
shiny::plotOutput('snmf.plot')
),
shiny::hr(),
shiny::headerPanel('PCA'),
shiny::sidebarPanel(
shiny::actionButton("pca", label = "run prcomp"),
shiny::selectInput('pca.x', 'X Variable', c("PC1", "PC2","PC3")),
shiny::selectInput('pca.y', 'Y Variable', c("PC1", "PC2","PC3"))
),
shiny::mainPanel(
shiny::plotOutput('pca.plot')
)
),
server = function(input, output,session) {
#data.name = input$select
output$data.info <- shiny::renderTable({ dplyr::select( dplyr::filter(data, name==input$select), name, description )})
# snmf
shiny::observeEvent(input$snmf, {
t = bench.snmf(bench.proj, input$select,K = input$K, again = TRUE)
})
output$snmf.plot <- shiny::renderPlot({
# Take a dependency on input$snmf
input$snmf
data.exploration = bench.getdata.exploration(bench.proj, input$select)
if(!is.null(data.exploration$snmf)){
# barplot(t(data.exploration$snmf$Q))
K = ncol(data.exploration$snmf$Q)
toplot = data.frame(data.exploration$snmf$Q)
names(toplot) = 1:K
toplot = dplyr::add_rownames(toplot)
toplot = tidyr::gather(toplot, "cluster", "coef", 2:(K+1))
ggplot2::ggplot(toplot, ggplot2::aes(x=rowname, y = coef, color = cluster, fill =cluster)) +
ggplot2::geom_bar(stat="identity") + ggplot2::xlab("Indiv")
}
})
# PCA
observeEvent(input$pca, {
t = bench.pca(bench.proj, input$select, again = TRUE)
})
output$pca.plot <- renderPlot({
# Take a dependency on input$snmf
input$pca
data.exploration = bench.getdata.exploration(bench.proj, input$select)
if(!is.null(data.exploration$pca)){
ggplot2::ggplot(data.frame(data.exploration$pca$x), ggplot2::aes(x = PC1, y = PC2)) +
ggplot2::geom_point()
}
})
},
options = list(height = 1250)
)
}
#' result viewer
#'
#'
#' TODO
#'
#' @return TODO
#'
#' @examples
#' TODO
#
#' @export
bench.resultviewer <- function(bench.proj) {
data = bench.proj$dataset()
methods = bench.proj$methods()
shiny::shinyApp(
ui = shiny::fluidPage(
shiny::titlePanel('Result'),
shiny::sidebarLayout(
shiny::sidebarPanel(
shiny::selectInput("data", label = shiny::h3("Select data set"),
choices = data$name,
selected = 1),
shiny::selectInput("method", label = shiny::h3("Select methods"),
choices = methods$name,
selected = 1)
),
shiny::mainPanel(
shiny::tableOutput(outputId="data.info")
)
),
shiny::hr(),
shiny::headerPanel('Result'),
shiny::sidebarPanel(
shiny::textInput("parameter", label = "Parameter", value = "parameter = list()"),
shiny::actionButton("run", label = "run"),
shiny::hr(),
shiny::selectInput('plot', 'Plot', c("histogram of pvalue", "manhattan plot","size effect"))
),
shiny::mainPanel(
shiny::plotOutput('result.plot')
)
),
server = function(input, output,session) {
#data.name = input$select
output$data.info <- shiny::renderTable({ dplyr::filter(bench.proj$summary(), data==input$data, method==input$method ) })
# plot result
shiny::observeEvent(input$run, {
eval(parse(text = input$parameter))
bench.run(bench.proj, data.name = input$data, method.name = input$method, again = TRUE,parameter = parameter)
#data.name = input$select
output$data.info <- shiny::renderTable({ dplyr::filter(bench.proj$summary(), data==input$data, method==input$method ) })
})
output$result.plot <- shiny::renderPlot({
# Take a dependency on input$snmf
input$run
plots = bench.plotres(bench.proj, data.name = input$data, method.name = input$method)
if(input$plot=="histogram of pvalue") {
plots$mplot
} else if(input$plot=="manhattan plot") {
plots$histpvalue
} else if(input$plot=="size effect") {
plots$b
}
})
},
options = list(height = 860)
)
}
#' result viewer
#'
#'
#' TODO
#'
#' @return TODO
#'
#' @examples
#' TODO
#
#' @export
bench.adddataviewer <- function(bench.proj) {
shiny::shinyApp(
ui = shiny::fluidPage(
shiny::headerPanel('Add/Remove Data Set'),
shiny::sidebarPanel(
shiny::h2("Add Data Set"),
shiny::fileInput("file.geno", label = "Genotype"),
shiny::fileInput("file.env", label = "Environmental Variable"),
shiny::fileInput("file.outlier", label = "Outlier"),
shiny::hr(),
shiny::h3("Remove Data Set"),
shiny::selectInput('plot', 'Plot', c("histogram of pvalue", "manhattan plot","size effect"))
),
shiny::mainPanel(
shiny::plotOutput('result.plot')
)
),
server = function(input, output,session) {
NULL
}
)
}
#' Comparaison viewer
#'
#'
#' TODO
#'
#' @return TODO
#'
#' @examples
#' TODO
#
#' @export
bench.comparaisonviewer <- function(bench.proj) {
methods = bench.proj$methods()
shiny::shinyApp(
ui = shiny::fluidPage(
shiny::headerPanel('Comparaison'),
shiny::sidebarPanel(
uiOutput("data"),
uiOutput("methods"),
shiny::hr(),
shiny::selectInput('plot', 'Plot', c("fdr", "power","fdr power", "F1 score", "correlation")),
shiny::sliderInput("fdr_lim", label = shiny::h3("Threshold"), min = 0,
max = 1.0, value = c(0.0, 0.25))
),
shiny::mainPanel(
shiny::plotOutput('comp.plot')
)
),
server = function(input, output,session) {
# select data
output$data <- renderUI({
data = bench.proj$dataset()
shiny::selectInput("data", label = shiny::h3("Select data set"), choices =
data$name)
})
# select method
output$methods <- renderUI({
sum = bench.proj$summary()
m = dplyr::filter(sum, data == input$data)$method
if(length(m) == 0) {
shiny::helpText("No run for this dataset")
} else {
shiny::checkboxGroupInput("methods", label = shiny::h3("Methods"), choices = m, selected = input$methods)
}
})
# comparaison plots
output$comp.plot <- shiny::renderPlot({
plots=bench.plotfdr_power(bench.proj, input$data, input$methods, input$fdr_lim)
if(input$plot=="fdr") {
plots$fdr
} else if(input$plot=="power") {
plots$power
} else if(input$plot=="fdr power") {
plots$fdr.power
} else if(input$plot=="F1 score") {
plots$f1.score
} else if(input$plot=="correlation") {
plots = bench.heatmap(bench.proj, input$data, input$methods)
plots$cor
}
})
},
options = list(height = 750)
)
}
#' run sampler viewer
#'
#'
#' TODO
#'
#' @return TODO
#'
#' @examples
#' TODO
#
#' @export
bench.samplerviewer <- function(bench.proj) {
sampler = bench.proj$sampler()
shiny::shinyApp(
ui = shiny::fluidPage(
shiny::headerPanel('Sampler'),
shiny::sidebarPanel(
shiny::selectInput("sampler", label = shiny::h3("Select sampler"),
choices = sampler$name,
selected = 1),
shiny::hr(),
uiOutput("param"),
shiny::actionButton("run", label = "run"),
shiny::hr(),
uiOutput("dataSelector"),
shiny::actionButton("remove", label = "remove")
),
shiny::mainPanel(
shiny::h3("Sampler"),
shiny::tableOutput(outputId="sampler.info"),
shiny::hr(),
shiny::h3("Dateset"),
shiny::tableOutput(outputId="data.info")
)
),
server = function(input, output,session) {
output$sampler.info <- shiny::renderTable({dplyr::select( dplyr::filter(sampler, name == input$sampler), name, description) })
output$param <- renderUI({
shiny::textInput("parameter", label = shiny::h3("Parameter"), value =
dplyr::select( dplyr::filter(sampler, name == input$sampler), default_parameter)[1])
})
shiny::observeEvent(input$run, {
eval(parse(text = input$parameter))
bench.runsampler(bench.proj, sampler.name = input$sampler, repetition = 1, parameter = parameter)
# data update
output$data.info <- shiny::renderTable({
data = bench.proj$dataset()
data[grep(input$sampler,data$name),c(1,2)]
})
output$dataSelector <- renderUI({
data = bench.proj$dataset()
names = data[grep(input$sampler,data$name),1]
shiny::selectInput("dataset", label = shiny::h3("Select dataset"),
choices = names,
selected = 1)
})
})
# data update
output$data.info <- shiny::renderTable({
data = bench.proj$dataset()
data[grep(input$sampler,data$name),c(1,2)]
})
output$dataSelector <- renderUI({
data = bench.proj$dataset()
names = data[grep(input$sampler,data$name),1]
shiny::selectInput("dataset", label = shiny::h3("Select dataset"),
choices = names,
selected = 1)
})
shiny::observeEvent(input$remove, {
bench.removedataset(bench.proj, input$dataset)
# data update
output$data.info <- shiny::renderTable({
data = bench.proj$dataset()
data[grep(input$sampler,data$name),c(1,2)]
})
output$dataSelector <- renderUI({
data = bench.proj$dataset()
names = data[grep(input$sampler,data$name),1]
shiny::selectInput("dataset", label = shiny::h3("Select dataset"),
choices = names,
selected = 1)
})
})
},
options = list(height = 750)
)
}
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