Global.R into dev
This commit is contained in:
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{
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"id": "00336B5B",
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"path": "~/plateflow/wizard/ui.R",
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"project_path": null,
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"type": "r_source",
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"hash": "0",
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"contents": "",
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"dirty": false,
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"created": 1777315188063.0,
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"source_on_save": false,
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"relative_order": 3,
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"properties": {
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"source_window_id": "",
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"Source": "Source",
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"cursorPosition": "149,33",
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"scrollLine": "0"
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},
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"folds": "",
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"lastKnownWriteTime": 1776610618,
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"encoding": "UTF-8",
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"collab_server": "",
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"source_window": "",
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"last_content_update": 1776610618,
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"read_only": false,
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"read_only_alternatives": []
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}
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library(shiny)
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library(shinyjs)
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library(shinyAce)
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library(bslib)
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version <- "1.0.0"
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function(req) {
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fluidPage(
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useShinyjs(),
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titlePanel("Dilution Wizard"),
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tags$head(tags$style((".shiny-notification {position: fixed; top: 20%;left: 50%; margin-top: -100px;
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margin-left: -250px; color: blue;font-size: 20px; font-style: italic;}")),
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tabsetPanel(id="toptab",
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tabPanel("Data entry",
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wellPanel(
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fluidRow(
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tags$head(tags$style(HTML("label {font-size:80%;margin-bottom: 3px;margin-top: 3px;}"))),
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column(2,
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tags$image(src="logo.png", class="adv_logo"),
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h4("upload EXCEL"),
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fileInput(inputId = "iFile", label = "", accept="ms-excel"),
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uiOutput(outputId = "sheetName"),
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div(checkboxInput("PureErr", "Should pure error be used for calculation of CIs?", FALSE),
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style = "font-size: 24px !important;color: red"),
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verbatimTextOutput("stats"),
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h5("\n\n\n Author: Franz Innerbichler, InnerAnalytics")),
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div(id="parameter",
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column(1,style = "background: lightgrey",
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#actionButton("StartCalc", "Click, when calculations to be started"),
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h4("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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),
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column(1,style = "background: lightgrey",
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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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column(1,style = "background: lightgreen",
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h4("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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),
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column(1,style = "background: lightgreen",
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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",NA),
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numericInput("CONC10", "10th concentration",NA),
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numericInput("CONC11", "11th concentration",NA),
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numericInput("CONC12", "lowest concentration",NA)
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),
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column(1,style = "background: lightblue",
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h4("geometric dilution scheme"),
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numericInput("ConcStart", "starting concentration",NA),
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numericInput("dilutionFac", "dilution factor",NA),
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numericInput("NoDil", "no. of dilutions",NA),
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numericInput("NoDilSer", "no. of dil. series",NA),
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verbatimTextOutput("dilutions")
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),
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column(4,
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h4("log-dilution scheme"),
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verbatimTextOutput("logdil"),
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h4("User help"),
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h5("If new dilutions are entered, please adjust EC50 to avoid calculation errors"))
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)
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)
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)),
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#### XLSX diagnostics ----
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tabPanel ("XLSX diagnostics",
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tags$style(HTML("pre { color: black; background-color: #FFE1FF;
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font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif;font-size: 12px;} ")),
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wellPanel(
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fluidRow(
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column(2,
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h5("Diagnostics only shown if EXCEL is uploaded"),
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htmlOutput("PureErrW2"),
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tags$head(tags$style("#PureErrW2{color: red;
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font-size: 16px;
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font_style: italic;}")),
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tableOutput("FileSAmpl"),
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downloadButton("downloadXLReport", label="Download PDF report", class="butt"),
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tags$style(type="text/css","#downloadXLReport {background-color: orange; color: black;font-family: COurier New}"),
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plotOutput("relpotTestPlot", width="300px", height="150px"),
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h4("Akaike Information Criterion"),
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tableOutput("AIC"),
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h5("First row: restricted model; 2nd row: unrestricted model"),
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h5("Smaller values of AIC indicate better fit to the data"),
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tableOutput("VarDiagn")
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),
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column(4,
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plotOutput("XLplot"),
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column(6,
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br(),
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"Regression results restricted",
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tableOutput("coeffs_r"),
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"Bend points restricted",
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tableOutput("coeffs_r2")),
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column(6,
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br(),
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"Regression results unrestricted",
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tableOutput("coeffs_unr"))),
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column(4,
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plotOutput("diagnplot"),
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column(6,
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tableOutput("logcoeffs_r"),
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tableOutput("coeffs_unr2")),
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column(6,
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tableOutput("logcoeffs_unr"))),
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column(2,
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tableOutput("ANOVAXLS"),
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DT::renderDataTable("EQtests"))
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)
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)),
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#### 4pl fits ----
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tabPanel("4pl-fit",
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wellPanel(
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fluidRow(
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column(6,
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tags$style(span(htmlOutput("PureErrW3"), style="color: red")),
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htmlOutput("PureErrW3"),
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tags$head(tags$style("#PureErrW2{color: red;
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font-size: 16px;
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font_style: italic;}")),
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plotOutput("plot"),
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DT::dataTableOutput("pottab4pl"),
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"Footnote: test performed on absolute CIs."),
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column(6,
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DT::dataTableOutput("secondary"), # SSTs
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h5("*...The estimate for F-test on regression and on non-linearity is the p-value"),
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h5("F-test on regression passes if F-value > F-crit and thus p < 0.05"),
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h5("F-test on non-linearity passes if F-value < F-crit and thus p > 0.05"),
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h5("Test results outcome: 0 ... test passed (for EQ tests: CI within limits);
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1 ... test failed (for EQ tests CI not within limits);
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-1 ... calculations unbound/denominator too close to 0"),
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#plotOutput("CIplot, height=50%")
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)
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))
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),
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#### Linear PLA ----
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tabPanel("Linear PLA",
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wellPanel(
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fluidRow(
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column(6,
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htmlOutput("PureErrW3"),
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tags$head(tags$style("#PureErrW2{color: red;
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font-size: 16px;
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font_style: italic;}")),
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plotOutput("plotLin"),
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"Delta method is used for potency CIs",
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DT::dataTableOutput("pottab"),
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h4("Unrestricted linear model (SSSI):"),
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tableOutput("SummaryModABu"),
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h4("Restricted linear model (CSSI):"),
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tableOutput("SummaryModAB")),
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column(3,
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h3("Tests for linear PLA):"),
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DT::dataTableOutput("TESTSlin"),
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h5("The estimate is the p-value of the test"),
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h5("F-tests on regression, significance of slopes, and preparation need to have a p-value <0.05 to pass"),
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h5("All other tests pass if p-value > 0.05"),
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"SST CI for difference of slopes:",
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tableOutput("SlopeDiffCI")),
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column(3,
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h3("ANOVA for parallel line assay"),
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DT::dataTableOutput("ANOVAlin"))
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)
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)),
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#### Dilution simulator ----
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tabPanel("Dilution simulator",
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wellPanel(
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fluidRow(
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column(4,
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h3("Confidence intervals"),
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tableOutput("CIs"),
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"The confidence intrval table is interaactive for changes in: variability slider (%SD), potency of test-slider,
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and 'Adjust the dilutions'-slider",
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tableOutput("optimalDils"),
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selectInput(inputId="scenario", label= "Select an 'optimal' scenario:", choices = c("scenario 2","scenario 3","scenario 6","steep slope"))),
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column(5,
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plotOutput("plotfordilutions"),
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h4("in grey: most extreme bend point lines of theoretical samples with 50% and 200% potency"),
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sliderInput("dilslider", "Adjust the dilutions(+-change in %)", min = -100,max=100, value=0, step=1, round=0),
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checkboxInput("fixupper","Fix highest concentration (if unticked, the center is fixed)",FALSE),
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h5("Dilution factors"),
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tableOutput("adjlogdil"),
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"Short guidance: wider dilution ranges increase the CIs of rel. potency, and decrease the CIs of upper and lower asymptote ratios, as well as Hill's slope ratios", br(),
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"Narrower dilution ranges decrease the CIs of rel. potency, and increase the CIs of upper and lower asymptote ratios, ands Hill's slope ratios",),
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column(3,
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h3("Bend points"),
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tableOutput("bps"),
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tableOutput("extremebps"),
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h4("Explanation of the plots")
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)
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)
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)),
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#### EQ limits simulation ----
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tabPanel("EQ-limit simulatioin",
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wellPanel(
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fluidRow(
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column(1, style="background: lightblue",
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numericInput("simN","number of datasets to simulate", 100, step=10, min=10, max=1000),
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numericInput("lowQuant", "lower quantile", 1, min = 0.01,max=20),
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numericInput("uppQuant", "upper quantile", 99, min = 801,max=99.99),
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actionButton('goSim', "Start simulation",class="btn-success")
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),
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column(4,
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h4("estimation of EACs for slope ratio, dynamic range-ratio, upper asymptote ratio, and potency"),
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plotOutput("plotHistuAs", width = "1400px", height = "400px"))
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)
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)),
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#### Documentation ----
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tabPanel("Documentation",
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h4("Information on dilution setting"),
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"(for details see:", a(href="ADONIS.pdf","Whitepaper", download=NA, target="_blank"),")",tags$br(),
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"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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#### setting lower panel ----
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wellPanel(
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fluidRow(
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column(2,
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h3("Settings"),
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helpText("Vary the slider to see the effect of special cause"),
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sliderInput("sdfac","Variability as % of lower to upper asymptote", max=10, value=3, min=0.1, step=0.1),
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checkboxInput("heterosked","heteroskedastic noise", FALSE),
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sliderInput("potencydiff","potency of test (%)", max=200, min=50, value=100, step=1),
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sliderInput("outlL","outlier in lower asymptote", min=0, max=1.5, value=0, step=0.1),
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sliderInput("outlM","outlier in mid part", min=0, max=1.5,value=0, step=0.1),
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sliderInput("outlU","outlier in upper asymptote", min=0, max=1.5,value=0, step=0.1)
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),
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column(1,
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tags$table(id="dose-table",
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numericInput("lEACdiffla","lower EAC for diff. of LA", -0.175, step=0.001),
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numericInput("uEACdiffla","upper EAC for diff. of LA", 0.189, step=0.001),
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numericInput("lEACratiola","lower EAC ratio of LAs", 0.005, step=0.001),
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numericInput("uEACratiola","upper EAC for ratio of LAs", 100, step=1),
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numericInput("lEACratioSlope","lower EAC for ratio of slopes", 0.55, step=0.01),
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numericInput("uEACratioSlope","upper EAC for ratio of slopes", 1.84, step=0.1),
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numericInput("lEACratioua","lower EAC for ratio of UAs", 0.75, step=0.1),
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numericInput("uEACratioua","upper EAC for ratio of UAs", 1.33, step=0.1),
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numericInput("lowerPot","lower EAC for potency", 75, step=1),
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numericInput("upperPot","upper EAC for potency", 133, step=1),
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numericInput("lEACratioAdiff","lower EAC of ratio of asymptote differences", 0.75, step=0.01),
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numericInput("uEACratioAdiff","upper EAC of ratio of asymptote differences", 1.33, step=0.01)
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)),
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column(4,
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"4 PL ANOVA unrestricted",
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DT::dataTableOutput("ANOVA"),
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h5("Please note that for the CIs of rel. potency the RSS of the restricted model is used"),
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h5("RSS ... 'Residual error' in the SumSquares column"),
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h5("MSE ... 'Residual error' in the MSs column"),
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h5("SSE ... 'Pure error' in the SumSquares column"),
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h5("RMSE ... Square root of the 'Residual Error' in the MS column"),
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verbatimTextOutput("RMSE")
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),
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column(5,
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DT::dataTableOutput("Conctab"))
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)
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)
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)
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)
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}
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@@ -0,0 +1,27 @@
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{
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"id": "2D702BEF",
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"path": "~/plateflow/wizard/server.R",
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"properties": {
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"expression": "slopeSt",
|
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"caption": "slopeSt",
|
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"cacheKey": "B95B358D",
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"object": "slopeSt",
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}
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@@ -0,0 +1,28 @@
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||||
{
|
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"id": "47543094",
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"path": "~/plateflow/NewApp/app.R",
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"project_path": "app.R",
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File diff suppressed because it is too large
Load Diff
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{
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"properties": {
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"caption": "pl_df",
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|
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"last_content_update": 1778393048148,
|
||||
"read_only": false,
|
||||
"read_only_alternatives": []
|
||||
}
|
||||
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,34 @@
|
||||
{
|
||||
"id": "9E593C09",
|
||||
"path": null,
|
||||
"project_path": null,
|
||||
"type": "r_dataframe",
|
||||
"hash": "0",
|
||||
"contents": "",
|
||||
"dirty": false,
|
||||
"created": 1778393675522.0,
|
||||
"source_on_save": false,
|
||||
"relative_order": 8,
|
||||
"properties": {
|
||||
"expression": "slopeTe",
|
||||
"caption": "slopeTe",
|
||||
"totalObservations": 10,
|
||||
"displayedObservations": 10,
|
||||
"variables": 2,
|
||||
"cacheKey": "E00BF6E9",
|
||||
"object": "slopeTe",
|
||||
"environment": "_rs_no_env",
|
||||
"contentUrl": "grid_resource/gridviewer.html?env=_rs_no_env&obj=slopeTe&cache_key=E00BF6E9&max_display_columns=50",
|
||||
"preview": 0,
|
||||
"source_window_id": "",
|
||||
"Source": "Source"
|
||||
},
|
||||
"folds": "",
|
||||
"lastKnownWriteTime": 0,
|
||||
"encoding": "",
|
||||
"collab_server": "",
|
||||
"source_window": "",
|
||||
"last_content_update": 1778393675522,
|
||||
"read_only": false,
|
||||
"read_only_alternatives": []
|
||||
}
|
||||
@@ -0,0 +1,51 @@
|
||||
#
|
||||
# This is a Shiny web application. You can run the application by clicking
|
||||
# the 'Run App' button above.
|
||||
#
|
||||
# Find out more about building applications with Shiny here:
|
||||
#
|
||||
# https://shiny.posit.co/
|
||||
#
|
||||
|
||||
library(shiny)
|
||||
|
||||
# Define UI for application that draws a histogram
|
||||
ui <- fluidPage(
|
||||
|
||||
# Application title
|
||||
titlePanel("Old Faithful Geyser Data"),
|
||||
|
||||
# Sidebar with a slider input for number of bins
|
||||
sidebarLayout(
|
||||
sidebarPanel(
|
||||
sliderInput("bins",
|
||||
"Number of bins:",
|
||||
min = 1,
|
||||
max = 50,
|
||||
value = 30)
|
||||
),
|
||||
|
||||
# Show a plot of the generated distribution
|
||||
mainPanel(
|
||||
plotOutput("distPlot")
|
||||
)
|
||||
)
|
||||
)
|
||||
|
||||
# Define server logic required to draw a histogram
|
||||
server <- function(input, output) {
|
||||
|
||||
output$distPlot <- renderPlot({
|
||||
# generate bins based on input$bins from ui.R
|
||||
x <- faithful[, 2]
|
||||
bins <- seq(min(x), max(x), length.out = input$bins + 1)
|
||||
|
||||
# draw the histogram with the specified number of bins
|
||||
hist(x, breaks = bins, col = 'darkgray', border = 'white',
|
||||
xlab = 'Waiting time to next eruption (in mins)',
|
||||
main = 'Histogram of waiting times')
|
||||
})
|
||||
}
|
||||
|
||||
# Run the application
|
||||
shinyApp(ui = ui, server = server)
|
||||
@@ -0,0 +1,27 @@
|
||||
{
|
||||
"id": "AFA288F2",
|
||||
"path": "~/plateflow/wizardNew/DataGenerator.R",
|
||||
"project_path": null,
|
||||
"type": "r_source",
|
||||
"hash": "0",
|
||||
"contents": "",
|
||||
"dirty": false,
|
||||
"created": 1777554257099.0,
|
||||
"source_on_save": false,
|
||||
"relative_order": 4,
|
||||
"properties": {
|
||||
"tempName": "Untitled1",
|
||||
"source_window_id": "",
|
||||
"Source": "Source",
|
||||
"cursorPosition": "53,0",
|
||||
"scrollLine": "32"
|
||||
},
|
||||
"folds": "",
|
||||
"lastKnownWriteTime": 1777557164,
|
||||
"encoding": "UTF-8",
|
||||
"collab_server": "",
|
||||
"source_window": "",
|
||||
"last_content_update": 1777557164367,
|
||||
"read_only": false,
|
||||
"read_only_alternatives": []
|
||||
}
|
||||
@@ -0,0 +1,54 @@
|
||||
Calc_DilRes <- function(as=3, bs=1, cs=-4, ds=10, at=3, bt=1, dt=10,r=0.0001,ct=cs-r,
|
||||
sd_fac=0.1, gt=1, gs=1, log_conc,
|
||||
heteroNoise=FALSE, noDilSeries, noDils) {
|
||||
yAxfac <- (ds-as)
|
||||
log_dose <- log_conc
|
||||
isRef <- rep(c(1,0),1,each=length(log_conc)*noDilSeries)
|
||||
isSample <- rep(c(0,1),1,each=length(log_conc)*noDilSeries)
|
||||
browser()
|
||||
av <- as*isRef + at*isSample + (ds*isRef + dt*isSample - as*isRef - at*isSample)/
|
||||
(1+isRef*exp(bs*(cs - log_dose)) + isSample*exp(bt*(ct-log_dose)))
|
||||
if (heteroNoise) {
|
||||
# heterosc noise
|
||||
ro_jit <- matrix(unlist(map(av, function(x) x+rnorm(1,0,x*sd_fac/100))), nrow=noDils, ncol=noDilSeries*2)
|
||||
} else {
|
||||
# homosc noise
|
||||
ro_jit <- matrix(unlist(map(av, function(x) x+rnorm(1,0,sd_fac*yAxfac/100))), nrow=noDils, ncol=noDilSeries*2)
|
||||
}
|
||||
ro_jit <- abs(ro_jit)
|
||||
|
||||
ro_jit2 <- cbind(ro_jit, log_dose)
|
||||
if (noDilSeries==3) {
|
||||
colnames(ro_jit2) <- c("R_dil1","R_dil2","R_dil3","T_dil1","T_dil2","T_dil3", "log_dose")
|
||||
} else {
|
||||
colnames(ro_jit2) <- c("R_dil1","R_dil2","T_dil1","T_dil2", "log_dose")
|
||||
}
|
||||
return(ro_jit2)
|
||||
}
|
||||
|
||||
library(openxlsx)
|
||||
Conc <- 9*1/(3^(1:11))
|
||||
Conc_ <- c(9, Conc)
|
||||
|
||||
ro_new <- list()
|
||||
ro_new[[1]] <- Calc_DilRes(as=1000, bs=-2, cs=-4, ds=10000, at=1000, bt=-2, dt=10000, log_conc = log(Conc_),
|
||||
sd_fac=3.3,
|
||||
# auslenkU=outlierU,
|
||||
# auslenkM=outlierM,
|
||||
# auslenkL=outlierL,
|
||||
heteroNoise = F, noDilSeries = 2, noDils = 12)
|
||||
ro_new[[2]] <- Calc_DilRes(as=1000, bs=-2, cs=-4, ds=10000, at=1000, bt=-2, dt=10000, log_conc = log(Conc_),
|
||||
sd_fac=3.3,r=0.1,
|
||||
# auslenkU=outlierU,
|
||||
# auslenkM=outlierM,
|
||||
# auslenkL=outlierL,
|
||||
heteroNoise = F, noDilSeries = 2, noDils = 12)
|
||||
ro_new[[3]] <- Calc_DilRes(as=1000, bs=-2, cs=-4, ds=10000, at=1000, bt=-2, dt=10000, log_conc = log(Conc_),
|
||||
sd_fac=3.2, r=-0.3,
|
||||
# auslenkU=outlierU,
|
||||
# auslenkM=outlierM,
|
||||
# auslenkL=outlierL,
|
||||
heteroNoise = F, noDilSeries = 2, noDils = 12)
|
||||
|
||||
write.xlsx(ro_new, "~/plateflow/wizard/Tests3Plates.xlsx")
|
||||
|
||||
@@ -0,0 +1,45 @@
|
||||
|
||||
library(shiny)
|
||||
library(shinydashboard)
|
||||
library(fontawesome)
|
||||
|
||||
ui <- dashboardPage(
|
||||
dashboardHeader("wizard"),
|
||||
dashboardSidebar(
|
||||
sidebarMenu(
|
||||
img(src="logo.png", width=230),
|
||||
menuItem("Home", tabName="home", icon=icon("home")),
|
||||
menuItem("Data template", tabName = "template", icon=icon("table"),
|
||||
menuSubItem( tags$li(a("EXCEL File", target="self",href="TestFIle.xlsx")))
|
||||
),
|
||||
menuItem("User Manual /Validation", tabName = "manual", icon=icon("book"),
|
||||
menuSubItem(icon = NULL, tags$li(a("Document", target="self",href="UserManual.pdf")))
|
||||
),
|
||||
menuItem("EXCEL upload", tabName="Dataupload", icon=icon("magnet", lib="glyphicon")),
|
||||
menuItem("4PL + report", tabName="4PL", icon=icon("chart-line", lib="font-awesome")),
|
||||
menuItem("Linear regression + report", tabName="pla", icon=icon("pencil", lib="glyphicon")),
|
||||
menuItem("Wizard", tabName="wizard", icon=icon("chart-column", lib="font-awesome")),
|
||||
menuItem("Documentation", tabName="documentation", icon=icon("chart-area", lib="font-awesome"))
|
||||
),
|
||||
tags$footer(HTML(paste("Owned by",tags$strong(tags$u("InnerAnalytics")), paste(rep(" ",9), collapse=""),
|
||||
"Developer:", paste(rep(" ",9), collapse=""),
|
||||
"Host on:", paste(rep(" ",9), collapse=""),
|
||||
"Version:")),
|
||||
align="left", style=
|
||||
"position:fixed; bottom_=;;width=100%; background: #7FAEFF; font-family: Times New Roman; font-size:100%;
|
||||
padding: 5px; color:#990000; box-sizing: border-box; z-index: 1000;")
|
||||
),
|
||||
dashboardBody(
|
||||
fluidPage(
|
||||
tabItems(
|
||||
tabItem(tabName = "home", htmlOutput("homePage")),
|
||||
tabItem(tabName = "Datapload", uiOutput("Dataupload")),
|
||||
tabItem(tabName = "fourPL", uiOutput("fourPL")),
|
||||
tabItem(tabName = "pla", uiOutput("pla")),
|
||||
tabItem(tabName = "wizard", uiOutput("wizard"))
|
||||
|
||||
)
|
||||
|
||||
)
|
||||
) , skin="blue"
|
||||
)
|
||||
@@ -0,0 +1,34 @@
|
||||
{
|
||||
"id": "FC76AEE8",
|
||||
"path": null,
|
||||
"project_path": null,
|
||||
"type": "r_dataframe",
|
||||
"hash": "0",
|
||||
"contents": "",
|
||||
"dirty": false,
|
||||
"created": 1778097939830.0,
|
||||
"source_on_save": false,
|
||||
"relative_order": 5,
|
||||
"properties": {
|
||||
"expression": "Conctab",
|
||||
"caption": "Conctab",
|
||||
"totalObservations": 12,
|
||||
"displayedObservations": 12,
|
||||
"variables": 8,
|
||||
"cacheKey": "E00A59C5",
|
||||
"object": "Conctab",
|
||||
"environment": "_rs_no_env",
|
||||
"contentUrl": "grid_resource/gridviewer.html?env=_rs_no_env&obj=Conctab&cache_key=E00A59C5&max_display_columns=50",
|
||||
"preview": 0,
|
||||
"source_window_id": "",
|
||||
"Source": "Source"
|
||||
},
|
||||
"folds": "",
|
||||
"lastKnownWriteTime": 0,
|
||||
"encoding": "",
|
||||
"collab_server": "",
|
||||
"source_window": "",
|
||||
"last_content_update": 1778097939830,
|
||||
"read_only": false,
|
||||
"read_only_alternatives": []
|
||||
}
|
||||
Reference in New Issue
Block a user