library(shiny)
library(shinythemes)
library(rhandsontable)
shinyUI(navbarPage(title = "dpcReport",
header = includeScript("ga.js"),
theme = shinytheme("cerulean"),
id = "navbar", windowTitle = "dpcReport", collapsible = TRUE,
tabPanel("Input file",
includeMarkdown("input_file1.md"),
fluidRow(
column(2, fileInput("input_file",
h4("Choose dPCR data"))),
column(2, selectInput("input_type", label = h4("Select data format"),
choices = list("REDF (raw format)" = "redf",
"QX100" = "QX100",
"QX200" = "QX200",
"BioMark (Detailed Table Results)" = "BioMark_det",
"BioMark (Summary Table Results)" = "BioMark_sum",
"Amplitude data (.zip)" = "amp"))),
column(3, htmlOutput("input_information"))
),
includeMarkdown("input_file2.md"),
rHandsontableOutput("input_table"),
br(),
br()
),
navbarMenu("Data summary",
tabPanel("Summary table",
DT::dataTableOutput("summary_input"),
# downloadButton("summary_table_download_button",
# "Save table (.csv)"),
includeMarkdown("./data_summary/data_summary_table1.md")),
#summary boxplot and stripchart
tabPanel("Summary charts",
includeMarkdown("./summary_plots/data_summary_scatterchart1.md"),
plotOutput("summary_plot",
dblclick = dblclickOpts(id = "summary_plot_dbl")),
fluidRow(
column(3, downloadButton("summary_plot_download_button",
"Save chart (.svg)")),
column(3, actionButton("summary_plot_reset",
"Reset chart"))
),
br(),
htmlOutput("summary_plot_dbl"),
includeMarkdown("./summary_plots/data_summary_scatterchart2.md"),
selectInput("CI_method", label = h4("Select method for CI calculation:"),
choices = list("Dube" = "dube", "Bhat" = "bhat")),
htmlOutput("summary_exprep_plot_ui"),
fluidRow(
column(3, downloadButton("summary_exprep_plot_download_button",
"Save chart (.svg)")),
column(3, actionButton("summary_exprep_plot_reset",
"Reset chart"))
),
htmlOutput("summary_exprep_plot_dbl"))),
#test counts
tabPanel("Comparison of runs",
includeMarkdown("./test_counts/test_counts1.md"),
DT::dataTableOutput("test_counts_res"),
# downloadButton("test_counts_res_download_button",
# "Save table (.csv)"),
includeMarkdown("./test_counts/test_counts2.md"),
DT::dataTableOutput("test_counts_groups"),
# downloadButton("test_counts_groups_download_button",
# "Save table (.csv)"),
htmlOutput("test_counts_plot_ui"),
fluidRow(
column(3, downloadButton("test_counts_plot_download_button",
"Save chart (.svg)")),
column(3, actionButton("test_counts_plot_reset",
"Reset chart"))
),
htmlOutput("test_count_dbl"),
includeMarkdown("./test_counts/test_counts3.md")),
navbarMenu("Advanced analysis",
tabPanel(title = "Array spatial analysis",
htmlOutput("plot_panel_tab")),
tabPanel(title = "Probability distribution",
includeMarkdown("./prob_distr/prob_distr1.md"),
htmlOutput("run_choice"),
includeMarkdown("./prob_distr/prob_distr2.md"),
DT::dataTableOutput("moments_table"),
# downloadButton("moments_table_download_button", "Save table (.csv)"),
includeMarkdown("./prob_distr/prob_distr3.md"),
fluidRow(
column(3, selectInput("density_plot_avg", label = h4("Select parameter:"),
choices = c("k" = FALSE, "lambda" = TRUE))),
column(3, selectInput("density_plot_methods", h4("Choose method of calculating CI:"),
choices = list("Agresti-Coull" = "agresti-coull",
"Asymptotic" = "asymptotic",
"Bayesian inference" = "bayes",
"Cloglog parameterization" = "cloglog",
"Logit parameterization" = "logit",
"Pearson-Klopper" = "exact",
"Probit parameterization" = "probit",
"Proportion test" = "prop.test",
"Wilson" = "wilson"),
"wilson")),
column(3, numericInput("density_plot_cil", h4("Confidence intervals level:"),
0.95, min = 0, max = 1,
step = 0.01)),
column(3, selectInput("density_plot_bars", label = h4("Plot bars:"),
choices = c("yes" = TRUE, "no" = FALSE)))
),
plotOutput("density_plot"),
downloadButton("density_plot_download_button",
"Save chart (.svg)"),
includeMarkdown("./prob_distr/prob_distr4.md")
)
),
tabPanel("Save report",
includeMarkdown("download_report1.md"),
checkboxInput("data_summary_table_rep", "Data summary table",
value = TRUE),
checkboxInput("data_summary_scatter_rep", "Data summary scatter charts",
value = TRUE),
checkboxInput("data_summary_test_counts", "Compare runs",
value = TRUE),
checkboxInput("plot_panel", "Visualise and analyze individually each array",
value = FALSE),
checkboxInput("poisson_distr", "Visualise and analyze probability distribution of each run",
value = FALSE),
checkboxInput("R_code", "R code used in the report generation",
value = TRUE),
p("Be patient. The generation of the report may take few minutes."),
downloadButton("report_download_button",
"Save report"),
downloadButton("input_download_button",
"Save input data (.csv)")),
tabPanel("About",
includeMarkdown("about.md"))
#tabPanel("Restart app", actionButton("quit_button", "Quit dpcReport"))
))
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