layout of explore & optimize
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explore_4pl <- tagList(
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div(),#empty, just for spacing
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navset_pill(
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id = "tab_menu_2",
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nav_panel("normal option TODO",
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tags$div("graphs 4pl TODO"),
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accordion(
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open = FALSE,
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accordion_panel(
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title = "4PL-Tests",
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p("This is the content inside the expandable box."),
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)
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),
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accordion(
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open = FALSE,
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accordion_panel(
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title = "unrestricted ANOVA for 4PL",
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p("This is the content inside the expandable box."),
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)
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),
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accordion(
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open = FALSE,
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accordion_panel(
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title = "Error calculations:", #TODO NAME?
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p("This is the content inside the expandable box."),
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)
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)
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),
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nav_panel("ln-transformed y",
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tags$div("graphs 4pl ln transformed y TODO"),
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accordion(
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open = FALSE,
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accordion_panel(
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title = "4PL-Tests for ln-transformed y",
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p("This is the content inside the expandable box."),
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)
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)
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),
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),
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)
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explore_linear <- tagList(
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tags$p("graphs linear TODO"),
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accordion(
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open = FALSE,
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accordion_panel(
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title = "Tests for linear PLA:",
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p("This is the content inside the expandable box."),
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)
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),
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accordion(
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open = FALSE,
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accordion_panel(
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title = "ANOVA for parallel line assay:",
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p("This is the content inside the expandable box."),
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)
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),
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accordion(
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open = FALSE,
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accordion_panel(
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title = "Unrestricted linear model (SSSI):",
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p("This is the content inside the expandable box."),
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)
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),
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accordion(
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open = FALSE,
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accordion_panel(
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title = "Restricted linear model (CSSI):",
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p("This is the content inside the expandable box."),
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)
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)
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)
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explore_page <- layout_sidebar(
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sidebar = sidebar(
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class = "sidebar",
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tags$div( class = "sidebar_collector",
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tags$h5( class = "sidebar_collector_header",
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"Exploration Settings"
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),
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sliderInput("sdfac", "Variability of lower to upper asymptote [%]:", min = 0, max = 100, value = 50),
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sliderInput("potencydiff", "Potency of test [%]:", min = 0, max = 200, value = 100),
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checkboxInput("PureErrMeta","Use pure error", FALSE),
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checkboxInput("heterosked","Heteroskedastic noise", FALSE),
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),
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tags$div( class = "sidebar_collector",
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tags$h5( class = "sidebar_collector_header", "Curve Settings"),
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numericInput("lowAsymptREF", "lower asymptote REF", 10, step = 1, min = 0),
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numericInput("lowAsymptTEST", "lower asymptote TEST", 10, step = 1, min = 0),
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numericInput("uppAsymptREF", "upper asymptote REF", 110, step = 1, min = 0),
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numericInput("uppAsymptTEST", "upper asymptote TEST", 110, step = 1, min = 0),
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numericInput("slopeREF", "slope REF", 1, step = 0.1, min = -10),
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numericInput("slopeTEST", "slope TEST", 1, step = 0.1, min = -10),
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numericInput("EC50", "EC50 REF", -3.5),
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numericInput("potDiff", "potency difference", 0)
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),
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tags$div( class = "sidebar_collector",
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tags$h5( class = "sidebar_collector_header", "Dilutions"),
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numericInput("CONC1", "highest concentration", 0.3, min = -3.5),
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numericInput("CONC2", "2nd concentration", 0.15),
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numericInput("CONC3", "3rd concentration", 0.075),
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numericInput("CONC4", "4th concentration", 0.0375),
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numericInput("CONC5", "5th concentration", 0.01875),
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numericInput("CONC6", "6th concentration", 0.00938),
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numericInput("CONC7", "7th concentration", 0.00469),
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numericInput("CONC8", "8thd concentration", 0.00235),
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numericInput("CONC9", "9thd concentration", value = NA),
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numericInput("CONC10", "10th concentration", value = NA),
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numericInput("CONC11", "11th concentration", value = NA),
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numericInput("CONC12", "lowest concentration", NA)
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),
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tags$div( class = "sidebar_collector",
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tags$h5( class = "sidebar_collector_header", "Geometric Dilution Scheme"),
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numericInput("ConcStart", "starting concentration", value = NA, min = 0),
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numericInput("dilutionFac", "dilution factor", value = NA, min = 0, max = 10),
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numericInput("NoDil", "no. of dilutions", value = NA, min = 8),
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numericInput("NoDilSer", "no. of dil. series", value = NA, min = 0), #TODO 1?
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),
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),
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# Main content goes here (can be multiple elements)
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navset_pill(
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id = "tab_menu_1",
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nav_panel("4PL", explore_4pl),
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nav_panel("LINEAR", explore_linear)
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),
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accordion(
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open = FALSE,
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accordion_panel(
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title = "Input-Data with added random noise:",
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box( # TODO
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title = "Simulated data per log-concentration", solidHeader = TRUE, width = 12, "incl. mean, sd and CV%",
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DT::dataTableOutput("ConctabMeta")
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),
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)
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)
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)
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@@ -0,0 +1,44 @@
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home_page <- tagList(
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tags$div( style = "align-self: center",
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tags$div( class = "home-text-section",
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tags$h3("Welcome to Plateflow"),
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tags$p("Plateflow allows you to EXPLORE, INSPECT and OPTIMIZE your data in
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the context of a 4 PL fit or a linear regression fit. "),
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),
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tags$div( class = "home-text-section",
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tags$h4("Readable formats and expected structure"),
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tags$p("Plateflow is optimized for uploadfiles in the folowing formats:
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.xlsx, .csv and .numbers."),
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tags$ul(
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tags$li("1 column with the dilution concentrations (first or last column) is expected"),
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tags$li("The column name of the dilution concentrations can be as follows: concentration, dose, log_concentration, log_dose (first letter can be capital).
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It is assumed, that the concentrations are in anti-log or in natural log mode."),
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tags$li("2 columns of reference and test sample readouts, respectively, in this order, are expected"),
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tags$li("The column names for reference and test are free to set, but must differ for all columns"),
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),
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tags$p("You can download an example", tags$a("TestFile.xlsx ", target = "self", href = "TestFile.xlsx"), "File here."),
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tags$h6("Example filestructure:"),
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tags$img(src= "example_file.png", width = "800px", alt="example filestructure for upload", style = " max-width:800px"),
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tags$br(),
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),
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tags$div( class = "home-text-section",
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tags$br(),
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tags$h4("Information on dilution settings"), #TODO
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tags$p("Bend points are calculated according to following formula:",
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withMathJax(" $$bp_{1/2} = \\pm\\frac{1.31696}{Hill's slope}$$"),
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"Please refer to this", a(href = "ADONIS.pdf", "Whitepaper", download = NA, target = "_blank"), "for further details.", #TODO this link does not work for me
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),
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tags$br(),
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),
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tags$div( class = "home-text-section",
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tags$h4("Plateflow Point of Contact"),
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tags$p("At InnerAnalytics, we are happy to hear from you. You can contact us under: ",
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tags$a("info@inner-analytics.eu", href = "mailto:info@inner-analytics.eu")),
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tags$p("If you would like to report a bug, we would appreciate it if you sent us the following infos to help us solve your request as fast as possible: "),
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verbatimTextOutput("sessioninfo"), #TODO actually output this
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),
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)
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)
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@@ -0,0 +1,61 @@
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optimize_4pl <- tagList(
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tags$p("graphs optimize 4pl TODO"),
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accordion(
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open = FALSE,
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accordion_panel(
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title = "Tests for linear PLA:",
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p("This is the content inside the expandable box."),
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)
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),
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)
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dilution_slider <- tagList(
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tags$h2("Finder for optimal dilutions"),
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tags$p("graphs optimize dilution-slider TODO"),
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accordion(
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open = FALSE,
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accordion_panel(
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title = "Adjusted dilution factors:",
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p("This is the content inside the expandable box."),
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)
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),
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)
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histograms <- tagList(
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accordion(
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open = FALSE,
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accordion_panel(
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title = "Parameter Histograms",
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p("This is the content inside the expandable box."),
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)
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),
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)
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optimize_report <- tagList(
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tags$p("download optimize report TODO"),
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)
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optimize_page <- layout_sidebar(
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sidebar = sidebar(
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class = "sidebar",
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tags$div( class = "sidebar_collector",
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tags$h5( class = "sidebar_collector_header",
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"Optimization Settings"
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),
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sliderInput("TODO", "Adjust the dilutions (+- change in %):", min = -100, max = 100, value = 0),
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checkboxInput("TODO2","Fix highest concentration instead of center", FALSE),
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p("Wider dilution ranges increase the CIs of the relative potency, and decrease the CIs of the upper and lower asymptotes ratios, as well as the Hill's slope ratios."),
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),
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),
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# Main content goes here (can be multiple elements)
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optimize_4pl,
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dilution_slider,
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histograms,
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optimize_report
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)
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