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| a | b/uieasyroc.R | ||
|---|---|---|---|
| 1 | shinyUI(pageWithSidebar( |
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| 2 | |||
| 3 | titlePanel("easyROC: a web-tool for ROC curve analysis (ver. 1.1)"), |
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| 4 | |||
| 5 | sidebarPanel( |
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| 6 | # Sol panelde nelerin yer alacağı bu bölümde belirleniyor. |
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| 7 | # Tab panellerden veya sol panel içindeki çeşitli radyo butonlar |
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| 8 | # checkbox'lar gibi seçimlerden sonra panelde nelerin değişeceği de |
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| 9 | # ayrıca bir conditionalPanel() bloğu ile burada tanımlanabiliyor. |
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| 10 | |||
| 11 | conditionalPanel(condition="input.tabs1=='Introduction'", |
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| 12 | HTML('<p><img src="multi.png" width=400 height=400></p>'), |
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| 13 | tags$head(includeScript("google-analytics.js")) |
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| 14 | |||
| 15 | ), |
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| 16 | |||
| 17 | conditionalPanel(condition="input.tabs1=='Data upload'", |
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| 18 | h4("Input data"), |
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| 19 | #radioButtons("dataInput", "", list("Load example data"=1, "Upload a file"=2, "Paste your data"=3), selected=1), |
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| 20 | radioButtons("dataInput", "", list("Load example data"=1, "Upload a file"=2), selected=1), |
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| 21 | |||
| 22 | selectizeInput("statusVar", "Name of the status variable", choices = NULL, multiple = FALSE), |
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| 23 | textInput("valueStatus", "Value of the status:", ""), |
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| 24 | HTML('<br>'), |
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| 25 | |||
| 26 | conditionalPanel(condition="input.dataInput=='1'", |
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| 27 | h5("Load example data:"), |
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| 28 | radioButtons("sampleData", "", list("Mayo data (n=312, p=4)"=1, "PBC data set (n=418, p=20)"=2), selected=1), |
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| 29 | HTML('<p>n: number of observations</p>'), |
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| 30 | HTML('<p>p: number of variables</p>') |
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| 31 | ), |
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| 32 | |||
| 33 | conditionalPanel(condition="input.dataInput=='2'", |
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| 34 | h5("Upload a delimited text file (max. 10MB): "), |
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| 35 | #HTML('<i class="fa fa-beer fa-lg"></i>'), |
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| 36 | fileInput("upload", "", multiple = FALSE), |
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| 37 | radioButtons("fileSepDF", "Delimiter:", list("Comma"=1, "Tab"=2, "Semicolon"=3, "Space"=4),selected=2), |
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| 38 | |||
| 39 | conditionalPanel(condition="input.fileSepDF!='1'", |
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| 40 | checkboxInput(inputId = "decimal", label = "Use comma as decimal", value = FALSE) |
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| 41 | ), |
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| 42 | |||
| 43 | HTML('<br>'), |
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| 44 | HTML('<p>You can upload your data as separated by comma, tab, semicolon or space.</p>'), |
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| 45 | HTML('<p><b>Note</b>: First row must be header.</p>') |
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| 46 | ), |
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| 47 | |||
| 48 | conditionalPanel(condition="input.dataInput=='3'", |
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| 49 | h5("Paste or enter your data below:"), |
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| 50 | tags$textarea(id="myData", rows=10, cols=5, ""), |
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| 51 | actionButton('clearText_button','Clear data'), |
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| 52 | HTML('<br>'), |
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| 53 | HTML('<br>'), |
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| 54 | |||
| 55 | radioButtons("fileSepP", "Separator:", list("Comma"=1,"Tab"=2,"Semicolon"=3), selected=2), |
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| 56 | HTML('<p>You can paste or manually enter your data as separated by comma, tab or semicolon.</p>'), |
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| 57 | HTML('<p>Note: First row must be header.</p>') |
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| 58 | ) |
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| 59 | ), |
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| 60 | |||
| 61 | conditionalPanel(condition="input.tabs1=='ROC curve'", |
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| 62 | |||
| 63 | selectizeInput("markerInput", "Select markers (*)", choices = NULL, multiple = TRUE), |
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| 64 | checkboxInput("lowhigh", "Higher values indicate disease", TRUE), |
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| 65 | |||
| 66 | HTML('<br>'), |
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| 67 | |||
| 68 | conditionalPanel(condition = "input.navbarROCcurve == 'Multiple Comparisons'", |
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| 69 | selectInput(inputId = "MultipleCompMethod", label = "Multiple Comparison Method", selected = "bonferroni", |
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| 70 | choices = c("Bonferroni" = "bonferroni", "False discovery rate" = "fdr", "None" = "none") |
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| 71 | ), |
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| 72 | HTML('<br>') |
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| 73 | ), |
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| 74 | |||
| 75 | |||
| 76 | helpText("(*) Multiple markers are allowed."), |
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| 77 | HTML('<br>'), |
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| 78 | |||
| 79 | |||
| 80 | checkboxInput(inputId = "advanced", label = "Advanced options", value = FALSE), |
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| 81 | |||
| 82 | conditionalPanel(condition = "input.advanced", |
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| 83 | radioButtons(inputId = "StdErr", label = "1. Select a method for SE estimation", |
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| 84 | choices = list("Mann-Whitney"="MW", "DeLong(1988)[+]"="DeLong", "Under Null Hyp."="Null", "Binomial"="Binomial"), selected = "DeLong"), |
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| 85 | |||
| 86 | radioButtons(inputId = "ConfInt", label = "2. Select a method for Conf. Interval", |
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| 87 | choices = list("Mann-Whitney"="MW", "DeLong(1988)[+]"="DeLong", "Under Null Hyp."="Null", "Binomial Exact"="Exact"), selected = "DeLong"), |
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| 88 | numericInput(inputId = "alpha", label = "Type I error", value = 0.05, min = 0, max = 1, step = 0.01), |
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| 89 | HTML('<br>'), |
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| 90 | HTML('<br>'), |
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| 91 | helpText("[+]: Default options."), |
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| 92 | HTML('<br>') |
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| 93 | ), |
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| 94 | |||
| 95 | checkboxInput(inputId = "ROCplotOpts", label = "Plot options", value = FALSE), |
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| 96 | |||
| 97 | |||
| 98 | |||
| 99 | conditionalPanel(condition = "input.ROCplotOpts", |
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| 100 | fluidRow(column(5,sliderInput("myheight", "Plot height:", value=400, min=200, max=1200)), |
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| 101 | column(2), |
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| 102 | column(5,sliderInput("mywidth", "Plot width:", value=400, min=200, max=1200 )) |
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| 103 | ), |
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| 104 | |||
| 105 | HTML('<br>'), |
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| 106 | |||
| 107 | fluidRow( |
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| 108 | column(10, selectizeInput("fontfamilyRC", "Font family", |
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| 109 | choices = c("Times New Roman" = "serif", "Arial" = "sans", |
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| 110 | "Corier New" = "mono"), selected = "sans")) |
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| 111 | ), |
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| 112 | |||
| 113 | HTML('<br>'), |
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| 114 | |||
| 115 | selectizeInput("subGrpsRC", "", choices = c("Edit x-axis" = "xAxis", "Edit y-axis" = "yAxis", |
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| 116 | "Other options" = "others"), selected = "xAxis"), |
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| 117 | |||
| 118 | conditionalPanel(condition = "input.subGrpsRC == 'others'", |
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| 119 | fluidRow( |
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| 120 | column(5, textInput("mainRC", "Graph title", "ROC Curve")), |
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| 121 | column(1), |
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| 122 | column(5, selectizeInput("font.mainRC", "Title font", choices = c("Regular" = "1", "Bold" = "2", |
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| 123 | "Italic" = "3", "Bold Italic" = "4"), |
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| 124 | selected = "2")) |
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| 125 | ), |
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| 126 | |||
| 127 | fluidRow( |
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| 128 | column(5, textInput("col.mainRC", "Title color", "black")), |
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| 129 | column(1), |
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| 130 | column(5, numericInput("cex.mainRC", "Title size", min=0.1, max=5, value = 1.2, step = 0.1)) |
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| 131 | ), |
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| 132 | |||
| 133 | fluidRow( |
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| 134 | column(5, textInput("ROCcolRC", "ROC line color", "black,red")), |
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| 135 | column(1), |
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| 136 | column(5, selectizeInput("ROCltyRC", "ROC line type", |
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| 137 | choices = c("\U2500\U2500\U2500\U2500\U2500\U2500\U2500" = "1", |
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| 138 | "\U2574 \U2574 \U2574 \U2574 \U2574 \U2574" = "2", |
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| 139 | "\U00B7 \U00B7 \U00B7 \U00B7 \U00B7 \U00B7 \U00B7 \U00B7 \U00B7" = "3", |
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| 140 | "\U2574 \U00B7 \U2574 \U00B7 \U2574 \U00B7 \U2574" = "4", |
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| 141 | "\U2500 \U2500 \U2500 \U2500 \U2500" = "5", |
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| 142 | "\U2500 \U2574 \U2500 \U2574 \U2500 \U2574" = "6"), |
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| 143 | selected = "1")) |
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| 144 | ), |
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| 145 | |||
| 146 | textInput(inputId = "legend.namesRC", label = "Legend names", value = "") |
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| 147 | ), |
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| 148 | |||
| 149 | conditionalPanel(condition = "input.subGrpsRC == 'xAxis'", |
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| 150 | h5('X-axis options:'), |
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| 151 | |||
| 152 | ## X axis label options |
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| 153 | fluidRow( |
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| 154 | column(5, textInput("xlabRC", "Axis label", "1-Specificity")), |
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| 155 | column(1), |
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| 156 | column(5, selectizeInput("xfont.labRC", "Label font", choices = c("Regular" = "1", "Bold" = "2", |
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| 157 | "Italic" = "3", "Bold Italic" = "4"), |
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| 158 | selected = "1")) |
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| 159 | ), |
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| 160 | |||
| 161 | fluidRow( |
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| 162 | column(5, textInput("xcol.labRC", "Label color", "black")), |
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| 163 | column(1), |
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| 164 | column(5, numericInput("xcex.labRC", "Label size", min=0.1, max=5, value = 1, step = 0.1)) |
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| 165 | ), |
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| 166 | |||
| 167 | ## X axis annotation options |
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| 168 | fluidRow( |
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| 169 | column(5, textInput("xcol.axisRC", "Annotation color", "black")), |
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| 170 | column(1), |
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| 171 | column(5, numericInput("xcex.axisRC", "Annotation size", min=0.1, max=5, value = 1, step = 0.1)) |
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| 172 | ) |
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| 173 | |||
| 174 | #fluidRow( |
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| 175 | # column(5, textInput("xcol11", "Axis color", "black")), |
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| 176 | # column(1), |
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| 177 | # column(5, textInput("xcol.ticks11", "Tickmarks color", "black")) |
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| 178 | #), |
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| 179 | ), |
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| 180 | |||
| 181 | conditionalPanel(condition = "input.subGrpsRC == 'yAxis'", |
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| 182 | h5('Y-axis options:'), |
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| 183 | |||
| 184 | ## Y axis label options |
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| 185 | fluidRow( |
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| 186 | column(5, textInput("ylabRC", "Axis label", "Sensitivity")), |
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| 187 | column(1), |
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| 188 | column(5, selectizeInput("yfont.labRC", "Label font", choices = c("Regular" = "1", "Bold" = "2", |
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| 189 | "Italic" = "3", "Bold Italic" = "4"), |
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| 190 | selected = "1")) |
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| 191 | ), |
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| 192 | |||
| 193 | fluidRow( |
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| 194 | column(5, textInput("ycol.labRC", "Label color", "black")), |
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| 195 | column(1), |
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| 196 | column(5, numericInput("ycex.labRC", "Label size", min=0.1, max=5, value = 1, step = 0.1)) |
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| 197 | ), |
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| 198 | |||
| 199 | ## Y axis annotation options |
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| 200 | fluidRow( |
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| 201 | column(5, textInput("ycol.axisRC", "Annotation color", "black")), |
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| 202 | column(1), |
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| 203 | column(5, numericInput("ycex.axisRC", "Annotation size", min=0.1, max=5, value = 1, step = 0.1)) |
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| 204 | ) |
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| 205 | ) |
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| 206 | |||
| 207 | ), |
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| 208 | |||
| 209 | conditionalPanel(condition = "input.navbarROCcurve == 'Partial AUC'", |
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| 210 | |||
| 211 | checkboxInput(inputId = "partialAUC", label = "Partial AUC", value = TRUE), |
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| 212 | |||
| 213 | conditionalPanel(condition = "input.partialAUC", |
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| 214 | |||
| 215 | fluidRow( |
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| 216 | column(5, numericInput("pointA", "Value 1", min=0, max=1, value = 0.5, step = 0.1)), |
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| 217 | column(1), |
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| 218 | column(5, numericInput("pointB", "Value 2", min=0, max=1, value = 1, step = 0.1)) |
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| 219 | ), |
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| 220 | |||
| 221 | selectizeInput("sensSpec", "Select a measure", choices = c("Sensitivity", "Specificity"), multiple = FALSE, selected = "Sensitivity") |
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| 222 | |||
| 223 | ) |
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| 224 | ) |
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| 225 | |||
| 226 | ), |
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| 227 | |||
| 228 | |||
| 229 | |||
| 230 | |||
| 231 | |||
| 232 | conditionalPanel(condition="input.tabs1=='Cut points'", |
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| 233 | h5("1. Select a marker"), |
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| 234 | selectizeInput("cutoffMarker", "", choices = NULL, multiple = FALSE), |
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| 235 | HTML('<br>'), |
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| 236 | h5("2. Select a method for optimal cut-off (*)"), |
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| 237 | selectizeInput("cutOffMethods", "", choices = c("Youden", "CB", "MCT", "MinValueSp", "MinValueSe", "ValueSe", "ValueSp", "MinValueSpSe", |
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| 238 | "MaxSp", "MaxSe", "MaxSpSe", "MaxProdSpSe", "ROC01", "SpEqualSe", "MaxEfficiency", |
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| 239 | "Minimax", "MaxDOR", "MaxKappa", "MinValueNPV", "MinValuePPV", "ValueNPV", "ValuePPV", |
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| 240 | "MinValueNPVPPV", "PROC01", "NPVEqualPPV", "MaxNPVPPV", "MaxSumNPVPPV", "MaxProdNPVPPV", |
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| 241 | "ValueDLR.Negative", "ValueDLR.Positive", "MinPvalue", "ObservedPrev", "MeanPrev", |
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| 242 | "PrevalenceMatching"), multiple = FALSE), |
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| 243 | #HTML('<br>'), |
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| 244 | |||
| 245 | conditionalPanel(condition="input.cutOffMethods=='Youden'", |
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| 246 | HTML('<p><b>Youden:</b> Youden index</p>'), |
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| 247 | HTML('<br>'), |
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| 248 | numericInput(inputId = "CFP_Youden", label = "Cost of a False Positive", value = 1, min = 0, max = 9999999), |
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| 249 | numericInput(inputId = "CFN_Youden", label = "Cost of a False Negative", value = 1, min = 0, max = 9999999), |
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| 250 | checkboxInput(inputId = "generalized_Youden", label = "Generalized Youden Index", value = FALSE), |
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| 251 | checkboxInput(inputId = "costs_benefits_Youden", label = "Cost-benefit based Youden Index", value = FALSE) |
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| 252 | ), |
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| 253 | |||
| 254 | conditionalPanel(condition="input.cutOffMethods=='CB'", |
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| 255 | HTML('<p><b>CB:</b> cost-benefit method</p>'), |
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| 256 | HTML('<br>'), |
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| 257 | numericInput(inputId = "costs_ratio", label = "Cost ratio", value = 1, min = 0, max = 99999999) |
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| 258 | ), |
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| 259 | |||
| 260 | conditionalPanel(condition="input.cutOffMethods=='MCT'", |
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| 261 | HTML('<p><b>MCT:</b> minimizes misclassification cost term</p>'), |
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| 262 | HTML('<br>'), |
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| 263 | numericInput(inputId = "CFP_MCT", label = "Cost of a False Positive", value = 1, min = 0, max = 9999999), |
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| 264 | numericInput(inputId = "CFN_MCT", label = "Cost of a False Negative", value = 1, min = 0, max = 9999999) |
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| 265 | ), |
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| 266 | |||
| 267 | conditionalPanel(condition="input.cutOffMethods=='MinValueSp'", |
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| 268 | HTML('<p><b>MinValueSp:</b> a minimum value set for specificity</p>'), |
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| 269 | HTML('<br>'), |
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| 270 | numericInput(inputId = "valueSp_MVSp", label = "Value of Specificity", value = 0.85, min = 0, max = 1, step = 0.01) |
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| 271 | ), |
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| 272 | |||
| 273 | conditionalPanel(condition="input.cutOffMethods=='MinValueSe'", |
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| 274 | HTML('<p><b>MinValueSe:</b> a minimum value set for sensitivity</p>'), |
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| 275 | HTML('<br>'), |
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| 276 | numericInput(inputId = "valueSe_MVSe", label = "Value of Sensitivity", value = 0.85, min = 0, max = 1, step = 0.01) |
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| 277 | ), |
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| 278 | |||
| 279 | conditionalPanel(condition="input.cutOffMethods=='ValueSe'", |
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| 280 | HTML('<p><b>ValueSe:</b> a value set for sensitivity</p>'), |
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| 281 | HTML('<br>'), |
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| 282 | numericInput(inputId = "valueSe_VSe", label = "Value of Sensitivity", value = 0.85, min = 0, max = 1, step = 0.01) |
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| 283 | ), |
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| 284 | |||
| 285 | conditionalPanel(condition="input.cutOffMethods=='ValueSp'", |
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| 286 | HTML('<p><b>ValueSp:</b> a value set for specificity</p>'), |
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| 287 | HTML('<br>'), |
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| 288 | numericInput(inputId = "valueSp_VSp", label = "Value of Specificity", value = 0.85, min = 0, max = 1, step = 0.01) |
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| 289 | ), |
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| 290 | |||
| 291 | conditionalPanel(condition="input.cutOffMethods=='MinValueSpSe'", |
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| 292 | HTML('<p><b>MinValueSpSe:</b> a minimum value set for specificity and sensitivity</p>'), |
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| 293 | HTML('<br>'), |
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| 294 | numericInput(inputId = "valueSe_MVSpSe", label = "Value of Sensitivity", value = 0.85, min = 0, max = 1, step = 0.01), |
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| 295 | numericInput(inputId = "valueSp_MVSpSe", label = "Value of Specificity", value = 0.85, min = 0, max = 1, step = 0.01), |
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| 296 | checkboxInput(inputId = "maxSp_MVSpSe", label = "Maximum specificity", value = TRUE) |
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| 297 | ), |
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| 298 | |||
| 299 | conditionalPanel(condition="input.cutOffMethods=='MaxSp'", |
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| 300 | HTML('<p><b>MaxSp:</b> maximizes specificity</p>') |
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| 301 | ), |
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| 302 | |||
| 303 | conditionalPanel(condition="input.cutOffMethods=='MaxSe'", |
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| 304 | HTML('<p><b>MaxSe:</b> maximizes sensitivity</p>') |
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| 305 | ), |
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| 306 | |||
| 307 | conditionalPanel(condition="input.cutOffMethods=='MaxSpSe'", |
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| 308 | HTML('<p><b>MaxSpSe:</b> maximizes sensitivity and specificity simultaneously</p>') |
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| 309 | ), |
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| 310 | |||
| 311 | conditionalPanel(condition="input.cutOffMethods=='MaxProdSpSe'", |
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| 312 | HTML('<p><b>MaxProdSpSe:</b> maximizes the product of sensitivity and specificity or accuracy area</p>') |
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| 313 | ), |
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| 314 | |||
| 315 | conditionalPanel(condition="input.cutOffMethods=='ROC01'", |
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| 316 | HTML('<p><b>ROC01:</b> minimizes distance between ROC plot and point (0,1)</p>') |
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| 317 | ), |
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| 318 | |||
| 319 | conditionalPanel(condition="input.cutOffMethods=='SpEqualSe'", |
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| 320 | HTML('<p><b>SpEqualSe:</b> sensitivity = specificity</p>') |
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| 321 | ), |
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| 322 | |||
| 323 | conditionalPanel(condition="input.cutOffMethods=='MaxEfficiency'", |
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| 324 | HTML('<p><b>MaxEfficiency:</b> maximizes efficiency or accuracy, similar to minimize error rate </p>'), |
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| 325 | HTML('<br>'), |
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| 326 | checkboxInput(inputId = "costs_benefits_Efficiency", label = "Cost-benefit based Efficiency", value = FALSE), |
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| 327 | checkboxInput(inputId = "standard_deviation_accuracy", label = "Standart deviation accuracy", value = FALSE) |
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| 328 | ), |
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| 329 | |||
| 330 | conditionalPanel(condition="input.cutOffMethods=='Minimax'", |
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| 331 | HTML('<p><b>Minimax:</b> minimizes the most frequent error</p>') |
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| 332 | ), |
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| 333 | |||
| 334 | conditionalPanel(condition="input.cutOffMethods=='MaxDOR'", |
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| 335 | HTML('<p><b>MaxDOR:</b> maximizes diagnostic odds ratio</p>') |
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| 336 | ), |
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| 337 | |||
| 338 | conditionalPanel(condition="input.cutOffMethods=='MaxKappa'", |
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| 339 | HTML('<p><b>MaxKappa:</b> maximizes kappa index</p>'), |
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| 340 | HTML('<br>'), |
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| 341 | numericInput(inputId = "CFP_MK", label = "Cost of a False Positive", value = 1, min = 0, max = 9999999), |
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| 342 | numericInput(inputId = "CFN_MK", label = "Cost of a False Negative", value = 1, min = 0, max = 9999999), |
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| 343 | checkboxInput(inputId = "weighted_Kappa", label = "Weighted Kappa", value = FALSE) |
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| 344 | ), |
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| 345 | |||
| 346 | conditionalPanel(condition="input.cutOffMethods=='MinValueNPV'", |
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| 347 | HTML('<p><b>MinValueNPV:</b> a minimum value set for negative predictive value</p>'), |
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| 348 | HTML('<br>'), |
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| 349 | numericInput(inputId = "valueNPV_MVNPV", label = "Value of NPV", value = 0.85, min = 0, max = 1, step = 0.01) |
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| 350 | ), |
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| 351 | |||
| 352 | conditionalPanel(condition="input.cutOffMethods=='MinValuePPV'", |
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| 353 | HTML('<p><b>MinValuePPV:</b> a minimum value set for positive predictive value</p>'), |
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| 354 | HTML('<br>'), |
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| 355 | numericInput(inputId = "valuePPV_MVPPV", label = "Value of PPV", value = 0.85, min = 0, max = 1, step = 0.01) |
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| 356 | ), |
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| 357 | |||
| 358 | conditionalPanel(condition="input.cutOffMethods=='ValueNPV'", |
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| 359 | HTML('<p><b>ValueNPV:</b> a value set for negative predictive value</p>'), |
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| 360 | HTML('<br>'), |
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| 361 | numericInput(inputId = "valueNPV_VNPV", label = "Value of NPV", value = 0.85, min = 0, max = 1, step = 0.01) |
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| 362 | ), |
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| 363 | |||
| 364 | conditionalPanel(condition="input.cutOffMethods=='ValuePPV'", |
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| 365 | HTML('<p><b>ValuePPV:</b> a value set for positive predictive value</p>'), |
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| 366 | HTML('<br>'), |
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| 367 | numericInput(inputId = "valuePPV_VPPV", label = "Value of PPV", value = 0.85, min = 0, max = 1, step = 0.01) |
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| 368 | ), |
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| 369 | |||
| 370 | conditionalPanel(condition="input.cutOffMethods=='MinValueNPVPPV'", |
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| 371 | HTML('<p><b>MinValueNPVPPV:</b> a minimum value set for predictive values</p>'), |
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| 372 | HTML('<br>'), |
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| 373 | numericInput(inputId = "valuePPV_MVNPVPPV", label = "Value of PPV", value = 0.85, min = 0, max = 1, step = 0.01), |
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| 374 | numericInput(inputId = "valueNPV_MVNPVPPV", label = "Value of NPV", value = 0.85, min = 0, max = 1, step = 0.01), |
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| 375 | checkboxInput(inputId = "maxNPV_MVNPVPPV", label = "Maximum NPV", value = TRUE) |
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| 376 | ), |
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| 377 | |||
| 378 | conditionalPanel(condition="input.cutOffMethods=='PROC01'", |
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| 379 | HTML('<p><b>PROC01:</b> minimizes distance between PROC plot and point (0,1)</p>') |
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| 380 | ), |
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| 381 | |||
| 382 | conditionalPanel(condition="input.cutOffMethods=='NPVEqualPPV'", |
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| 383 | HTML('<p><b>NPVEqualPPV:</b> negative predictive value = positive predictive value</p>') |
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| 384 | ), |
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| 385 | |||
| 386 | conditionalPanel(condition="input.cutOffMethods=='MaxNPVPPV'", |
||
| 387 | HTML('<p><b>MaxNPVPPV:</b> maximizes positive predictive value and negative predictive value simultaneously</p>') |
||
| 388 | ), |
||
| 389 | |||
| 390 | conditionalPanel(condition="input.cutOffMethods=='MaxSumNPVPPV'", |
||
| 391 | HTML('<p><b>MaxSumNPVPPV:</b> maximizes the sum of the predictive values</p>') |
||
| 392 | ), |
||
| 393 | |||
| 394 | conditionalPanel(condition="input.cutOffMethods=='MaxProdNPVPPV'", |
||
| 395 | HTML('<p><b>MaxProdNPVPPV:</b> maximizes the product of predictive values</p>') |
||
| 396 | ), |
||
| 397 | |||
| 398 | conditionalPanel(condition="input.cutOffMethods=='ValueDLR.Negative'", |
||
| 399 | HTML('<p><b>ValueDLR.Negative:</b> a value set for negative diagnostic likelihood ratio</p>'), |
||
| 400 | HTML('<br>'), |
||
| 401 | numericInput(inputId = "valueDLR_Negative", label = "Value of Negative DLR", value = 0.5, min = 0, max = 999999) |
||
| 402 | ), |
||
| 403 | |||
| 404 | conditionalPanel(condition="input.cutOffMethods=='ValueDLR.Positive'", |
||
| 405 | HTML('<p><b>ValueDLR.Positive:</b> a value set for positive diagnostic likelihood ratio</p>'), |
||
| 406 | HTML('<br>'), |
||
| 407 | numericInput(inputId = "valueDLR_Positive", label = "Value of Positive DLR", value = 2, min = 0, max = 999999) |
||
| 408 | ), |
||
| 409 | |||
| 410 | conditionalPanel(condition="input.cutOffMethods=='MinPvalue'", |
||
| 411 | HTML('<p><b>MinPvalue:</b> minimizes p-value associated with the statistical Chi-squared test which measures the association between the marker and the binary result obtained on using the cutpoint</p>'), |
||
| 412 | HTML('<br>'), |
||
| 413 | selectInput(inputId = "adjusted_pvalue", label = "Adjustment method for p-value", |
||
| 414 | choices = c("Miller and Siegmund" = "PADJMS", "Altman_5" = "PALT5", "Altman_10" = "PALT10"), |
||
| 415 | multiple = FALSE, selected = "PADJMS") |
||
| 416 | ), |
||
| 417 | |||
| 418 | conditionalPanel(condition="input.cutOffMethods=='ObservedPrev'", |
||
| 419 | HTML('<p><b>ObservedPrev:</b> the closest value to observed prevalence</p>') |
||
| 420 | ), |
||
| 421 | |||
| 422 | conditionalPanel(condition="input.cutOffMethods=='MeanPrev'", |
||
| 423 | HTML('<p><b>MeanPrev:</b> the closest value to the mean of the diagnostic test values</p>') |
||
| 424 | ), |
||
| 425 | |||
| 426 | conditionalPanel(condition="input.cutOffMethods=='PrevalenceMatching'", |
||
| 427 | HTML('<p><b>PrevalenceMatching:</b> the value for which predicted prevalence is practically equal to observed prevalence</p>') |
||
| 428 | ), |
||
| 429 | |||
| 430 | HTML('<br>'), |
||
| 431 | HTML('<p>(*) See <a href="http://cran.r-project.org/web/packages/OptimalCutpoints/index.html" target="_blank"> OptimalCutpoints</a> package from R</p>'), |
||
| 432 | HTML('<br>'), |
||
| 433 | |||
| 434 | checkboxInput("showPlots", "Include plots.", FALSE), |
||
| 435 | |||
| 436 | conditionalPanel(condition="input.showPlots", |
||
| 437 | fluidRow( |
||
| 438 | column(1), |
||
| 439 | column(5, sliderInput("myheightCutoff", "Plot height:", value=600, min=400, max=1400)), |
||
| 440 | column(1), |
||
| 441 | column(5, sliderInput("mywidthCutoff", "Plot width:", value=800, min=400, max=1400 )) |
||
| 442 | ), |
||
| 443 | |||
| 444 | HTML('<br>'), |
||
| 445 | checkboxInput("cutoffPlotsOpts", "More plot options (See Manual)", FALSE), |
||
| 446 | HTML('<br>') |
||
| 447 | ), |
||
| 448 | |||
| 449 | conditionalPanel(condition="input.cutoffPlotsOpts", |
||
| 450 | fluidRow( |
||
| 451 | column(10, selectizeInput("fontfamily", "Font family", |
||
| 452 | choices = c("Times New Roman" = "serif", "Arial" = "sans", |
||
| 453 | "Corier New" = "mono"), selected = "sans")) |
||
| 454 | ), |
||
| 455 | |||
| 456 | radioButtons("selectedGraph", "", list("Top Left \U2003 \U2003" = 1, "Top Right \U2003 \U2003" = 2, |
||
| 457 | "Bottom Left \U2002\U2008" = 3, "Bottom Right" = 4), selected=1), |
||
| 458 | |||
| 459 | HTML('<br>'), |
||
| 460 | |||
| 461 | selectizeInput("subGrps", "", choices = NULL, selected = NULL), |
||
| 462 | |||
| 463 | ## First graph options (11) |
||
| 464 | conditionalPanel(condition = "input.selectedGraph == '1'", |
||
| 465 | |||
| 466 | conditionalPanel(condition = "input.subGrps == 'others'", |
||
| 467 | fluidRow( |
||
| 468 | column(5, textInput("main11", "Graph title", "ROC Curve")), |
||
| 469 | column(1), |
||
| 470 | column(5, selectizeInput("font.main11", "Title font", choices = c("Regular" = "1", "Bold" = "2", |
||
| 471 | "Italic" = "3", "Bold Italic" = "4"), |
||
| 472 | selected = "2")) |
||
| 473 | ), |
||
| 474 | |||
| 475 | fluidRow( |
||
| 476 | column(5, textInput("col.main11", "Title color", "black")), |
||
| 477 | column(1), |
||
| 478 | column(5, numericInput("cex.main11", "Title size", min=0.1, max=5, value = 1.2, step = 0.1)) |
||
| 479 | ), |
||
| 480 | |||
| 481 | fluidRow( |
||
| 482 | column(5, textInput("ROCcol11", "ROC line color", "black")), |
||
| 483 | column(1), |
||
| 484 | column(5, selectizeInput("ROClty11", "ROC line type", |
||
| 485 | choices = c("\U2500\U2500\U2500\U2500\U2500\U2500\U2500" = "1", |
||
| 486 | "\U2574 \U2574 \U2574 \U2574 \U2574 \U2574" = "2", |
||
| 487 | "\U00B7 \U00B7 \U00B7 \U00B7 \U00B7 \U00B7 \U00B7 \U00B7 \U00B7" = "3", |
||
| 488 | "\U2574 \U00B7 \U2574 \U00B7 \U2574 \U00B7 \U2574" = "4", |
||
| 489 | "\U2500 \U2500 \U2500 \U2500 \U2500" = "5", |
||
| 490 | "\U2500 \U2574 \U2500 \U2574 \U2500 \U2574" = "6"), |
||
| 491 | selected = "1")) |
||
| 492 | ) |
||
| 493 | ), |
||
| 494 | |||
| 495 | conditionalPanel(condition = "input.subGrps == 'xAxis'", |
||
| 496 | h5('X-axis options:'), |
||
| 497 | |||
| 498 | ## X axis label options |
||
| 499 | fluidRow( |
||
| 500 | column(5, textInput("xlab11", "Axis label", "1-Specificity")), |
||
| 501 | column(1), |
||
| 502 | column(5, selectizeInput("xfont.lab11", "Label font", choices = c("Regular" = "1", "Bold" = "2", |
||
| 503 | "Italic" = "3", "Bold Italic" = "4"), |
||
| 504 | selected = "1")) |
||
| 505 | ), |
||
| 506 | |||
| 507 | fluidRow( |
||
| 508 | column(5, textInput("xcol.lab11", "Label color", "black")), |
||
| 509 | column(1), |
||
| 510 | column(5, numericInput("xcex.lab11", "Label size", min=0.1, max=5, value = 1, step = 0.1)) |
||
| 511 | ), |
||
| 512 | |||
| 513 | ## X axis annotation options |
||
| 514 | fluidRow( |
||
| 515 | column(5, textInput("xcol.axis11", "Annotation color", "black")), |
||
| 516 | column(1), |
||
| 517 | column(5, numericInput("xcex.axis11", "Annotation size", min=0.1, max=5, value = 1, step = 0.1)) |
||
| 518 | ) |
||
| 519 | |||
| 520 | #fluidRow( |
||
| 521 | # column(5, textInput("xcol11", "Axis color", "black")), |
||
| 522 | # column(1), |
||
| 523 | # column(5, textInput("xcol.ticks11", "Tickmarks color", "black")) |
||
| 524 | #), |
||
| 525 | ), |
||
| 526 | |||
| 527 | conditionalPanel(condition = "input.subGrps == 'yAxis'", |
||
| 528 | h5('Y-axis options:'), |
||
| 529 | |||
| 530 | ## Y axis label options |
||
| 531 | fluidRow( |
||
| 532 | column(5, textInput("ylab11", "Axis label", "Sensitivity")), |
||
| 533 | column(1), |
||
| 534 | column(5, selectizeInput("yfont.lab11", "Label font", choices = c("Regular" = "1", "Bold" = "2", |
||
| 535 | "Italic" = "3", "Bold Italic" = "4"), |
||
| 536 | selected = "1")) |
||
| 537 | ), |
||
| 538 | |||
| 539 | fluidRow( |
||
| 540 | column(5, textInput("ycol.lab11", "Label color", "black")), |
||
| 541 | column(1), |
||
| 542 | column(5, numericInput("ycex.lab11", "Label size", min=0.1, max=5, value = 1, step = 0.1)) |
||
| 543 | ), |
||
| 544 | |||
| 545 | ## Y axis annotation options |
||
| 546 | fluidRow( |
||
| 547 | column(5, textInput("ycol.axis11", "Annotation color", "black")), |
||
| 548 | column(1), |
||
| 549 | column(5, numericInput("ycex.axis11", "Annotation size", min=0.1, max=5, value = 1, step = 0.1)) |
||
| 550 | ) |
||
| 551 | ) |
||
| 552 | ), |
||
| 553 | |||
| 554 | ## Second graph options (12) |
||
| 555 | conditionalPanel(condition = "input.selectedGraph == '2'", |
||
| 556 | |||
| 557 | conditionalPanel(condition = "input.subGrps == 'others'", |
||
| 558 | fluidRow( |
||
| 559 | column(5, textInput("main12", "Graph title", "Sens. & Spec. Curve")), |
||
| 560 | column(1), |
||
| 561 | column(5, selectizeInput("font.main12", "Title font", choices = c("Regular" = "1", "Bold" = "2", |
||
| 562 | "Italic" = "3", "Bold Italic" = "4"), |
||
| 563 | selected = "2")) |
||
| 564 | ), |
||
| 565 | |||
| 566 | fluidRow( |
||
| 567 | column(5, textInput("col.main12", "Title color", "black")), |
||
| 568 | column(1), |
||
| 569 | column(5, numericInput("cex.main12", "Title size", min=0.1, max=5, value = 1.2, step = 0.1)) |
||
| 570 | ), |
||
| 571 | |||
| 572 | fluidRow( |
||
| 573 | column(5, textInput("specCol", "Spec. line color", "blue")), |
||
| 574 | column(1), |
||
| 575 | column(5, selectizeInput("specType", "Spec. line type", |
||
| 576 | choices = c("\U2500\U2500\U2500\U2500\U2500\U2500\U2500" = "1", |
||
| 577 | "\U2574 \U2574 \U2574 \U2574 \U2574 \U2574" = "2", |
||
| 578 | "\U00B7 \U00B7 \U00B7 \U00B7 \U00B7 \U00B7 \U00B7 \U00B7 \U00B7" = "3", |
||
| 579 | "\U2574 \U00B7 \U2574 \U00B7 \U2574 \U00B7 \U2574" = "4", |
||
| 580 | "\U2500 \U2500 \U2500 \U2500 \U2500" = "5", |
||
| 581 | "\U2500 \U2574 \U2500 \U2574 \U2500 \U2574" = "6"), |
||
| 582 | selected = "1")) |
||
| 583 | ), |
||
| 584 | |||
| 585 | fluidRow( |
||
| 586 | column(5, textInput("sensCol", "Sens. line color", "red")), |
||
| 587 | column(1), |
||
| 588 | column(5, selectizeInput("sensType", "Sens. line type", |
||
| 589 | choices = c("\U2500\U2500\U2500\U2500\U2500\U2500\U2500" = "1", |
||
| 590 | "\U2574 \U2574 \U2574 \U2574 \U2574 \U2574" = "2", |
||
| 591 | "\U00B7 \U00B7 \U00B7 \U00B7 \U00B7 \U00B7 \U00B7 \U00B7 \U00B7" = "3", |
||
| 592 | "\U2574 \U00B7 \U2574 \U00B7 \U2574 \U00B7 \U2574" = "4", |
||
| 593 | "\U2500 \U2500 \U2500 \U2500 \U2500" = "5", |
||
| 594 | "\U2500 \U2574 \U2500 \U2574 \U2500 \U2574" = "6"), |
||
| 595 | selected = "1")) |
||
| 596 | ) |
||
| 597 | ), |
||
| 598 | |||
| 599 | conditionalPanel(condition = "input.subGrps == 'Legend'", |
||
| 600 | fluidRow( |
||
| 601 | column(5, selectizeInput("legendPos12", "Position", choices = c("Top right" = "topright", "Top left" = "topleft", "Bottom right" = "bottomright", "Bottom left" = "bottomleft", "xy coord." = "xy"), |
||
| 602 | selected = "topright")), |
||
| 603 | column(1), |
||
| 604 | column(2, |
||
| 605 | conditionalPanel(condition = "input.legendPos12 == 'xy'", |
||
| 606 | numericInput("legendXpos12", "x", value = 0, step = 0.1) |
||
| 607 | ) |
||
| 608 | ), |
||
| 609 | column(1), |
||
| 610 | column(2, |
||
| 611 | conditionalPanel(condition = "input.legendPos12 == 'xy'", |
||
| 612 | numericInput("legendYpos12", "y", value = 0, step = 0.02) |
||
| 613 | ) |
||
| 614 | ) |
||
| 615 | ), |
||
| 616 | |||
| 617 | fluidRow( |
||
| 618 | column(7, textInput("legendNames12", "Leg. labels (comma sep.)", "Sens.,Spec.")), |
||
| 619 | column(1), |
||
| 620 | column(3, numericInput("cex.legend12", "Leg. size", min = 0.5, max = 5, step = 0.1, value = 1)) |
||
| 621 | ), |
||
| 622 | |||
| 623 | fluidRow( |
||
| 624 | column(5, textInput("legendTitle12", "Title", "")), |
||
| 625 | column(1), |
||
| 626 | column(5, textInput("col.legendTitle12", "Title color", "black")) |
||
| 627 | ), |
||
| 628 | |||
| 629 | checkboxInput("borderless12", label = "Remove borders.", value = FALSE) |
||
| 630 | ), |
||
| 631 | |||
| 632 | conditionalPanel(condition = "input.subGrps == 'xAxis'", |
||
| 633 | h5('X-axis options:'), |
||
| 634 | |||
| 635 | ## X axis label options |
||
| 636 | fluidRow( |
||
| 637 | column(5, textInput("xlab12", "Axis label", "Marker Name")), |
||
| 638 | column(1), |
||
| 639 | column(5, selectizeInput("xfont.lab12", "Label font", choices = c("Regular" = "1", "Bold" = "2", |
||
| 640 | "Italic" = "3", "Bold Italic" = "4"), |
||
| 641 | selected = "1")) |
||
| 642 | ), |
||
| 643 | |||
| 644 | fluidRow( |
||
| 645 | column(5, textInput("xcol.lab12", "Label color", "black")), |
||
| 646 | column(1), |
||
| 647 | column(5, numericInput("xcex.lab12", "Label size", min=0.1, max=5, value = 1, step = 0.1)) |
||
| 648 | ), |
||
| 649 | |||
| 650 | ## X axis annotation options |
||
| 651 | fluidRow( |
||
| 652 | column(5, textInput("xcol.axis12", "Annotation color", "black")), |
||
| 653 | column(1), |
||
| 654 | column(5, numericInput("xcex.axis12", "Annotation size", min=0.1, max=5, value = 1, step = 0.1)) |
||
| 655 | ) |
||
| 656 | ), |
||
| 657 | |||
| 658 | conditionalPanel(condition = "input.subGrps == 'yAxis'", |
||
| 659 | h5('Y-axis options:'), |
||
| 660 | |||
| 661 | ## Y axis label options |
||
| 662 | fluidRow( |
||
| 663 | column(5, textInput("ylab12", "Axis label", "Value")), |
||
| 664 | column(1), |
||
| 665 | column(5, selectizeInput("yfont.lab12", "Label font", choices = c("Regular" = "1", "Bold" = "2", |
||
| 666 | "Italic" = "3", "Bold Italic" = "4"), |
||
| 667 | selected = "1")) |
||
| 668 | ), |
||
| 669 | |||
| 670 | fluidRow( |
||
| 671 | column(5, textInput("ycol.lab12", "Label color", "black")), |
||
| 672 | column(1), |
||
| 673 | column(5, numericInput("ycex.lab12", "Label size", min=0.1, max=5, value = 1, step = 0.1)) |
||
| 674 | ), |
||
| 675 | |||
| 676 | ## Y axis annotation options |
||
| 677 | fluidRow( |
||
| 678 | column(5, textInput("ycol.axis12", "Annotation color", "black")), |
||
| 679 | column(1), |
||
| 680 | column(5, numericInput("ycex.axis12", "Annotation size", min=0.1, max=5, value = 1, step = 0.1)) |
||
| 681 | ) |
||
| 682 | ) |
||
| 683 | ), |
||
| 684 | |||
| 685 | ## Third graph options (21) |
||
| 686 | conditionalPanel(condition = "input.selectedGraph == '3'", |
||
| 687 | |||
| 688 | conditionalPanel(condition = "input.subGrps == 'others'", |
||
| 689 | fluidRow( |
||
| 690 | column(5, textInput("main21", "Graph title", "Distribution Graph")), |
||
| 691 | column(1), |
||
| 692 | column(5, selectizeInput("font.main21", "Title font", choices = c("Regular" = "1", "Bold" = "2", |
||
| 693 | "Italic" = "3", "Bold Italic" = "4"), |
||
| 694 | selected = "2")) |
||
| 695 | ), |
||
| 696 | |||
| 697 | fluidRow( |
||
| 698 | column(5, textInput("col.main21", "Title color", "black")), |
||
| 699 | column(1), |
||
| 700 | column(5, numericInput("cex.main21", "Title size", min=0.1, max=5, value = 1.2, step = 0.1)) |
||
| 701 | ), |
||
| 702 | |||
| 703 | fluidRow( |
||
| 704 | column(6, textInput("lineColD", "Line color (Diseased)", "red")), |
||
| 705 | column(1), |
||
| 706 | column(5, selectizeInput("lineTypeD", "Line type", |
||
| 707 | choices = c("\U2500\U2500\U2500\U2500\U2500\U2500\U2500" = "1", |
||
| 708 | "\U2574 \U2574 \U2574 \U2574 \U2574 \U2574" = "2", |
||
| 709 | "\U00B7 \U00B7 \U00B7 \U00B7 \U00B7 \U00B7 \U00B7 \U00B7 \U00B7" = "3", |
||
| 710 | "\U2574 \U00B7 \U2574 \U00B7 \U2574 \U00B7 \U2574" = "4", |
||
| 711 | "\U2500 \U2500 \U2500 \U2500 \U2500" = "5", |
||
| 712 | "\U2500 \U2574 \U2500 \U2574 \U2500 \U2574" = "6"), |
||
| 713 | selected = "1")) |
||
| 714 | ), |
||
| 715 | |||
| 716 | fluidRow( |
||
| 717 | column(6, textInput("lineColH", "Line color (Healthy)", "blue")), |
||
| 718 | column(1), |
||
| 719 | column(5, selectizeInput("lineTypeH", "Line type", |
||
| 720 | choices = c("\U2500\U2500\U2500\U2500\U2500\U2500\U2500" = "1", |
||
| 721 | "\U2574 \U2574 \U2574 \U2574 \U2574 \U2574" = "2", |
||
| 722 | "\U00B7 \U00B7 \U00B7 \U00B7 \U00B7 \U00B7 \U00B7 \U00B7 \U00B7" = "3", |
||
| 723 | "\U2574 \U00B7 \U2574 \U00B7 \U2574 \U00B7 \U2574" = "4", |
||
| 724 | "\U2500 \U2500 \U2500 \U2500 \U2500" = "5", |
||
| 725 | "\U2500 \U2574 \U2500 \U2574 \U2500 \U2574" = "6"), |
||
| 726 | selected = "1")) |
||
| 727 | ) |
||
| 728 | ), |
||
| 729 | |||
| 730 | conditionalPanel(condition = "input.subGrps == 'Legend'", |
||
| 731 | fluidRow( |
||
| 732 | column(5, selectizeInput("legendPos21", "Position", choices = c("Top right" = "topright", "Top left" = "topleft", "Bottom right" = "bottomright", "Bottom left" = "bottomleft", "xy coord." = "xy"), |
||
| 733 | selected = "topright")), |
||
| 734 | column(1), |
||
| 735 | column(2, |
||
| 736 | conditionalPanel(condition = "input.legendPos21 == 'xy'", |
||
| 737 | numericInput("legendXpos21", "x", value = 0, step = 0.1) |
||
| 738 | ) |
||
| 739 | ), |
||
| 740 | column(1), |
||
| 741 | column(2, |
||
| 742 | conditionalPanel(condition = "input.legendPos21 == 'xy'", |
||
| 743 | numericInput("legendYpos21", "y", value = 0, step = 0.1) |
||
| 744 | ) |
||
| 745 | ) |
||
| 746 | ), |
||
| 747 | |||
| 748 | fluidRow( |
||
| 749 | column(7, textInput("legendNames21", "Leg. labels (comma sep.)", "Diseased,Healthy")), |
||
| 750 | column(1), |
||
| 751 | column(3, numericInput("cex.legend21", "Leg. Size", min = 0.5, max = 5, step = 0.1, value = 1)) |
||
| 752 | ), |
||
| 753 | |||
| 754 | fluidRow( |
||
| 755 | column(5, textInput("legendTitle21", "Title", "")), |
||
| 756 | column(1), |
||
| 757 | column(5, textInput("col.legendTitle21", "Title color", "black")) |
||
| 758 | ), |
||
| 759 | |||
| 760 | checkboxInput("borderless21", label = "Remove borders.", value = FALSE) |
||
| 761 | ), |
||
| 762 | |||
| 763 | conditionalPanel(condition = "input.subGrps == 'xAxis'", |
||
| 764 | h5('X-axis options:'), |
||
| 765 | |||
| 766 | ## X axis label options |
||
| 767 | fluidRow( |
||
| 768 | column(5, textInput("xlab21", "Axis label", "Marker Name")), |
||
| 769 | column(1), |
||
| 770 | column(5, selectizeInput("xfont.lab21", "Label font", choices = c("Regular" = "1", "Bold" = "2", |
||
| 771 | "Italic" = "3", "Bold Italic" = "4"), |
||
| 772 | selected = "1")) |
||
| 773 | ), |
||
| 774 | |||
| 775 | fluidRow( |
||
| 776 | column(5, textInput("xcol.lab21", "Label color", "black")), |
||
| 777 | column(1), |
||
| 778 | column(5, numericInput("xcex.lab21", "Label size", min=0.1, max=5, value = 1, step = 0.1)) |
||
| 779 | ), |
||
| 780 | |||
| 781 | ## X axis annotation options |
||
| 782 | fluidRow( |
||
| 783 | column(5, textInput("xcol.axis21", "Annotation color", "black")), |
||
| 784 | column(1), |
||
| 785 | column(5, numericInput("xcex.axis21", "Annotation size", min=0.1, max=5, value = 1, step = 0.1)) |
||
| 786 | ) |
||
| 787 | ), |
||
| 788 | |||
| 789 | conditionalPanel(condition = "input.subGrps == 'yAxis'", |
||
| 790 | h5('Y-axis options:'), |
||
| 791 | |||
| 792 | ## Y axis label options |
||
| 793 | fluidRow( |
||
| 794 | column(5, textInput("ylab21", "Axis label", "Density")), |
||
| 795 | column(1), |
||
| 796 | column(5, selectizeInput("yfont.lab21", "Label font", choices = c("Regular" = "1", "Bold" = "2", |
||
| 797 | "Italic" = "3", "Bold Italic" = "4"), |
||
| 798 | selected = "1")) |
||
| 799 | ), |
||
| 800 | |||
| 801 | fluidRow( |
||
| 802 | column(5, textInput("ycol.lab21", "Label color", "black")), |
||
| 803 | column(1), |
||
| 804 | column(5, numericInput("ycex.lab21", "Label size", min=0.1, max=5, value = 1, step = 0.1)) |
||
| 805 | ), |
||
| 806 | |||
| 807 | ## Y axis annotation options |
||
| 808 | fluidRow( |
||
| 809 | column(5, textInput("ycol.axis21", "Annotation color", "black")), |
||
| 810 | column(1), |
||
| 811 | column(5, numericInput("ycex.axis21", "Annotation size", min=0.1, max=5, value = 1, step = 0.1)) |
||
| 812 | ) |
||
| 813 | ) |
||
| 814 | ), |
||
| 815 | |||
| 816 | ## Fourth graph options (22) |
||
| 817 | conditionalPanel(condition = "input.selectedGraph == '4'", |
||
| 818 | conditionalPanel(condition = "input.subGrps == 'others'", |
||
| 819 | fluidRow( |
||
| 820 | column(5, textInput("main22", "Graph title", "Distribution Graph")), |
||
| 821 | column(1), |
||
| 822 | column(5, selectizeInput("font.main22", "Title font", choices = c("Regular" = "1", "Bold" = "2", |
||
| 823 | "Italic" = "3", "Bold Italic" = "4"), |
||
| 824 | selected = "2")) |
||
| 825 | ), |
||
| 826 | |||
| 827 | fluidRow( |
||
| 828 | column(5, textInput("col.main22", "Title color", "black")), |
||
| 829 | column(1), |
||
| 830 | column(5, numericInput("cex.main22", "Title size", min=0.1, max=5, value = 1.2, step = 0.1)) |
||
| 831 | ), |
||
| 832 | |||
| 833 | numericInput("jitterAmount", "Amount of jittering", min=0.01, max = 0.5, value = 0.05, step = 0.01), |
||
| 834 | |||
| 835 | ## pch options for Healthy and Diseased subjects |
||
| 836 | fluidRow( |
||
| 837 | column(8, textInput("colPoints", "Point colors (comma sep.)", "black,black")), |
||
| 838 | column(1), |
||
| 839 | column(2, numericInput("pchPoints", "Type", min = 0, max = 25, step = 1, value = 1)) |
||
| 840 | ), |
||
| 841 | |||
| 842 | fluidRow( |
||
| 843 | column(3, numericInput("pchSize", "Point size", min = 0.1, max = 5, step = 0.1, value = 1)), |
||
| 844 | column(1), |
||
| 845 | column(7, |
||
| 846 | conditionalPanel(condition = "input.pchPoints > 20", |
||
| 847 | textInput("pchFill", "Fill points with color" ,"white,white") |
||
| 848 | ) |
||
| 849 | ) |
||
| 850 | ) |
||
| 851 | ), |
||
| 852 | |||
| 853 | conditionalPanel(condition = "input.subGrps == 'xAxis'", |
||
| 854 | h5('X-axis options:'), |
||
| 855 | |||
| 856 | ## X axis label options |
||
| 857 | fluidRow( |
||
| 858 | column(5, textInput("xlab22", "Axis label", "Disease Status")), |
||
| 859 | column(1), |
||
| 860 | column(5, selectizeInput("xfont.lab22", "Label font", choices = c("Regular" = "1", "Bold" = "2", |
||
| 861 | "Italic" = "3", "Bold Italic" = "4"), |
||
| 862 | selected = "1")) |
||
| 863 | ), |
||
| 864 | |||
| 865 | fluidRow( |
||
| 866 | column(5, textInput("xcol.lab22", "Label color", "black")), |
||
| 867 | column(1), |
||
| 868 | column(5, numericInput("xcex.lab22", "Label size", min=0.1, max=5, value = 1, step = 0.1)) |
||
| 869 | ), |
||
| 870 | |||
| 871 | ## X axis annotation options |
||
| 872 | fluidRow( |
||
| 873 | column(12, textInput("xlabels22", "Annotation names (comma seperated)", "Healthy,Diseased")) |
||
| 874 | ), |
||
| 875 | |||
| 876 | fluidRow( |
||
| 877 | column(5, textInput("xcol.axis22", "Annotation color", "black")), |
||
| 878 | column(1), |
||
| 879 | column(5, numericInput("xcex.axis22", "Annotation size", min=0.1, max=5, value = 1, step = 0.1)) |
||
| 880 | ) |
||
| 881 | ), |
||
| 882 | |||
| 883 | conditionalPanel(condition = "input.subGrps == 'yAxis'", |
||
| 884 | h5('Y-axis options:'), |
||
| 885 | |||
| 886 | ## Y axis label options |
||
| 887 | fluidRow( |
||
| 888 | column(5, textInput("ylab22", "Axis label", "Marker Name")), |
||
| 889 | column(1), |
||
| 890 | column(5, selectizeInput("yfont.lab22", "Label font", choices = c("Regular" = "1", "Bold" = "2", |
||
| 891 | "Italic" = "3", "Bold Italic" = "4"), |
||
| 892 | selected = "1")) |
||
| 893 | ), |
||
| 894 | |||
| 895 | fluidRow( |
||
| 896 | column(5, textInput("ycol.lab22", "Label color", "black")), |
||
| 897 | column(1), |
||
| 898 | column(5, numericInput("ycex.lab22", "Label size", min=0.1, max=5, value = 1, step = 0.1)) |
||
| 899 | ), |
||
| 900 | |||
| 901 | ## Y axis annotation options |
||
| 902 | fluidRow( |
||
| 903 | column(5, textInput("ycol.axis22", "Annotation color", "black")), |
||
| 904 | column(1), |
||
| 905 | column(5, numericInput("ycex.axis22", "Annotation size", min=0.1, max=5, value = 1, step = 0.1)) |
||
| 906 | ) |
||
| 907 | ) |
||
| 908 | ) |
||
| 909 | ) |
||
| 910 | ), |
||
| 911 | |||
| 912 | |||
| 913 | conditionalPanel(condition="input.tabs1=='Sample size'", |
||
| 914 | |||
| 915 | h5("Choose one of the following methods (*):"), |
||
| 916 | HTML('<br>'), |
||
| 917 | |||
| 918 | |||
| 919 | checkboxInput("singleTest", "Single diagnostic test", FALSE), |
||
| 920 | |||
| 921 | conditionalPanel(condition="input.singleTest", |
||
| 922 | |||
| 923 | numericInput(inputId = "alpha1", label = "Type I error", value = 0.05, min = 0, max = 1, step = 0.01), |
||
| 924 | numericInput(inputId = "power1", label = "Power", value = 0.80, min = 0, max = 1, step = 0.1), |
||
| 925 | numericInput(inputId = "auc", label = "Area under the ROC curve", value = 0.60, min = 0.5, max = 1, step = 0.1), |
||
| 926 | numericInput(inputId = "ratio", label = "Allocation ratio", value = 1, min = 0, step = 0.1) |
||
| 927 | |||
| 928 | ), |
||
| 929 | |||
| 930 | HTML('<br>'), |
||
| 931 | |||
| 932 | checkboxInput("twoTests", "Comparison of two diagnostic tests", FALSE), |
||
| 933 | |||
| 934 | conditionalPanel(condition="input.twoTests", |
||
| 935 | |||
| 936 | numericInput(inputId = "alpha2", label = "Type I error", value = 0.05, min = 0, max = 1, step = 0.01), |
||
| 937 | numericInput(inputId = "power2", label = "Power", value = 0.80, min = 0, max = 1, step = 0.1), |
||
| 938 | numericInput(inputId = "auc01", label = "AUC for 1st test under null hypothesis", value = 0.80, min = 0.5, max = 1, step = 0.1), |
||
| 939 | numericInput(inputId = "auc02", label = "AUC for 2nd test under null hypothesis", value = 0.80, min = 0.5, max = 1, step = 0.1), |
||
| 940 | numericInput(inputId = "auc11", label = "AUC for 1st test under alternative hypothesis", value = 0.90, min = 0.5, max = 1, step = 0.1), |
||
| 941 | numericInput(inputId = "auc12", label = "AUC for 2nd test under alternative hypothesis", value = 0.70, min = 0.5, max = 1, step = 0.1), |
||
| 942 | numericInput(inputId = "ratio2", label = "Allocation ratio", value = 1, min = 0, step = 0.1) |
||
| 943 | |||
| 944 | ), |
||
| 945 | HTML('<br>'), |
||
| 946 | |||
| 947 | |||
| 948 | checkboxInput("StandardVsNew", "Noninferiority of a new test to a standard test", FALSE), |
||
| 949 | |||
| 950 | |||
| 951 | conditionalPanel(condition="input.StandardVsNew", |
||
| 952 | |||
| 953 | numericInput(inputId = "alpha3", label = "Type I error", value = 0.05, min = 0, max = 1, step = 0.01), |
||
| 954 | numericInput(inputId = "power3", label = "Power", value = 0.80, min = 0, max = 1, step = 0.1), |
||
| 955 | numericInput(inputId = "aucs", label = "AUC for standard test", value = 0.80, min = 0.5, max = 1, step = 0.1), |
||
| 956 | numericInput(inputId = "aucn", label = "AUC for new test", value = 0.80, min = 0.5, max = 1, step = 0.1), |
||
| 957 | numericInput(inputId = "sd", label = "Smallest difference", value = 0.1, step = 0.1), |
||
| 958 | numericInput(inputId = "ratio3", label = "Allocation ratio", value = 1, min = 0, step = 0.1) |
||
| 959 | |||
| 960 | ), |
||
| 961 | |||
| 962 | HTML('<br>'), |
||
| 963 | HTML('<p>(*) See <a href="http://66.199.228.237/boundary/complex_decision_making_and_ethics/ROC_Analysis.pdf" target="_blank"> Obuchowski, 2005</a> for further details.</p>'), |
||
| 964 | HTML('<br>') |
||
| 965 | |||
| 966 | |||
| 967 | ), |
||
| 968 | |||
| 969 | |||
| 970 | conditionalPanel(condition="input.tabs1=='Manual'", |
||
| 971 | HTML('<p align="center"><img src="manual.png" width=200 height=200></p>') |
||
| 972 | ), |
||
| 973 | |||
| 974 | conditionalPanel(condition="input.tabs1=='Authors & News'", |
||
| 975 | HTML('<p align="center"> <a href="https://www.hacettepe.edu.tr/english/" target="_blank"><img src="hulogo.JPEG" width=150 height=150></a> </p>') |
||
| 976 | ) |
||
| 977 | ), |
||
| 978 | |||
| 979 | |||
| 980 | mainPanel( |
||
| 981 | # Tab panelinden herhangi bir sekme seçildiği zaman ana bölmede (Ekranın orta kısmı) |
||
| 982 | # nelerin görüneceği bu kısımda tanımlanıyor. Belirli koşullar tanımlanmak istenir ise |
||
| 983 | # ayrıca bir conditionalPanel() bloğu burada tanımlanabilir. |
||
| 984 | tabsetPanel( |
||
| 985 | tabPanel(title="Introduction", |
||
| 986 | h5("The easiest way to perform ROC analysis!"), |
||
| 987 | HTML('<p> A receiver operating characteristics (ROC) curve is a graphical approach which |
||
| 988 | assess the performance of a binary classifier system. The ROC curve analysis is widely |
||
| 989 | used in medicine, radiology, biometrics and various application of machine learning. </p>'), |
||
| 990 | HTML('<p align="justify"> Here we developed an easy way to carry out ROC analysis. |
||
| 991 | This application creates ROC curves, calculates area under the curve (AUC) |
||
| 992 | values and confidence intervals for the AUC values, and performs multiple comparisons |
||
| 993 | for ROC curves in a user-friendly, up-to-date and comprehensive way. Moreover, |
||
| 994 | easyROC computes and compares partial AUCs. It can also perform sample size calculation.</p>'), |
||
| 995 | |||
| 996 | HTML('<p> An important feature of this application is to determine cut-off values especially |
||
| 997 | for diagnostic tests. For this task, we made use of |
||
| 998 | <a href="http://cran.r-project.org/web/packages/OptimalCutpoints/index.html" target="_blank">OptimalCutpoints</a> package (Lopez-Raton et al, 2014) of R [1].</p>'), |
||
| 999 | |||
| 1000 | #HTML('<br>'), |
||
| 1001 | |||
| 1002 | HTML('<p><div align="center"><table cellpadding="0" cellspacing="0"><tr><td><img src="ROCplot.png" width="300" height="300" border="10000"></td><td><img src="CutOff_Plots.png" width="400" height="400" border="70"></td></tr></table></div></p>'), |
||
| 1003 | |||
| 1004 | # HTML('<br>'), |
||
| 1005 | |||
| 1006 | |||
| 1007 | h6("[1] Monica Lopez-Raton, Maria Xose Rodriguez-Alvarez, Carmen Cadarso Suarez, Francisco Gude Sampedro (2014). OptimalCutpoints: An R Package for Selecting Optimal Cutpoints in Diagnostic Tests. Journal of Statistical Software, 61(8), 1-36.") |
||
| 1008 | ), |
||
| 1009 | |||
| 1010 | tabPanel("Data upload", |
||
| 1011 | navbarPage(title = '', |
||
| 1012 | tabPanel('Data', dataTableOutput('RawData')) |
||
| 1013 | ) |
||
| 1014 | ), |
||
| 1015 | |||
| 1016 | tabPanel("ROC curve", |
||
| 1017 | downloadButton("downloadROCStats", "Download ROC statistics as txt-file"), |
||
| 1018 | downloadButton("downloadROCData", "Download ROC coordinates as txt-file"), |
||
| 1019 | downloadButton("downloadROCPlot", "Download plot as pdf-file"), |
||
| 1020 | |||
| 1021 | h4(textOutput(outputId = "section1")), |
||
| 1022 | navbarPage(id = "navbarROCcurve", |
||
| 1023 | title = '', |
||
| 1024 | tabPanel('Statistics', dataTableOutput('ROCstatistics')), |
||
| 1025 | tabPanel('ROC Coordinates', dataTableOutput('ROCcoordinates')), |
||
| 1026 | tabPanel('Multiple Comparisons', dataTableOutput('ROCcomparisons')), |
||
| 1027 | tabPanel('Partial AUC', dataTableOutput('resultPAuc')) |
||
| 1028 | |||
| 1029 | |||
| 1030 | |||
| 1031 | ), |
||
| 1032 | |||
| 1033 | conditionalPanel(condition = "input.navbarROCcurve != 'ROC Coordinates'", |
||
| 1034 | textOutput(outputId = "CIreminderLine1"), |
||
| 1035 | h6(textOutput(outputId = "CIreminderLine2")) |
||
| 1036 | ), |
||
| 1037 | |||
| 1038 | HTML('<br>'), |
||
| 1039 | h4(textOutput(outputId = "section2")), |
||
| 1040 | plotOutput("ROCplot") |
||
| 1041 | |||
| 1042 | |||
| 1043 | |||
| 1044 | #verbatimTextOutput("resultPAuc") |
||
| 1045 | ), |
||
| 1046 | |||
| 1047 | tabPanel("Cut points", |
||
| 1048 | downloadButton("downloadCutOffresults", "Download results as txt-file"), |
||
| 1049 | downloadButton("downloadCutOffPlotPDF", "Download plots as pdf-file"), |
||
| 1050 | verbatimTextOutput("cutPoints"), |
||
| 1051 | |||
| 1052 | ## İçeriği sayfada ortalamak için kullanılan HTML kodu. |
||
| 1053 | HTML('<div align="center">'), |
||
| 1054 | plotOutput("cutPointsPlot"), |
||
| 1055 | HTML('</div>') |
||
| 1056 | ), |
||
| 1057 | |||
| 1058 | tabPanel(title="Sample size", |
||
| 1059 | |||
| 1060 | downloadButton("downloadSampleSizeResults", "Download results as txt-file"), |
||
| 1061 | verbatimTextOutput("SampleSizeForRoc") |
||
| 1062 | |||
| 1063 | |||
| 1064 | ), |
||
| 1065 | |||
| 1066 | tabPanel(title="Manual", |
||
| 1067 | h5("Detailed manual will be released soon...") |
||
| 1068 | ), |
||
| 1069 | |||
| 1070 | tabPanel("Authors & News", |
||
| 1071 | h4("Authors"), |
||
| 1072 | HTML('<p><a href="http://www.biostatistics.hacettepe.edu.tr/cv/Dincer_Goksuluk_CV_Eng.pdf" target="_blank"> <b>Dincer Goksuluk</b></a><p>'), |
||
| 1073 | HTML('<p>Hacettepe University Faculty of Medicine <a href="http://www.biostatistics.hacettepe.edu.tr" target="_blank"> Department of Biostatistics</a><p>'), |
||
| 1074 | HTML('<p><a href="mailto:dincer.goksuluk@hacettepe.edu.tr" target="_blank">dincer.goksuluk@hacettepe.edu.tr</a><p>'), |
||
| 1075 | HTML('<p><a href="http://yunus.hacettepe.edu.tr/~selcuk.korkmaz/" target="_blank"> <b>Selcuk Korkmaz</b></a><p>'), |
||
| 1076 | HTML('<p>Hacettepe University Faculty of Medicine <a href="http://www.biostatistics.hacettepe.edu.tr" target="_blank"> Department of Biostatistics</a><p>'), |
||
| 1077 | HTML('<p><a href="mailto:selcuk.korkmaz@hacettepe.edu.tr" target="_blank">selcuk.korkmaz@hacettepe.edu.tr</a><p>'), |
||
| 1078 | HTML('<p><a href="http://www.biostatistics.hacettepe.edu.tr/cv/Gokmen_Zararsiz_CV_Eng.pdf" target="_blank"> <b>Gokmen Zararsiz</b></a><p>'), |
||
| 1079 | HTML('<p>Hacettepe University Faculty of Medicine <a href="http://www.biostatistics.hacettepe.edu.tr" target="_blank"> Department of Biostatistics</a><p>'), |
||
| 1080 | HTML('<p><a href="mailto:gokmen.zararsiz@hacettepe.edu.tr" target="_blank">gokmen.zararsiz@hacettepe.edu.tr</a><p>'), |
||
| 1081 | HTML('<br>'), |
||
| 1082 | h4("News"), |
||
| 1083 | HTML('<br>'), |
||
| 1084 | HTML('<p><b> Version 1.1 (June 23, 2015) </b><p>'), |
||
| 1085 | HTML('<p> (1) Partial AUC feature has been added.<p>'), |
||
| 1086 | HTML('<p> (2) Sample size calculation tab has been added.<p>'), |
||
| 1087 | HTML('<p> (3) Minor improvements and bug fixes.<p>'), |
||
| 1088 | |||
| 1089 | HTML('<br>'), |
||
| 1090 | HTML('<p><b> Version 1.0 (March 19, 2015)</b><p>'), |
||
| 1091 | HTML('<p> (1) Initial version has been released.<p>'), |
||
| 1092 | HTML('<br>'), |
||
| 1093 | |||
| 1094 | |||
| 1095 | h5("Other Tools"), |
||
| 1096 | |||
| 1097 | HTML('<p><a href="http://www.biosoft.hacettepe.edu.tr/MLViS/" target="_blank"> <b>MLViS: a machine learning-based virtual screening tool</b></a><p>'), |
||
| 1098 | HTML('<p><a href="http://www.biosoft.hacettepe.edu.tr/MVN/" target="_blank"> <b>MVN: a web-tool for assessing multivariate normality </b></a><p>'), |
||
| 1099 | HTML('<p><a href="http://www.biosoft.hacettepe.edu.tr/DDNAA/" target="_blank"> <b>DDNAA: Decision support system for differential diagnosis of nontraumatic acute abdomen </b></a><p>'), |
||
| 1100 | HTML('<br>'), |
||
| 1101 | |||
| 1102 | h6("Please feel free to send us bugs and feature requests.") |
||
| 1103 | ), |
||
| 1104 | |||
| 1105 | #tabPanel("News", |
||
| 1106 | # h4("New Features") |
||
| 1107 | #), |
||
| 1108 | id="tabs1" |
||
| 1109 | ), |
||
| 1110 | |||
| 1111 | tags$head(tags$style(type="text/css", "label.radio { display: inline-block; }", ".radio input[type=\"radio\"] { float: none; }"), |
||
| 1112 | tags$style(type="text/css", "select { max-width: 200px; }"), |
||
| 1113 | tags$style(type="text/css", "textarea { max-width: 185px; }"), |
||
| 1114 | tags$style(type="text/css", ".jslider { max-width: 200px; }"), |
||
| 1115 | tags$style(type='text/css', ".well { max-width: 330px; }"), |
||
| 1116 | tags$style(type='text/css', ".span4 { max-width: 330px; }")), |
||
| 1117 | |||
| 1118 | tags$head( |
||
| 1119 | tags$link(rel = "shortcut icon", href = "favicon-2.ico")) |
||
| 1120 | |||
| 1121 | ) |
||
| 1122 | )) |
||
| 1123 | |||
| 1124 | |||
| 1125 | |||
| 1126 |