Nothing
inst/app/ui.R
In compareGroups: Descriptive Analysis by Groups
ui <- fluidPage(
useShinyjs(),
# verbatimTextOutput("xxx"),
HTML("<style type='text/css'> #ResponseVariableORPanel, #LoadDataOptionsExcel, #LoadDataOptionsTxt, #extralabelsPanel {color:white;background-color:rgba(60,141,188,1)}</style>"),
HTML("<style type='text/css'> #ratioAccordion, #formatAccordion, #decimalsAccordion {color:rgba(60,141,188,1)}</style>"),
# get window sizes.
tags$head(tags$script('var dimension = [0, 0];
$(document).on("shiny:connected", function(e) {
dimension[0] = window.innerWidth;
dimension[1] = window.innerHeight;
Shiny.onInputChange("dimension", dimension);
});
$(window).resize(function(e) {
dimension[0] = window.innerWidth;
dimension[1] = window.innerHeight;
Shiny.onInputChange("dimension", dimension);
});
')),
HTML("<link href='https://fonts.googleapis.com/css?family=Knewave' rel='stylesheet'>"),
titlePanel(HTML("<p style='margin-top:-20px'></p>"), windowTitle="compareGroups | Explore and Summarise Epidemiological Data in R"),
dashboardPage(
# md = TRUE,
preloader=NULL,
skin="blue",
#sidebar_background=NULL,
#sidebar_fullCollapse=FALSE,
header = dashboardHeader(
# title = logo_cg,
title=tagList(
span(class = "logo-lg",
HTML("<img src='logo.png' width=35 style='margin-right:10px;margin-bottom:10px'/><format style='text-align: left; font-family: Knewave; font-size: 30px; font-style: normal; font-variant: normal;'>compareGroups<br>xxx</format>")),
# <br><format style='color:yellow'>R package to easily build publication-ready univariate or bivariate descriptive tables from a data set</format>")),
img(src = "logo.png", width=35)
),
titleWidth = 300,
fixed = FALSE,
#enable_rightsidebar = TRUE,
controlbarIcon = shiny::icon("gears")
,
leftUi=tagList(
hidden(div(id="dropdownData",
tags$table(
tags$tr(
tags$td(style="padding-right:5px",
dropdownButton(inputId="valuextoptionsaction", circle=FALSE, status="primary", label=HTML("<format style='font-size:13pt'>View options</format>"),
checkboxInput("showlabels","Show variable labels",TRUE),
sliderInput("valueextsize", "Resize (%):", min=10, max=300, value=100, step=10),
sliderInput("valueextwidth", "Width (%)", value=100, min=50, max=200)
)
),
tags$td(style="padding-right:5px",
bsButton("udpateSelection",HTML("<format style='font-size:13pt'>Update Selection</format>"),style="primary")
)
)
)
)),
hidden(div(id="dropdownDescriptives",
tags$table(
tags$tr(
tags$td(style="padding-right:5px",
bsButton("varinfotabbtn",HTML("<format style='font-size:13pt'>Names/Labels</format>"),style="primary")
),
tags$td(style="padding-right:5px",
shinyWidgets::dropdownButton(circle=FALSE, label=HTML("<format style='font-size:13pt'>Options</format>"), icon=icon("gears"), width=600, status="primary",
sliderInput("htmlsizerestab", "Resize:", min=7, max=30, value=16, step=1),
sliderInput("htmlwidthrestab", "Variable column width (cm):", min=2, max=20, value=8, step=0.5),
radioButtons("position", "Table position", c("left","center","right"), inline=TRUE),
fluidRow(
column(6,colorSelectorInput("header.background","Header background colour:",choices=choices_brewer,selected="#F7FBFF",display_label=FALSE)),
column(6, colorSelectorInput("header.color","Header colour:",choices=choices_brewer,selected="#000000",display_label=FALSE))
),
checkboxInput("strip", "Strip variables", FALSE),
conditionalPanel("input.strip",
colorSelectorInput("strip.color","Strip colour:",choices=choices_brewer,selected="#F0F0F0",display_label=FALSE)
)
)
),
tags$td(style="padding-right:5px",
shinyWidgets::dropdownButton(circle=FALSE, label=HTML("<format style='font-size:13pt'>Save</format>"), icon=icon("save"), status="primary",
h3("Save table"),
hr(),
div(id="SavePanel",
selectInput("downloadtabletype", "Select format", choices = c("PDF","CSV","HTML","TXT","Word","Excel"),selectize=FALSE),
conditionalPanel(
condition="input.downloadtabletype == 'PDF'",
wellPanel(
selectInput('sizepdf', 'Resize', c("tiny","scriptsize","footnotesize","small","normalsize","large","Large","LARGE","huge","Huge"),"normalsize", selectize=FALSE),
h4(""),
checkboxInput('landscape', 'Landscape', FALSE)
)
),
conditionalPanel(
condition="input.downloadtabletype == 'CSV'",
wellPanel(
radioButtons('sepcsv', 'Separator', c(Comma=',', Semicolon=';', Tab='\t'), ',')
)
),
downloadButton('actiondownloadtable', 'Download'),
bsAlert("downloadtablealert")
)
)
)
)
)
)),
hidden(div(id="dropdownPlot",
fluidRow(
column(6,
shinyWidgets::dropdownButton(circle=FALSE,icon = icon("down"),label = HTML("<format style='font-size:13pt'>Download</format>"),inputId = "downPlotOptionsBtn", status="primary",
tooltip = "Click here to download the plot. You can choose also the format.",
selectInput("downloadplottype", "Select format", choices = c('pdf','bmp','jpg','png','tif'), selectize=FALSE),
div(style="width:80px",downloadButton('actiondownloadplot', 'OK'))
)
),
column(6,
shinyjs::hidden(checkboxInput("perc",HTML("<format style='color:white;font-size:13pt'>Show percentage</format>"),TRUE))
)
)
)),
hidden(div(id="dropdownSNPs",
downloadButton('actiondownloadSNPtable', HTML("<format style='font-size:13pt'>Download</format>"), style="color:white; background-color:#3C8DBC;border:2px solid #357CA5")
))
)
,userOutput("github")
),
## sidebar
sidebar = dashboardSidebar(
sidebarMenu(id="leftmenu",
menuItem(HTML("<format style='font-size:13pt'>Home</format>"), tabName="Home", icon=icon("home")),
div(id="DataHeader",style="padding-top:5px;",
uiOutput("DataHeaderText"),
div(style="border: 1px solid white;height:0px; margin-top:-3px; margin-bottom:0px")
),
menuItem(HTML("<format style='font-size:13pt'>Load data</format>"), tabName="LoadData", icon = icon("upload")),
menuItem(HTML("<format style='font-size:13pt'>Filter Data</format>"), tabName="FilterData", icon = icon("filter")),
menuItem(HTML("<format style='font-size:13pt'>Recode variables</format>"), tabName="RecodeVars", icon = icon("calculator")),
##
div(id="TableHeader",style="padding-top:5px",
uiOutput("TableHeaderText"),
div(style="border: 1px solid white;height:0px; margin-top:-3px; margin-bottom:0px")
),
menuItem(HTML("<format style='font-size:13pt'>Variables</format>"), tabName="Variables", icon = icon("bars"), startExpanded=FALSE,
menuSubItem(HTML("<format style='font-size:12pt'>Described variables</format>"), tabName="DescribedVariables"),
menuSubItem(HTML("<format style='font-size:12pt'>Response / groups</format>"), tabName="ResponseVariable"),
menuSubItem(HTML("<format style='font-size:12pt'>Stratas</format>"), tabName="StrataVariable")
),
menuItem(HTML("<format style='font-size:13pt'>Settings</format>"), tabName="Settings", icon = icon("cogs"),
menuSubItem(HTML("<format style='font-size:12pt'>Type</format>"), tabName="Type"),
menuSubItem(HTML("<format style='font-size:12pt'>Hide</format>"), tabName="Hide"),
menuSubItem(HTML("<format style='font-size:12pt'>Subset</format>"), tabName="Subset"),
menuSubItem(HTML("<format style='font-size:12pt'>Odds/Hazard/Risk Ratio</format>"), tabName="ORHR")
),
menuItem(HTML("<format style='font-size:13pt'>Display</format>"), tabName="Display", icon = icon("eye"),
menuSubItem(HTML("<format style='font-size:12pt'>Show</format>"), tabName="Show"),
menuSubItem(HTML("<format style='font-size:12pt'>Format</format>"), tabName="Format"),
menuSubItem(HTML("<format style='font-size:12pt'>Decimals</format>"), tabName="Decimals"),
menuSubItem(HTML("<format style='font-size:12pt'>Labels</format>"), tabName="Labels")
),
##
div(id="PlotHeader",style="padding-top:5px",
uiOutput("PlotHeaderText"),
div(style="border: 1px solid white;height:0px; margin-top:-3px; margin-bottom:0px")
),
menuItem(HTML("<format style='font-size:13pt'>Variable</format>"), tabName="PlotVariables", icon = icon("bars")),
menuItem(HTML("<format style='font-size:13pt'>Groups</format>"), tabName="PlotGroups", icon = icon("user-friends")),
##
div(id="SNPsHeader",style="padding-top:5px",
uiOutput("SNPsHeaderText"),
div(style="border: 1px solid white;height:0px; margin-top:-3px; margin-bottom:0px")
),
menuItem(HTML("<format style='font-size:13pt'>Variables</format>"), tabName="SNPsVariables", icon = icon("bars")),
menuItem(HTML("<format style='font-size:13pt'>Groups</format>"), tabName="SNPsGroups", icon = icon("user-friends")),
menuItem(HTML("<format style='font-size:13pt'>Options</format>"), tabName="SNPsOptions", icon=icon("gears"))
)
),
## body
body = dashboardBody(
setShadow(class = "dropdown-menu"),
# cg_theme,
tags$head(tags$style(HTML('.content-wrapper, .right-side {background-color: white;}'))),
### Home ####
div(id="homePanel",
HTML("<p style='text-align: center;><format color:#357CA5; font-family: Knewave; font-size: 40pt; font-style: normal; font-variant: normal;'>compareGroups WUI</format></p>"),
HTML("<h3 style='text-align: center;><format style='text-align: center'><i><strong>Web User Interface to explore data and create descriptive tables with <code>compareGroups</code> package</strong></format></i></h3>"),
includeMarkdown("home.md")
),
### Table ####
shinyjs::hidden(div(style="margin-top:1%", id="descrTableBox",
shinyhelper::helper(flipBox(id=1,
main_img = "",
header_img = "",
front_title = "Descriptive table",
back_title = "Variable information",
front_btn_text="Go to variable information",
back_btn_text="Go to descriptive table",
uiOutput("table"),
back_content=tagList(
uiOutput("sumtab")
)
),title="Descriptive table", type="markdown", content="descrTablehelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px")
)),
#### Data ####
shinyjs::hidden(div(id="showDataPanel",
shinyhelper::helper(uiOutput("valuesextui"),title="Data Panel", type="markdown", content="DataPanelhelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
bsAlert("dataAlert")
)),
#### Plot #####
shinyjs::hidden(div(id="showPlotPanel",
shinyhelper::helper(plotOutput("plot", height=600, width=800),title="Plot Panel", type="markdown", content="PlotPanelhelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px")
)),
##### SNPs #####
shinyjs::hidden(div(id="showSNPsPanel",
shinyhelper::helper(verbatimTextOutput("restabSNPs"),title="SNPs Panel", type="markdown", content="SNPsPanelhelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px")
))
),
#########################################
########### right side bar ##############
controlbar = dashboardControlbar(id="rightPanel",
skin = "dark",overlay = FALSE, width=400,
hidden(div(style="margin-left:10%; margin-right:-10%; width:70%",sliderInput("leftPanelWidth", HTML("<format style='color:white'>Middle Panel width</format>"), value=30, min=0, max=100))),
# bsButton("toggleLeftPanel","",type = "action",icon=icon("angle-double-left"),size="extra-small"),
# shinyBS::bsTooltip("toggleLeftPanel","Hide panel"),
column(1, " "),
column(11,
#### Load data #####
conditionalPanel("input.leftmenu=='LoadData'",
shinyhelper::helper(h3("Load data"), title="Load data", type="markdown", content="loadhelp", size="l", colour="#3c8dbc", style="font-size:14pt; margin-right:10px"),
hr(),
hidden(div(id="resetbtnPanel",
actionButton("resetbtn","Load a new dataset"),
br(),
"In order to read a new data set, all parameteres will be resetted",
hr()
)),
div(id="LoadDataPanel",
HTML(
'<div id="exampledata" class="form-group shiny-input-radiogroup shiny-input-container" style="width:100%;text-align:justify">
<label class="control-label" for="exampledata"></label>
<div class="shiny-options-group">
<div class="radio">
<label>
<input type="radio" name="exampledata" value="Own data" checked="checked"/>
<span>Upload your own data set from a file</span>
</label>
<div><br><font style="weight:bold">...or choose an example data set</font></p></div>
</div>
<div class="radio" style="margin-left:10px">
<label>
<input type="radio" name="exampledata" value="REGICOR"/>
<span>REGICOR</span>
</label>
</div>
<div class="radio" style="margin-left:10px">
<label>
<input type="radio" name="exampledata" value="SNPS"/>
<span>SNPS</span>
</label>
</div>
</div>
</div>'
),
fileInput("files", ""),
div(id="ownPanel",
selectInput("datatype", "Data format", c('SPSS'='*.sav', 'TEXT'='*.txt','EXCEL'='*.xls','Stata'='*.dta','R'='*.rda'),'*.sav'),
conditionalPanel("input.datatype=='*.xls'", # EXCELL
wellPanel(id="LoadDataOptionsExcel",
HTML('<p style="font-style:Bold; font-size:18px">Excel options</p>'),
selectInput("tablenames", "Choose the table to read:", choices = NULL, selectize=FALSE),
checkboxInput('headerexcel', 'Has column headers', TRUE),
numericInput("skipexcel", "Number of rows to skip", value=0),
textInput("missvalueexcel", HTML("Missing Data String (e.g. <i>NA</i>)"), ""),
checkboxInput("stringToFactorexcel", "Convert string variables to factor", value=TRUE)
)
),
conditionalPanel("input.datatype=='*.txt'",
wellPanel(id="LoadDataOptionsTxt",
HTML('<p style="font-style:Bold; font-size:18px">TEXT options</p>'),
downloadButton("previewtxtdown","Preview data"),
checkboxInput('header', 'Has column headers', TRUE),
numericInput("skip", "Number of rows to skip", value=0),
textInput("missvalue", HTML("Missing Data String (e.g. <i>NA</i>)"), ""),
selectInput('sep', 'Column Separator', c(Comma=',', Semicolon=';', Tab='\t', Other='o'), ','),
conditionalPanel(
condition = "input.sep == 'o'",
textInput("sepother", "Specify separator character","")
),
selectInput('dechar', 'Decimal point character', c('Comma'=',', 'Dot'='.'), '.'),
selectInput('quote', 'Values in Quotes?', c("None"=1, "Double"=2, "Single"=3), 2),
radioButtons("encoding", "Encoding", c('default'='default','latin1'='latin1','utf8'='utf8'),'default',inline=TRUE)
)
)
),
actionButton("loadok","Read data")
),
br()
),
#### Filter data ######
conditionalPanel("input.leftmenu=='FilterData'",
shinyhelper::helper(h3("Filter data"), title="Filter data", type="markdown", content="filterhelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
textAreaInput("filterexpr", "Write R code", placeholder = "Some R code or left in blank to remove the filter"),
tags$table(
tags$tr(
tags$td(shinyBS::bsButton("filterdataok", "Filter", width=80)),
tags$td(HTML(" ")),
tags$td(shinyBS::bsButton("removefilterdataok", "Clean", icon=icon("brush"), width=80, style="warning"))
)
),
br()
),
#### Recode variables ######
conditionalPanel("input.leftmenu=='RecodeVars'",
shinyhelper::helper(h3("Recode variables"), title="Recode variables", type="markdown", content="recodehelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
textInput("newvarname", "Variable name"),
textInput("newvarlabel", "Variable label"),
textAreaInput("newvarexpr", "Write R code"),
tags$table(
tags$tr(
tags$td(shinyBS::bsButton("newvarok", "Create", width=80)),
tags$td(HTML(" ")),
tags$td(shinyBS::bsButton("removenewvarok", "Clean", icon=icon("brush"), width=80, style="warning"))
)
),
br(),
hr(),
selectInput("vartofactor","Choose variable to convert to factor",choices = NULL),
actionButton("vartofactorbtn","Convert")
),
#### Described variables ######
conditionalPanel("input.leftmenu=='DescribedVariables'",
shinyhelper::helper(h3("Selected described variables"), title="Selected described variables", type="markdown", content="selecthelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
div(id="DescribedVariablesPanel",
fluidRow(
fluidRow(
tags$table(
tags$tr(
tags$td(HTML("  ")),
tags$td(width="50px",shinyBS::bsButton("selevarsAll","All",style="info",size="extra-small",block=TRUE)),
tags$td(HTML(" ")),
tags$td(width="50px",shinyBS::bsButton("selevarsNone","None",style="danger",size="extra-small",block=TRUE))
)
)
),
fluidRow(
column(12,
selectizeInput("selevars",NULL,width="100%",choices=NULL,multiple=TRUE,options=list(plugins=list('remove_button', 'drag_drop')))
)
),
column(3, offset=0,
shinyBS::bsButton("changeselevarsok","Update")
)
)
),
br()
),
#### Response Variable ######
conditionalPanel("input.leftmenu=='ResponseVariable'",
shinyhelper::helper(h3("Define groups"), title="Define groups", type="markdown", content="responsehelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
div(id="ResponseVariablePanel",
radioGroupButtons("resptype", "", c("None","Group","Survival"),justified=TRUE, checkIcon=list(yes=icon("ok",lib = "glyphicon"))),
conditionalPanel("input.resptype == 'Group'",
numericInput('maxgroups',"Maximum number of groups:",value=5,min=2,max=10),
selectInput("gvar", "Choose the grouping variable:", choices = NULL, selectize=FALSE),
actionLink("ResponseVariableORPanelBtn",HTML("<format style='color:white'>OR/RR options</format>")),
wellPanel(id="ResponseVariableORPanel",
checkboxInput('computeratio', 'Compute OR/RR:', FALSE),
conditionalPanel(
condition = "input.computeratio == true",
selectInput("gvarcat", "OR/RR ref. cat:", choices = NULL, selectize=FALSE),
radioButtons("riskratio","OR or RR", c("OR", "RR"), inline=TRUE),
conditionalPanel(
"input.riskratio=='OR'",
selectInput("oddsratiomethod","OR method",c("midp", "fisher", "wald", "small"))
),
conditionalPanel(
"input.riskratio=='RR'",
selectInput("riskratiomethod","RR method",c("wald", "small", "boot"))
)
)
)
),
conditionalPanel("input.resptype=='Survival'",
selectInput("varseletime", "Select time-to-event variable", choices = NULL, multiple = FALSE, selectize=FALSE),
selectInput("varselestatus", "Select status variable", choices = NULL, multiple = FALSE, selectize=FALSE),
selectInput("statuscat", "Select event category/ies", choices=NULL, multiple = TRUE, selectize=FALSE)
),
actionButton("changeresp","Update")
),
br()
),
#### Stratas ######
conditionalPanel("input.leftmenu=='StrataVariable'",
shinyhelper::helper(h3("Define strata"), title="Define strata", type="markdown", content="stratahelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
div(id="StrataVariablePanel",
radioGroupButtons("stratatype", "", c("None","Strata"), justified=TRUE, checkIcon=list(yes=icon("ok",lib = "glyphicon"))),
conditionalPanel("input.stratatype=='Strata'",
numericInput('maxstrata',"Maximum number of stratas:",value=5,min=2,max=10),
selectInput("svar", "Choose the strata variable:", choices = NULL, selectize=FALSE)
),
actionButton("changestrata","Update")
),
br()
),
#### Type ####
conditionalPanel("input.leftmenu=='Type'",
shinyhelper::helper(h3("Define the type of variables"), title="Define the type of variables", type="markdown", content="typehelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
div(id="TypePanel",
shinyWidgets::pickerInput("varselemethod", "Select variables", choices=NULL, multiple=TRUE,
options = pickerOptions(actionsBox=TRUE, title="Select variables", header="",liveSearch=TRUE)
),
selectInput("method", "Select type of chosen variable/s", c("Normal","Non-normal","Categorical","NA"), selectize=FALSE),
conditionalPanel("input.method=='NA'",
fluidRow(
column(6,numericInput("alpha","alpha",value=0.05,min=0,max=1,step=0.005)),
column(6,numericInput("mindis","min categories",value=5,min=1,max=10))
)
),
actionButton("changemethod","Update")
),
br()
),
#### Hide ####
conditionalPanel("input.leftmenu=='Hide'",
shinyhelper::helper(h3("Hide settings"), title="Hide settings", type="markdown", content="hidehelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
div(id="HidePanel",
div(
fluidRow(
column(6, selectInput("varselehide", "variable", choices = NULL, multiple = FALSE, selectize=FALSE)),
column(6, selectInput("hidecat", "category", choices = NULL, "<<None>>", selectize=FALSE))
),
textInput('hideno', "Hide 'no' category", ''),
actionButton("changehide","Update")
)
),
br()
),
#### Subset ####
conditionalPanel("input.leftmenu=='Subset'",
shinyhelper::helper(h3("Variable subset settings"), title="Variable subset settings", type="markdown", content="subsethelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
div(id="SubsetPanel",
HTML('<div style="height:10px"></div>'),
shinyWidgets::pickerInput("varselevarsubset", "Select variables", choices=NULL, multiple=TRUE,
options = pickerOptions(actionsBox=TRUE, title="Select variables", header="",liveSearch=TRUE)
),
br(),
textAreaInput("varsubset", label="Write subset expression", value = ""),
tags$table(
tags$tr(
tags$td(shinyBS::bsButton("changevarsubset","Update", width=80)),
tags$td(HTML(" ")),
tags$td(shinyBS::bsButton("removechangevarsubset","Clean", width=80, icon=icon("brush"), style="warning"))
)
)
),
br()
),
#### Odds Ratio / Hazard Ratio ####
conditionalPanel("input.leftmenu=='ORHR'",
shinyhelper::helper(h3("Odds/Risk/Hazard Ratio settings"), title="Odds/Risk/Hazard Ratio settings", type="markdown", content="ratiohelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
div(id="RatioPanel",
conditionalPanel("input.computeratio || input.resptype=='Survival'",
HTML('<div style="height:10px"></div>'),
bsCollapse(id="ratioAccordion", open="xxx", multiple=FALSE,
bsCollapsePanel(value="Reference category", style="primary", title=HTML('<p style="font-color:black; height:10px">Reference category</p>'),
fluidRow(
column(6, selectInput("varselerefratio", "variable", choices=NULL, multiple=FALSE, selectize=FALSE)),
column(6, selectInput("refratiocat", "category", choices=NULL, selectize=FALSE))
),
actionButton("changeratiocat","Update")
),
bsCollapsePanel(value="Multiplying factor", style="primary", title=HTML('<p style="font-color:black; height:10px">Multiplying factor</p>'),
shinyWidgets::pickerInput("varselefactratio", "Select variables", choices=NULL, multiple=TRUE,
options = pickerOptions(actionsBox=TRUE, title="Select variables", header="",liveSearch=TRUE)
),
numericInput("factratio", label=NULL, value = 1, min=1, max=100, width=100),
actionButton("changefactratio","Update")
)
)
),
conditionalPanel("!input.computeratio && input.resptype!='Survival'",
helpText("No binary non survival response variable selected")
)
),
br()
),
#### Show ####
conditionalPanel("input.leftmenu=='Show'",
shinyhelper::helper(h3("Show settings"), title="Show settings", type="markdown", content="showhelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
div(id="ShowPanel",
fluidRow(
column(6,checkboxInput('showall', 'ALL', TRUE)),
column(6,checkboxInput('showpoverall', 'p-overall', TRUE))
),
fluidRow(
column(6,checkboxInput('showdesc', 'Descriptives', TRUE)),
column(6,checkboxInput('showptrend', 'p-trend', FALSE))
),
fluidRow(
column(6,checkboxInput('showratio', 'OR/RR/HR', FALSE)),
column(6,
conditionalPanel("input.showratio == true",
checkboxInput('showpratio', 'OR/RR/HR p-value', FALSE)
)
)
),
fluidRow(
column(6,checkboxInput('shown', 'Available', FALSE)),
column(6,checkboxInput('includemiss', "Add 'Missing' category", FALSE))
),
fluidRow(
column(6,checkboxInput('showpmul', 'Pairwise p-value', FALSE)),
column(6,
conditionalPanel("input.showpmul == true",
checkboxInput('pcorrected', 'Correct pairwise p-values', FALSE)
)
)
),
fluidRow(
column(6,checkboxInput('simplify', 'Simplify', FALSE)),
column(6,"")
),
actionButton("changeshow","Update")
),
br()
),
#### Format ####
conditionalPanel("input.leftmenu=='Format'",
shinyhelper::helper(h3("Format settings"), title="Format settings", type="markdown", content="formathelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
div(id="FormatPanel",
HTML('<div style="height:10px"></div>'),
fluidRow(
column(6,checkboxInput('showci', 'Report Confidence Interval', FALSE)),
column(6,
conditionalPanel('input.showci',
div(style="color:white",sliderInput('conflevel', 'Confidence level', min=50, max=100, value=95, step=1))
)
)
),
numericInput("timemax","Time for survival variables",NA),
conditionalPanel("!input.showci",
bsCollapse(id="formatAccordion",multiple=FALSE,open="xxx",
bsCollapsePanel(value="Frequencies", style="primary", title=HTML('<p style="font-color:black; height:10px">Frequencies</p>'),
radioButtons("type", "", c("%" = 1, "n (%)" = 2, "n"=3), selected="n (%)",inline = TRUE),
radioButtons("byrow", "Percentages by:", choices=c("columns","rows","total"), inline = TRUE)
),
bsCollapsePanel(value="Mean, standard deviation", style="primary", title=HTML('<p style="font-color:black; height:10px">Mean, standard deviation</p>'),
radioButtons("sdtype", "", c("Mean (SD)"=1,"Mean\u00B1SD"=2), selected="Mean (SD)",inline = TRUE)
),
bsCollapsePanel(value="Median [a, b]", style="primary", title=HTML('<p style="font-color:black; height:10px">Median [a, b]</p>'),
fluidRow(
column(6,numericInput("Q1", label="[a, ]:", value = 25, min=0, max=49)),
column(6,numericInput("Q3", label="[ , b]:", value = 75, min=51, max=100))
),
fluidRow(
column(6,radioButtons("qtype1", "brackets", c("Squared"=1,"Rounded"=2), selected="Squared")),
column(6,radioButtons("qtype2", "separator", c("Semicolon"=1,"Comma"=2,"Slash"=3), selected="Semicolon"))
)
),
bsCollapsePanel(value="Date variables", style="primary", title=HTML('<p style="font-color:black; height:10px">Date variables</p>'),
selectInput("Dateformat", "Date format", choices=c("d-m-Y","m-d-Y","Y-m-d","d-mon-Y","mon-d-Y"), selected="d-mon-Y")
)
)
),
checkboxInput("extralabels","Show variable format indicators", FALSE),
conditionalPanel("input.extralabels",
wellPanel(id="extralabelsPanel",
textInput("extralabelmean","Mean and standard deviation", "Mean (SD)"),
textInput("extralabelmedian","Median and quartiles", "Median [25th; 75th]"),
textInput("extralabelperc","Frequencies", "N (%)"),
textInput("extralabelsurv","Survival variable", "Incidence")
)
),
actionButton("changeformat","Update")
),
br()
),
#### Decimals ####
conditionalPanel("input.leftmenu=='Decimals'",
shinyhelper::helper(h3("Decimals"), title="Decimals", type="markdown", content="decimalshelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
div(id="DecimalsPanel",
HTML('<div style="height:10px"></div>'),
bsCollapse(id="decimalsAccordion", open="xxx", multiple=FALSE,
bsCollapsePanel(value="p-values", style="primary", title=HTML('<p style="font-color:white; height:10px">p-values</p>'),
numericInput("pvaldigits", label="Number of decimals", value = 3, min=1, max=20),
actionButton("changepvalsdigits","Update")
),
bsCollapsePanel(value="Descriptives", style="primary", title=HTML('<p style="font-color:white; height:10px">Descriptives</p>'),
shinyWidgets::pickerInput("varseledescdigits", "", choices=NULL, multiple=TRUE,
options = pickerOptions(actionsBox=TRUE, title="Select variables", header="",liveSearch=TRUE)
),
numericInput("descdigits", label=NULL, value = -1, min=-1, max=10, width=100),
actionButton("changedescdigits","Update")
),
bsCollapsePanel(value="OR/RR/HR", style="primary", title=HTML('<p style="font-color:white; height:10px">OR/RR/HR</p>'),
shinyWidgets::pickerInput("varseleratiodigits", "", choices=NULL, multiple=TRUE,
options = pickerOptions(actionsBox=TRUE, title="Select variables", header="",liveSearch=TRUE)
),
numericInput("ratiodigits", label=NULL, value = -1, min=-1, max=10, width=100),
actionButton("changeratiodigits","Update")
)
)
),
br()
),
#### Labels ####
conditionalPanel("input.leftmenu=='Labels'",
shinyhelper::helper(h3("Labels"), title="Labels", type="markdown", content="labelshelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
div(id="LabelsPanel",
textInput("alllabel", label="All:", value="[ALL]"),
textInput("poveralllabel", label="overall p-value:", value="p.overall"),
textInput("ptrendlabel", label="p-value for trend:", value="p.trend"),
textInput("pratiolabel", label="OR/RR/HR p-value:", value="p.ratio"),
textInput("Nlabel", label="Available data:", value="N"),
textInput("captionlabel", label="Caption:", value="NULL"),
tags$table(
tags$tr(
tags$td(shinyBS::bsButton("changeLabels","Apply", width=80)),
tags$td(HTML(" ")),
tags$td(shinyBS::bsButton("refreshLabels","Refresh", style="warning", width=80))
)
)
),
br()
),
#### PlotVariables #####
conditionalPanel("input.leftmenu=='PlotVariables'",
shinyhelper::helper(h3("Plot variable"), title="Plot variable", type="markdown", content="PlotVariableshelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
div(id="PlotVariablesPanel",
HTML('<div style="height:10px"></div>'),
selectInput("plotselevars", "Select variable", choices=NULL),
actionButton("plotvarchange","Update")
),
br()
),
#### PlotGroups #####
conditionalPanel("input.leftmenu=='PlotGroups'",
shinyhelper::helper(h3("Plot Groups"), title="Plot Groups", type="markdown", content="PlotGroupshelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
div(id="PlotGroupsPanel",
HTML('<div style="height:10px"></div>'),
radioGroupButtons("plotresptype", "", c("None","Group","Survival"),justified=TRUE, checkIcon=list(yes=icon("ok",lib = "glyphicon"))),
br(),
conditionalPanel("input.plotresptype == 'Group'",
numericInput('plotmaxgroups',"Maximum number of groups:",value=5,min=2,max=10),
selectInput("plotgvar", "Choose the grouping variable:", choices = NULL, selectize=FALSE)
),
conditionalPanel("input.plotresptype=='Survival'",
selectInput("plotvarseletime", "Select time-to-event variable", choices = NULL, multiple = FALSE, selectize=FALSE),
selectInput("plotvarselestatus", "Select status variable", choices = NULL, multiple = FALSE, selectize=FALSE),
selectInput("plotstatuscat", "Select event category", choices=NULL, multiple = TRUE, selectize=FALSE)
),
actionButton("plotgroupschange","Update")
),
br()
),
#### SNPs Variables #####
conditionalPanel("input.leftmenu=='SNPsVariables'",
shinyhelper::helper(h3("SNPs Variables"), title="SNPs Variables", type="markdown", content="SNPsVariableshelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
div(id="SNPsVariablesPanel",
HTML('<div style="height:10px"></div>'),
fluidRow(
tags$table(
tags$tr(
tags$td(HTML("  ")),
tags$td(width="50px",shinyBS::bsButton("snpsselevarsAll","All",style="info",size="extra-small",block=TRUE)),
tags$td(HTML(" ")),
tags$td(width="50px",shinyBS::bsButton("snpsselevarsNone","None",style="danger",size="extra-small",block=TRUE))
)
)
),
fluidRow(
selectizeInput("snpsselevars",NULL,width="100%",choices=NULL,multiple=TRUE,options=list(plugins=list('remove_button', 'drag_drop')))
),
actionButton("snpsvarchange","Update")
),
br()
),
#### SNPs Groups #####
conditionalPanel("input.leftmenu=='SNPsGroups'",
shinyhelper::helper(h3("SNPs Groups"), title="SNPs Groups", type="markdown", content="SNPsGroupshelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
div(id="SNPsGroupsPanel",
HTML('<div style="height:10px"></div>'),
radioGroupButtons("snpsresptype", "", c("None","Group"),justified=TRUE, checkIcon=list(yes=icon("ok",lib = "glyphicon"))),
conditionalPanel("input.snpsresptype == 'Group'",
numericInput('snpsmaxgroups',"Maximum number of groups:",value=5,min=2,max=10),
selectInput("snpsgvar", "Choose the grouping variable:", choices = NULL, selectize=FALSE)
),
actionButton("snpsgroupschange","Update")
),
br()
),
##### SNPs options #####
conditionalPanel("input.leftmenu=='SNPsOptions'",
shinyhelper::helper(h3("SNPs Options"), title="SNPs Options", type="markdown", content="SNPsOptionshelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
div(id="SNPsOptionsPanel",
textInput("sepSNPs","Allele separator"),
bsButton("snpsoptionschange","Update")
),
br()
)
)
),
### footer ###
footer = dashboardFooter(
left = HTML("
<b>By Isaac Subirana</b><br>CIBERCV, IMIM-Parc de Salut Mar, Barcelona<br>
<hr>
<table style='margin-left: auto;margin-right: auto'>
<tr>
<td style='margin-left:5px'><a title='CIBERCV' href='https://www.cibercv.es/'><img alt='CIBERCV' src='logo-cibercv.png' width='80%'/></a></td>
<td style='margin-left:10px'><a title='IMIM' href='https://imim.cat/'><img alt='IMIM' src='logo_imim_capsalera.gif' width='80%'/></a></td>
<td style='margin-left:10px'><a title='REGICOR' href='https://regicor.cat//'><img alt='IMIM' src='regicor_logo125.png' width='80%'/></a></td>
</tr>
</table>
"),
right = HTML("Powered by <a href='https://shiny.rstudio.com/'>Shiny</a>")
)
# ,
# ### preloader ###
# enable_preloader = FALSE
)
)
Try the compareGroups package in your browser
Any scripts or data that you put into this service are public.
compareGroups documentation built on Oct. 12, 2023, 1:08 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
ui <- fluidPage(
useShinyjs(),
# verbatimTextOutput("xxx"),
HTML("<style type='text/css'> #ResponseVariableORPanel, #LoadDataOptionsExcel, #LoadDataOptionsTxt, #extralabelsPanel {color:white;background-color:rgba(60,141,188,1)}</style>"),
HTML("<style type='text/css'> #ratioAccordion, #formatAccordion, #decimalsAccordion {color:rgba(60,141,188,1)}</style>"),
# get window sizes.
tags$head(tags$script('var dimension = [0, 0];
$(document).on("shiny:connected", function(e) {
dimension[0] = window.innerWidth;
dimension[1] = window.innerHeight;
Shiny.onInputChange("dimension", dimension);
});
$(window).resize(function(e) {
dimension[0] = window.innerWidth;
dimension[1] = window.innerHeight;
Shiny.onInputChange("dimension", dimension);
});
')),
HTML("<link href='https://fonts.googleapis.com/css?family=Knewave' rel='stylesheet'>"),
titlePanel(HTML("<p style='margin-top:-20px'></p>"), windowTitle="compareGroups | Explore and Summarise Epidemiological Data in R"),
dashboardPage(
# md = TRUE,
preloader=NULL,
skin="blue",
#sidebar_background=NULL,
#sidebar_fullCollapse=FALSE,
header = dashboardHeader(
# title = logo_cg,
title=tagList(
span(class = "logo-lg",
HTML("<img src='logo.png' width=35 style='margin-right:10px;margin-bottom:10px'/><format style='text-align: left; font-family: Knewave; font-size: 30px; font-style: normal; font-variant: normal;'>compareGroups<br>xxx</format>")),
# <br><format style='color:yellow'>R package to easily build publication-ready univariate or bivariate descriptive tables from a data set</format>")),
img(src = "logo.png", width=35)
),
titleWidth = 300,
fixed = FALSE,
#enable_rightsidebar = TRUE,
controlbarIcon = shiny::icon("gears")
,
leftUi=tagList(
hidden(div(id="dropdownData",
tags$table(
tags$tr(
tags$td(style="padding-right:5px",
dropdownButton(inputId="valuextoptionsaction", circle=FALSE, status="primary", label=HTML("<format style='font-size:13pt'>View options</format>"),
checkboxInput("showlabels","Show variable labels",TRUE),
sliderInput("valueextsize", "Resize (%):", min=10, max=300, value=100, step=10),
sliderInput("valueextwidth", "Width (%)", value=100, min=50, max=200)
)
),
tags$td(style="padding-right:5px",
bsButton("udpateSelection",HTML("<format style='font-size:13pt'>Update Selection</format>"),style="primary")
)
)
)
)),
hidden(div(id="dropdownDescriptives",
tags$table(
tags$tr(
tags$td(style="padding-right:5px",
bsButton("varinfotabbtn",HTML("<format style='font-size:13pt'>Names/Labels</format>"),style="primary")
),
tags$td(style="padding-right:5px",
shinyWidgets::dropdownButton(circle=FALSE, label=HTML("<format style='font-size:13pt'>Options</format>"), icon=icon("gears"), width=600, status="primary",
sliderInput("htmlsizerestab", "Resize:", min=7, max=30, value=16, step=1),
sliderInput("htmlwidthrestab", "Variable column width (cm):", min=2, max=20, value=8, step=0.5),
radioButtons("position", "Table position", c("left","center","right"), inline=TRUE),
fluidRow(
column(6,colorSelectorInput("header.background","Header background colour:",choices=choices_brewer,selected="#F7FBFF",display_label=FALSE)),
column(6, colorSelectorInput("header.color","Header colour:",choices=choices_brewer,selected="#000000",display_label=FALSE))
),
checkboxInput("strip", "Strip variables", FALSE),
conditionalPanel("input.strip",
colorSelectorInput("strip.color","Strip colour:",choices=choices_brewer,selected="#F0F0F0",display_label=FALSE)
)
)
),
tags$td(style="padding-right:5px",
shinyWidgets::dropdownButton(circle=FALSE, label=HTML("<format style='font-size:13pt'>Save</format>"), icon=icon("save"), status="primary",
h3("Save table"),
hr(),
div(id="SavePanel",
selectInput("downloadtabletype", "Select format", choices = c("PDF","CSV","HTML","TXT","Word","Excel"),selectize=FALSE),
conditionalPanel(
condition="input.downloadtabletype == 'PDF'",
wellPanel(
selectInput('sizepdf', 'Resize', c("tiny","scriptsize","footnotesize","small","normalsize","large","Large","LARGE","huge","Huge"),"normalsize", selectize=FALSE),
h4(""),
checkboxInput('landscape', 'Landscape', FALSE)
)
),
conditionalPanel(
condition="input.downloadtabletype == 'CSV'",
wellPanel(
radioButtons('sepcsv', 'Separator', c(Comma=',', Semicolon=';', Tab='\t'), ',')
)
),
downloadButton('actiondownloadtable', 'Download'),
bsAlert("downloadtablealert")
)
)
)
)
)
)),
hidden(div(id="dropdownPlot",
fluidRow(
column(6,
shinyWidgets::dropdownButton(circle=FALSE,icon = icon("down"),label = HTML("<format style='font-size:13pt'>Download</format>"),inputId = "downPlotOptionsBtn", status="primary",
tooltip = "Click here to download the plot. You can choose also the format.",
selectInput("downloadplottype", "Select format", choices = c('pdf','bmp','jpg','png','tif'), selectize=FALSE),
div(style="width:80px",downloadButton('actiondownloadplot', 'OK'))
)
),
column(6,
shinyjs::hidden(checkboxInput("perc",HTML("<format style='color:white;font-size:13pt'>Show percentage</format>"),TRUE))
)
)
)),
hidden(div(id="dropdownSNPs",
downloadButton('actiondownloadSNPtable', HTML("<format style='font-size:13pt'>Download</format>"), style="color:white; background-color:#3C8DBC;border:2px solid #357CA5")
))
)
,userOutput("github")
),
## sidebar
sidebar = dashboardSidebar(
sidebarMenu(id="leftmenu",
menuItem(HTML("<format style='font-size:13pt'>Home</format>"), tabName="Home", icon=icon("home")),
div(id="DataHeader",style="padding-top:5px;",
uiOutput("DataHeaderText"),
div(style="border: 1px solid white;height:0px; margin-top:-3px; margin-bottom:0px")
),
menuItem(HTML("<format style='font-size:13pt'>Load data</format>"), tabName="LoadData", icon = icon("upload")),
menuItem(HTML("<format style='font-size:13pt'>Filter Data</format>"), tabName="FilterData", icon = icon("filter")),
menuItem(HTML("<format style='font-size:13pt'>Recode variables</format>"), tabName="RecodeVars", icon = icon("calculator")),
##
div(id="TableHeader",style="padding-top:5px",
uiOutput("TableHeaderText"),
div(style="border: 1px solid white;height:0px; margin-top:-3px; margin-bottom:0px")
),
menuItem(HTML("<format style='font-size:13pt'>Variables</format>"), tabName="Variables", icon = icon("bars"), startExpanded=FALSE,
menuSubItem(HTML("<format style='font-size:12pt'>Described variables</format>"), tabName="DescribedVariables"),
menuSubItem(HTML("<format style='font-size:12pt'>Response / groups</format>"), tabName="ResponseVariable"),
menuSubItem(HTML("<format style='font-size:12pt'>Stratas</format>"), tabName="StrataVariable")
),
menuItem(HTML("<format style='font-size:13pt'>Settings</format>"), tabName="Settings", icon = icon("cogs"),
menuSubItem(HTML("<format style='font-size:12pt'>Type</format>"), tabName="Type"),
menuSubItem(HTML("<format style='font-size:12pt'>Hide</format>"), tabName="Hide"),
menuSubItem(HTML("<format style='font-size:12pt'>Subset</format>"), tabName="Subset"),
menuSubItem(HTML("<format style='font-size:12pt'>Odds/Hazard/Risk Ratio</format>"), tabName="ORHR")
),
menuItem(HTML("<format style='font-size:13pt'>Display</format>"), tabName="Display", icon = icon("eye"),
menuSubItem(HTML("<format style='font-size:12pt'>Show</format>"), tabName="Show"),
menuSubItem(HTML("<format style='font-size:12pt'>Format</format>"), tabName="Format"),
menuSubItem(HTML("<format style='font-size:12pt'>Decimals</format>"), tabName="Decimals"),
menuSubItem(HTML("<format style='font-size:12pt'>Labels</format>"), tabName="Labels")
),
##
div(id="PlotHeader",style="padding-top:5px",
uiOutput("PlotHeaderText"),
div(style="border: 1px solid white;height:0px; margin-top:-3px; margin-bottom:0px")
),
menuItem(HTML("<format style='font-size:13pt'>Variable</format>"), tabName="PlotVariables", icon = icon("bars")),
menuItem(HTML("<format style='font-size:13pt'>Groups</format>"), tabName="PlotGroups", icon = icon("user-friends")),
##
div(id="SNPsHeader",style="padding-top:5px",
uiOutput("SNPsHeaderText"),
div(style="border: 1px solid white;height:0px; margin-top:-3px; margin-bottom:0px")
),
menuItem(HTML("<format style='font-size:13pt'>Variables</format>"), tabName="SNPsVariables", icon = icon("bars")),
menuItem(HTML("<format style='font-size:13pt'>Groups</format>"), tabName="SNPsGroups", icon = icon("user-friends")),
menuItem(HTML("<format style='font-size:13pt'>Options</format>"), tabName="SNPsOptions", icon=icon("gears"))
)
),
## body
body = dashboardBody(
setShadow(class = "dropdown-menu"),
# cg_theme,
tags$head(tags$style(HTML('.content-wrapper, .right-side {background-color: white;}'))),
### Home ####
div(id="homePanel",
HTML("<p style='text-align: center;><format color:#357CA5; font-family: Knewave; font-size: 40pt; font-style: normal; font-variant: normal;'>compareGroups WUI</format></p>"),
HTML("<h3 style='text-align: center;><format style='text-align: center'><i><strong>Web User Interface to explore data and create descriptive tables with <code>compareGroups</code> package</strong></format></i></h3>"),
includeMarkdown("home.md")
),
### Table ####
shinyjs::hidden(div(style="margin-top:1%", id="descrTableBox",
shinyhelper::helper(flipBox(id=1,
main_img = "",
header_img = "",
front_title = "Descriptive table",
back_title = "Variable information",
front_btn_text="Go to variable information",
back_btn_text="Go to descriptive table",
uiOutput("table"),
back_content=tagList(
uiOutput("sumtab")
)
),title="Descriptive table", type="markdown", content="descrTablehelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px")
)),
#### Data ####
shinyjs::hidden(div(id="showDataPanel",
shinyhelper::helper(uiOutput("valuesextui"),title="Data Panel", type="markdown", content="DataPanelhelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
bsAlert("dataAlert")
)),
#### Plot #####
shinyjs::hidden(div(id="showPlotPanel",
shinyhelper::helper(plotOutput("plot", height=600, width=800),title="Plot Panel", type="markdown", content="PlotPanelhelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px")
)),
##### SNPs #####
shinyjs::hidden(div(id="showSNPsPanel",
shinyhelper::helper(verbatimTextOutput("restabSNPs"),title="SNPs Panel", type="markdown", content="SNPsPanelhelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px")
))
),
#########################################
########### right side bar ##############
controlbar = dashboardControlbar(id="rightPanel",
skin = "dark",overlay = FALSE, width=400,
hidden(div(style="margin-left:10%; margin-right:-10%; width:70%",sliderInput("leftPanelWidth", HTML("<format style='color:white'>Middle Panel width</format>"), value=30, min=0, max=100))),
# bsButton("toggleLeftPanel","",type = "action",icon=icon("angle-double-left"),size="extra-small"),
# shinyBS::bsTooltip("toggleLeftPanel","Hide panel"),
column(1, " "),
column(11,
#### Load data #####
conditionalPanel("input.leftmenu=='LoadData'",
shinyhelper::helper(h3("Load data"), title="Load data", type="markdown", content="loadhelp", size="l", colour="#3c8dbc", style="font-size:14pt; margin-right:10px"),
hr(),
hidden(div(id="resetbtnPanel",
actionButton("resetbtn","Load a new dataset"),
br(),
"In order to read a new data set, all parameteres will be resetted",
hr()
)),
div(id="LoadDataPanel",
HTML(
'<div id="exampledata" class="form-group shiny-input-radiogroup shiny-input-container" style="width:100%;text-align:justify">
<label class="control-label" for="exampledata"></label>
<div class="shiny-options-group">
<div class="radio">
<label>
<input type="radio" name="exampledata" value="Own data" checked="checked"/>
<span>Upload your own data set from a file</span>
</label>
<div><br><font style="weight:bold">...or choose an example data set</font></p></div>
</div>
<div class="radio" style="margin-left:10px">
<label>
<input type="radio" name="exampledata" value="REGICOR"/>
<span>REGICOR</span>
</label>
</div>
<div class="radio" style="margin-left:10px">
<label>
<input type="radio" name="exampledata" value="SNPS"/>
<span>SNPS</span>
</label>
</div>
</div>
</div>'
),
fileInput("files", ""),
div(id="ownPanel",
selectInput("datatype", "Data format", c('SPSS'='*.sav', 'TEXT'='*.txt','EXCEL'='*.xls','Stata'='*.dta','R'='*.rda'),'*.sav'),
conditionalPanel("input.datatype=='*.xls'", # EXCELL
wellPanel(id="LoadDataOptionsExcel",
HTML('<p style="font-style:Bold; font-size:18px">Excel options</p>'),
selectInput("tablenames", "Choose the table to read:", choices = NULL, selectize=FALSE),
checkboxInput('headerexcel', 'Has column headers', TRUE),
numericInput("skipexcel", "Number of rows to skip", value=0),
textInput("missvalueexcel", HTML("Missing Data String (e.g. <i>NA</i>)"), ""),
checkboxInput("stringToFactorexcel", "Convert string variables to factor", value=TRUE)
)
),
conditionalPanel("input.datatype=='*.txt'",
wellPanel(id="LoadDataOptionsTxt",
HTML('<p style="font-style:Bold; font-size:18px">TEXT options</p>'),
downloadButton("previewtxtdown","Preview data"),
checkboxInput('header', 'Has column headers', TRUE),
numericInput("skip", "Number of rows to skip", value=0),
textInput("missvalue", HTML("Missing Data String (e.g. <i>NA</i>)"), ""),
selectInput('sep', 'Column Separator', c(Comma=',', Semicolon=';', Tab='\t', Other='o'), ','),
conditionalPanel(
condition = "input.sep == 'o'",
textInput("sepother", "Specify separator character","")
),
selectInput('dechar', 'Decimal point character', c('Comma'=',', 'Dot'='.'), '.'),
selectInput('quote', 'Values in Quotes?', c("None"=1, "Double"=2, "Single"=3), 2),
radioButtons("encoding", "Encoding", c('default'='default','latin1'='latin1','utf8'='utf8'),'default',inline=TRUE)
)
)
),
actionButton("loadok","Read data")
),
br()
),
#### Filter data ######
conditionalPanel("input.leftmenu=='FilterData'",
shinyhelper::helper(h3("Filter data"), title="Filter data", type="markdown", content="filterhelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
textAreaInput("filterexpr", "Write R code", placeholder = "Some R code or left in blank to remove the filter"),
tags$table(
tags$tr(
tags$td(shinyBS::bsButton("filterdataok", "Filter", width=80)),
tags$td(HTML(" ")),
tags$td(shinyBS::bsButton("removefilterdataok", "Clean", icon=icon("brush"), width=80, style="warning"))
)
),
br()
),
#### Recode variables ######
conditionalPanel("input.leftmenu=='RecodeVars'",
shinyhelper::helper(h3("Recode variables"), title="Recode variables", type="markdown", content="recodehelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
textInput("newvarname", "Variable name"),
textInput("newvarlabel", "Variable label"),
textAreaInput("newvarexpr", "Write R code"),
tags$table(
tags$tr(
tags$td(shinyBS::bsButton("newvarok", "Create", width=80)),
tags$td(HTML(" ")),
tags$td(shinyBS::bsButton("removenewvarok", "Clean", icon=icon("brush"), width=80, style="warning"))
)
),
br(),
hr(),
selectInput("vartofactor","Choose variable to convert to factor",choices = NULL),
actionButton("vartofactorbtn","Convert")
),
#### Described variables ######
conditionalPanel("input.leftmenu=='DescribedVariables'",
shinyhelper::helper(h3("Selected described variables"), title="Selected described variables", type="markdown", content="selecthelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
div(id="DescribedVariablesPanel",
fluidRow(
fluidRow(
tags$table(
tags$tr(
tags$td(HTML("  ")),
tags$td(width="50px",shinyBS::bsButton("selevarsAll","All",style="info",size="extra-small",block=TRUE)),
tags$td(HTML(" ")),
tags$td(width="50px",shinyBS::bsButton("selevarsNone","None",style="danger",size="extra-small",block=TRUE))
)
)
),
fluidRow(
column(12,
selectizeInput("selevars",NULL,width="100%",choices=NULL,multiple=TRUE,options=list(plugins=list('remove_button', 'drag_drop')))
)
),
column(3, offset=0,
shinyBS::bsButton("changeselevarsok","Update")
)
)
),
br()
),
#### Response Variable ######
conditionalPanel("input.leftmenu=='ResponseVariable'",
shinyhelper::helper(h3("Define groups"), title="Define groups", type="markdown", content="responsehelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
div(id="ResponseVariablePanel",
radioGroupButtons("resptype", "", c("None","Group","Survival"),justified=TRUE, checkIcon=list(yes=icon("ok",lib = "glyphicon"))),
conditionalPanel("input.resptype == 'Group'",
numericInput('maxgroups',"Maximum number of groups:",value=5,min=2,max=10),
selectInput("gvar", "Choose the grouping variable:", choices = NULL, selectize=FALSE),
actionLink("ResponseVariableORPanelBtn",HTML("<format style='color:white'>OR/RR options</format>")),
wellPanel(id="ResponseVariableORPanel",
checkboxInput('computeratio', 'Compute OR/RR:', FALSE),
conditionalPanel(
condition = "input.computeratio == true",
selectInput("gvarcat", "OR/RR ref. cat:", choices = NULL, selectize=FALSE),
radioButtons("riskratio","OR or RR", c("OR", "RR"), inline=TRUE),
conditionalPanel(
"input.riskratio=='OR'",
selectInput("oddsratiomethod","OR method",c("midp", "fisher", "wald", "small"))
),
conditionalPanel(
"input.riskratio=='RR'",
selectInput("riskratiomethod","RR method",c("wald", "small", "boot"))
)
)
)
),
conditionalPanel("input.resptype=='Survival'",
selectInput("varseletime", "Select time-to-event variable", choices = NULL, multiple = FALSE, selectize=FALSE),
selectInput("varselestatus", "Select status variable", choices = NULL, multiple = FALSE, selectize=FALSE),
selectInput("statuscat", "Select event category/ies", choices=NULL, multiple = TRUE, selectize=FALSE)
),
actionButton("changeresp","Update")
),
br()
),
#### Stratas ######
conditionalPanel("input.leftmenu=='StrataVariable'",
shinyhelper::helper(h3("Define strata"), title="Define strata", type="markdown", content="stratahelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
div(id="StrataVariablePanel",
radioGroupButtons("stratatype", "", c("None","Strata"), justified=TRUE, checkIcon=list(yes=icon("ok",lib = "glyphicon"))),
conditionalPanel("input.stratatype=='Strata'",
numericInput('maxstrata',"Maximum number of stratas:",value=5,min=2,max=10),
selectInput("svar", "Choose the strata variable:", choices = NULL, selectize=FALSE)
),
actionButton("changestrata","Update")
),
br()
),
#### Type ####
conditionalPanel("input.leftmenu=='Type'",
shinyhelper::helper(h3("Define the type of variables"), title="Define the type of variables", type="markdown", content="typehelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
div(id="TypePanel",
shinyWidgets::pickerInput("varselemethod", "Select variables", choices=NULL, multiple=TRUE,
options = pickerOptions(actionsBox=TRUE, title="Select variables", header="",liveSearch=TRUE)
),
selectInput("method", "Select type of chosen variable/s", c("Normal","Non-normal","Categorical","NA"), selectize=FALSE),
conditionalPanel("input.method=='NA'",
fluidRow(
column(6,numericInput("alpha","alpha",value=0.05,min=0,max=1,step=0.005)),
column(6,numericInput("mindis","min categories",value=5,min=1,max=10))
)
),
actionButton("changemethod","Update")
),
br()
),
#### Hide ####
conditionalPanel("input.leftmenu=='Hide'",
shinyhelper::helper(h3("Hide settings"), title="Hide settings", type="markdown", content="hidehelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
div(id="HidePanel",
div(
fluidRow(
column(6, selectInput("varselehide", "variable", choices = NULL, multiple = FALSE, selectize=FALSE)),
column(6, selectInput("hidecat", "category", choices = NULL, "<<None>>", selectize=FALSE))
),
textInput('hideno', "Hide 'no' category", ''),
actionButton("changehide","Update")
)
),
br()
),
#### Subset ####
conditionalPanel("input.leftmenu=='Subset'",
shinyhelper::helper(h3("Variable subset settings"), title="Variable subset settings", type="markdown", content="subsethelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
div(id="SubsetPanel",
HTML('<div style="height:10px"></div>'),
shinyWidgets::pickerInput("varselevarsubset", "Select variables", choices=NULL, multiple=TRUE,
options = pickerOptions(actionsBox=TRUE, title="Select variables", header="",liveSearch=TRUE)
),
br(),
textAreaInput("varsubset", label="Write subset expression", value = ""),
tags$table(
tags$tr(
tags$td(shinyBS::bsButton("changevarsubset","Update", width=80)),
tags$td(HTML(" ")),
tags$td(shinyBS::bsButton("removechangevarsubset","Clean", width=80, icon=icon("brush"), style="warning"))
)
)
),
br()
),
#### Odds Ratio / Hazard Ratio ####
conditionalPanel("input.leftmenu=='ORHR'",
shinyhelper::helper(h3("Odds/Risk/Hazard Ratio settings"), title="Odds/Risk/Hazard Ratio settings", type="markdown", content="ratiohelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
div(id="RatioPanel",
conditionalPanel("input.computeratio || input.resptype=='Survival'",
HTML('<div style="height:10px"></div>'),
bsCollapse(id="ratioAccordion", open="xxx", multiple=FALSE,
bsCollapsePanel(value="Reference category", style="primary", title=HTML('<p style="font-color:black; height:10px">Reference category</p>'),
fluidRow(
column(6, selectInput("varselerefratio", "variable", choices=NULL, multiple=FALSE, selectize=FALSE)),
column(6, selectInput("refratiocat", "category", choices=NULL, selectize=FALSE))
),
actionButton("changeratiocat","Update")
),
bsCollapsePanel(value="Multiplying factor", style="primary", title=HTML('<p style="font-color:black; height:10px">Multiplying factor</p>'),
shinyWidgets::pickerInput("varselefactratio", "Select variables", choices=NULL, multiple=TRUE,
options = pickerOptions(actionsBox=TRUE, title="Select variables", header="",liveSearch=TRUE)
),
numericInput("factratio", label=NULL, value = 1, min=1, max=100, width=100),
actionButton("changefactratio","Update")
)
)
),
conditionalPanel("!input.computeratio && input.resptype!='Survival'",
helpText("No binary non survival response variable selected")
)
),
br()
),
#### Show ####
conditionalPanel("input.leftmenu=='Show'",
shinyhelper::helper(h3("Show settings"), title="Show settings", type="markdown", content="showhelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
div(id="ShowPanel",
fluidRow(
column(6,checkboxInput('showall', 'ALL', TRUE)),
column(6,checkboxInput('showpoverall', 'p-overall', TRUE))
),
fluidRow(
column(6,checkboxInput('showdesc', 'Descriptives', TRUE)),
column(6,checkboxInput('showptrend', 'p-trend', FALSE))
),
fluidRow(
column(6,checkboxInput('showratio', 'OR/RR/HR', FALSE)),
column(6,
conditionalPanel("input.showratio == true",
checkboxInput('showpratio', 'OR/RR/HR p-value', FALSE)
)
)
),
fluidRow(
column(6,checkboxInput('shown', 'Available', FALSE)),
column(6,checkboxInput('includemiss', "Add 'Missing' category", FALSE))
),
fluidRow(
column(6,checkboxInput('showpmul', 'Pairwise p-value', FALSE)),
column(6,
conditionalPanel("input.showpmul == true",
checkboxInput('pcorrected', 'Correct pairwise p-values', FALSE)
)
)
),
fluidRow(
column(6,checkboxInput('simplify', 'Simplify', FALSE)),
column(6,"")
),
actionButton("changeshow","Update")
),
br()
),
#### Format ####
conditionalPanel("input.leftmenu=='Format'",
shinyhelper::helper(h3("Format settings"), title="Format settings", type="markdown", content="formathelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
div(id="FormatPanel",
HTML('<div style="height:10px"></div>'),
fluidRow(
column(6,checkboxInput('showci', 'Report Confidence Interval', FALSE)),
column(6,
conditionalPanel('input.showci',
div(style="color:white",sliderInput('conflevel', 'Confidence level', min=50, max=100, value=95, step=1))
)
)
),
numericInput("timemax","Time for survival variables",NA),
conditionalPanel("!input.showci",
bsCollapse(id="formatAccordion",multiple=FALSE,open="xxx",
bsCollapsePanel(value="Frequencies", style="primary", title=HTML('<p style="font-color:black; height:10px">Frequencies</p>'),
radioButtons("type", "", c("%" = 1, "n (%)" = 2, "n"=3), selected="n (%)",inline = TRUE),
radioButtons("byrow", "Percentages by:", choices=c("columns","rows","total"), inline = TRUE)
),
bsCollapsePanel(value="Mean, standard deviation", style="primary", title=HTML('<p style="font-color:black; height:10px">Mean, standard deviation</p>'),
radioButtons("sdtype", "", c("Mean (SD)"=1,"Mean\u00B1SD"=2), selected="Mean (SD)",inline = TRUE)
),
bsCollapsePanel(value="Median [a, b]", style="primary", title=HTML('<p style="font-color:black; height:10px">Median [a, b]</p>'),
fluidRow(
column(6,numericInput("Q1", label="[a, ]:", value = 25, min=0, max=49)),
column(6,numericInput("Q3", label="[ , b]:", value = 75, min=51, max=100))
),
fluidRow(
column(6,radioButtons("qtype1", "brackets", c("Squared"=1,"Rounded"=2), selected="Squared")),
column(6,radioButtons("qtype2", "separator", c("Semicolon"=1,"Comma"=2,"Slash"=3), selected="Semicolon"))
)
),
bsCollapsePanel(value="Date variables", style="primary", title=HTML('<p style="font-color:black; height:10px">Date variables</p>'),
selectInput("Dateformat", "Date format", choices=c("d-m-Y","m-d-Y","Y-m-d","d-mon-Y","mon-d-Y"), selected="d-mon-Y")
)
)
),
checkboxInput("extralabels","Show variable format indicators", FALSE),
conditionalPanel("input.extralabels",
wellPanel(id="extralabelsPanel",
textInput("extralabelmean","Mean and standard deviation", "Mean (SD)"),
textInput("extralabelmedian","Median and quartiles", "Median [25th; 75th]"),
textInput("extralabelperc","Frequencies", "N (%)"),
textInput("extralabelsurv","Survival variable", "Incidence")
)
),
actionButton("changeformat","Update")
),
br()
),
#### Decimals ####
conditionalPanel("input.leftmenu=='Decimals'",
shinyhelper::helper(h3("Decimals"), title="Decimals", type="markdown", content="decimalshelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
div(id="DecimalsPanel",
HTML('<div style="height:10px"></div>'),
bsCollapse(id="decimalsAccordion", open="xxx", multiple=FALSE,
bsCollapsePanel(value="p-values", style="primary", title=HTML('<p style="font-color:white; height:10px">p-values</p>'),
numericInput("pvaldigits", label="Number of decimals", value = 3, min=1, max=20),
actionButton("changepvalsdigits","Update")
),
bsCollapsePanel(value="Descriptives", style="primary", title=HTML('<p style="font-color:white; height:10px">Descriptives</p>'),
shinyWidgets::pickerInput("varseledescdigits", "", choices=NULL, multiple=TRUE,
options = pickerOptions(actionsBox=TRUE, title="Select variables", header="",liveSearch=TRUE)
),
numericInput("descdigits", label=NULL, value = -1, min=-1, max=10, width=100),
actionButton("changedescdigits","Update")
),
bsCollapsePanel(value="OR/RR/HR", style="primary", title=HTML('<p style="font-color:white; height:10px">OR/RR/HR</p>'),
shinyWidgets::pickerInput("varseleratiodigits", "", choices=NULL, multiple=TRUE,
options = pickerOptions(actionsBox=TRUE, title="Select variables", header="",liveSearch=TRUE)
),
numericInput("ratiodigits", label=NULL, value = -1, min=-1, max=10, width=100),
actionButton("changeratiodigits","Update")
)
)
),
br()
),
#### Labels ####
conditionalPanel("input.leftmenu=='Labels'",
shinyhelper::helper(h3("Labels"), title="Labels", type="markdown", content="labelshelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
div(id="LabelsPanel",
textInput("alllabel", label="All:", value="[ALL]"),
textInput("poveralllabel", label="overall p-value:", value="p.overall"),
textInput("ptrendlabel", label="p-value for trend:", value="p.trend"),
textInput("pratiolabel", label="OR/RR/HR p-value:", value="p.ratio"),
textInput("Nlabel", label="Available data:", value="N"),
textInput("captionlabel", label="Caption:", value="NULL"),
tags$table(
tags$tr(
tags$td(shinyBS::bsButton("changeLabels","Apply", width=80)),
tags$td(HTML(" ")),
tags$td(shinyBS::bsButton("refreshLabels","Refresh", style="warning", width=80))
)
)
),
br()
),
#### PlotVariables #####
conditionalPanel("input.leftmenu=='PlotVariables'",
shinyhelper::helper(h3("Plot variable"), title="Plot variable", type="markdown", content="PlotVariableshelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
div(id="PlotVariablesPanel",
HTML('<div style="height:10px"></div>'),
selectInput("plotselevars", "Select variable", choices=NULL),
actionButton("plotvarchange","Update")
),
br()
),
#### PlotGroups #####
conditionalPanel("input.leftmenu=='PlotGroups'",
shinyhelper::helper(h3("Plot Groups"), title="Plot Groups", type="markdown", content="PlotGroupshelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
div(id="PlotGroupsPanel",
HTML('<div style="height:10px"></div>'),
radioGroupButtons("plotresptype", "", c("None","Group","Survival"),justified=TRUE, checkIcon=list(yes=icon("ok",lib = "glyphicon"))),
br(),
conditionalPanel("input.plotresptype == 'Group'",
numericInput('plotmaxgroups',"Maximum number of groups:",value=5,min=2,max=10),
selectInput("plotgvar", "Choose the grouping variable:", choices = NULL, selectize=FALSE)
),
conditionalPanel("input.plotresptype=='Survival'",
selectInput("plotvarseletime", "Select time-to-event variable", choices = NULL, multiple = FALSE, selectize=FALSE),
selectInput("plotvarselestatus", "Select status variable", choices = NULL, multiple = FALSE, selectize=FALSE),
selectInput("plotstatuscat", "Select event category", choices=NULL, multiple = TRUE, selectize=FALSE)
),
actionButton("plotgroupschange","Update")
),
br()
),
#### SNPs Variables #####
conditionalPanel("input.leftmenu=='SNPsVariables'",
shinyhelper::helper(h3("SNPs Variables"), title="SNPs Variables", type="markdown", content="SNPsVariableshelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
div(id="SNPsVariablesPanel",
HTML('<div style="height:10px"></div>'),
fluidRow(
tags$table(
tags$tr(
tags$td(HTML("  ")),
tags$td(width="50px",shinyBS::bsButton("snpsselevarsAll","All",style="info",size="extra-small",block=TRUE)),
tags$td(HTML(" ")),
tags$td(width="50px",shinyBS::bsButton("snpsselevarsNone","None",style="danger",size="extra-small",block=TRUE))
)
)
),
fluidRow(
selectizeInput("snpsselevars",NULL,width="100%",choices=NULL,multiple=TRUE,options=list(plugins=list('remove_button', 'drag_drop')))
),
actionButton("snpsvarchange","Update")
),
br()
),
#### SNPs Groups #####
conditionalPanel("input.leftmenu=='SNPsGroups'",
shinyhelper::helper(h3("SNPs Groups"), title="SNPs Groups", type="markdown", content="SNPsGroupshelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
div(id="SNPsGroupsPanel",
HTML('<div style="height:10px"></div>'),
radioGroupButtons("snpsresptype", "", c("None","Group"),justified=TRUE, checkIcon=list(yes=icon("ok",lib = "glyphicon"))),
conditionalPanel("input.snpsresptype == 'Group'",
numericInput('snpsmaxgroups',"Maximum number of groups:",value=5,min=2,max=10),
selectInput("snpsgvar", "Choose the grouping variable:", choices = NULL, selectize=FALSE)
),
actionButton("snpsgroupschange","Update")
),
br()
),
##### SNPs options #####
conditionalPanel("input.leftmenu=='SNPsOptions'",
shinyhelper::helper(h3("SNPs Options"), title="SNPs Options", type="markdown", content="SNPsOptionshelp", size="l", colour="#3C8DBC", style="font-size:14pt; margin-right:10px"),
hr(),
div(id="SNPsOptionsPanel",
textInput("sepSNPs","Allele separator"),
bsButton("snpsoptionschange","Update")
),
br()
)
)
),
### footer ###
footer = dashboardFooter(
left = HTML("
<b>By Isaac Subirana</b><br>CIBERCV, IMIM-Parc de Salut Mar, Barcelona<br>
<hr>
<table style='margin-left: auto;margin-right: auto'>
<tr>
<td style='margin-left:5px'><a title='CIBERCV' href='https://www.cibercv.es/'><img alt='CIBERCV' src='logo-cibercv.png' width='80%'/></a></td>
<td style='margin-left:10px'><a title='IMIM' href='https://imim.cat/'><img alt='IMIM' src='logo_imim_capsalera.gif' width='80%'/></a></td>
<td style='margin-left:10px'><a title='REGICOR' href='https://regicor.cat//'><img alt='IMIM' src='regicor_logo125.png' width='80%'/></a></td>
</tr>
</table>
"),
right = HTML("Powered by <a href='https://shiny.rstudio.com/'>Shiny</a>")
)
# ,
# ### preloader ###
# enable_preloader = FALSE
)
)
Try the compareGroups package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.