inst/website/ui.R
In oncoclass/hemaClass: One-by-one normalization and classification of hematological malignacies
library(shiny)
library(shinysky)
library(RLumShiny)
#title <- "hemaClass" # Old title :)
title <- HTML(paste0('<span class="rand"',
'style="color: #FF6060; text-decoration: none">',
icon("tint", lib = "glyphicon"), ' hemaClass</span>'))
# Conditions using in classification panel
abc.cond <- "input.getClassifications.indexOf('ABCGCB') != -1"
rtx.cond <- "input.getClassifications.indexOf('Rituximab (R)') != -1"
cyc.cond <- "input.getClassifications.indexOf('Cyclophosphamide (C)') != -1"
dox.cond <- "input.getClassifications.indexOf('Doxorubicin (H)') != -1"
vin.cond <- "input.getClassifications.indexOf('Vincristine (O)') != -1"
dex.cond <- "input.getClassifications.indexOf('Dexamethasone') != -1"
cho.cond <- "input.getClassifications.indexOf('Combined (CHO)') != -1"
shinyUI(
navbarPage(
title = title,
theme = "bootstrap.css",
tabPanel(
'Home',
sidebarLayout(
sidebarPanel(
navlistPanel(
"Information:",
tabPanel("Welcome"),
tabPanel("News"),
tabPanel("Help"),
tabPanel("Publications"),
tabPanel("About"),
well = FALSE,
id = "nlp",
widths = c(12,1)),
width = 4),
mainPanel(
htmlOutput("mpContent")
)
)
), # End tabPanel "Home"
tabPanel(
'Load data',
navbarPage(
'Type of data',
tabPanel(
'CEL files',
sidebarLayout(
sidebarPanel(
h3("Upload .CEL files"),
busyIndicator("Pre-processing .CEL files", wait = 1000),
fileInput("usrFiles",
"Please choose your .CEL files to classify:",
accept = "", multiple = TRUE),
tags$hr(),
conditionalPanel(
condition = "output.showNormMethods == 0",
h4("Please click here to download 4 .CEL files available for
test use"),
tags$a(href = 'http://hemaclass.org/celfiles.zip',
class = "btn btn-default shiny-download-link",
target = "_blank", icon("download"),
'Download test data.')
),
conditionalPanel(
condition = "output.showNormMethods!=0",
h3("RMA Pre-processing"),
selectInput(
"ChooseMethod", "Choose method",
list("Please select" = "blah",
"Use build-in reference" = "standardReference",
"Build a new reference" = "build",
"Upload a reference" = "upload",
"Cohort based RMA" = "RMA"
)
),
conditionalPanel(
condition = "input.ChooseMethod == 'build'",
fileInput("refFiles",
label = "To build a laboratory specific
reference, please upload .CEL files:",
accept = "", multiple = TRUE),
conditionalPanel(
condition = "output.showBuildRefButton!=0",
actionButton("buildreferenceButton",
HTML(paste(icon("cog", lib = "glyphicon"),
"Build reference"))),
conditionalPanel(
condition = "output.showDownloadRefButton!=0",
tags$hr(),
helpText("Download reference to save time on next run:"),
downloadButton('downloadReference',
'Download reference for later use.')
)
)
),
tags$hr()
),
conditionalPanel(
condition = "input.ChooseMethod == 'upload'",
fileInput("refUpload",
"Upload the file containing the reference:",
accept = "", multiple = FALSE),
tags$hr()
),
conditionalPanel(
condition = "input.ChooseMethod == 'standardReference'",
selectInput(
"ChooseReference", "Choose a reference",
list("LLMPP CHOP" = "LLMPPCHOP",
"LLMPP R-CHOP" = "LLMPPRCHOP",
"IDRC" = "IDRC",
"MDFCI" = "MDFCI",
"CHEPRETRO" = "CHEPRETRO",
"UAMS" = "UAMS"
)),
tags$hr()
),
conditionalPanel(
condition = "output.showNormButton!=0",
helpText("Normalize the files according to the chosen
reference:"),
actionButton("normalizeButton",
HTML(paste(icon("cog", lib = "glyphicon"),
"Normalize files"))),
tags$br(),
tags$hr(),
sliderInput("rle.iqr.threshold",
"Keep samples with RLE IQR less than:",
step = 0.01,
min = 0, max = 1.5, value = 0.6)
)
),
mainPanel(
shinyalert("shinyalertUploadCel",
click.hide = FALSE),
shinyalert("shinyalertSelectReference",
click.hide = FALSE),
shinyalert("shinyalertUploadCelSucces",
auto.close.after = 10),
shinyalert("shinyalertSelectReferenceSucess",
auto.close.after = 10),
shinyalert("shinyalertNormalizationSuccess",
click.hide = FALSE, auto.close.after = 10),
dataTableOutput("rle.stats"),
conditionalPanel(
condition = "output.showErrorprints!=0",
verbatimTextOutput("start"),
verbatimTextOutput("start2"),
verbatimTextOutput("showBuildRefButton"),
verbatimTextOutput("showNormButton"),
verbatimTextOutput("showDownloadRefButton"),
verbatimTextOutput("showNormMethods"),
verbatimTextOutput("showErrorprints"))
)
)
), # End tabPanel "CEL files"
# navbarMenu(
# 'Metadata',
# tabPanel(
# 'Input manually',
# sidebarLayout(
# sidebarPanel(
# helpText("You may also calculate IPI from clinical features."),
# checkboxInput(inputId = "IPIcalc",
# label = "Calculate IPI", value = FALSE),
# helpText("Additional columns"),
# select2Input("Additionalcolumns",
# "Type in the names.",
# choices = c("Age","LDH"),
# selected = "IPI"),
# conditionalPanel(
# condition = "input.IPIcalc",
# helpText("You may change the settings for the IPI calculation."),
# numericInput(inputId = "AGE.cut", label = "Get point when age > x", 60),
# numericInput(inputId = "ECOG.cut", label = "Get point when ECOG > x", 1),
# numericInput(inputId = "LDH.cut", label = "Get point when LDH > x", 1),
# numericInput(inputId = "N.Extra.Nodal.cut",
# label = "Get point when number of extra nodal sites > x", 1),
# numericInput(inputId = "Stage.cut", label = "Get point when Stage > x", 2)
# ),
# tags$hr(),
# downloadButton('downloadMetadataManual', 'Download metadata')
# ),
# mainPanel(
# shinyalert("shinyalertInputMeta", click.hide = FALSE),
# conditionalPanel(
# condition = "input.IPIcalc",
# helpText("Input the clinical features for each patient below.",
# "The IPI values are calculated automatically.")
# ),
# conditionalPanel(
# condition = "!input.IPIcalc",
# helpText("Input the IPI scores for each patient below.")
# ),
# div(class = "well container-fluid",
# hotable("hotableMetadataManual"))
# )
# )
# ), # End tabPanel "Input manually"
# tabPanel(
# 'Upload metadata',
# sidebarPanel(
# h4("Upload file containing metadata"),
# busyIndicator("Processing the metadata", wait = 1000),
# fileInput("usrMeta",
# "Please upload the file storing the metadata",
# accept = "", multiple = FALSE),
# conditionalPanel(
# condition = "output.showReadMetaMethods=='txt'",
# helpText("Does the file contain a header"),
# checkboxInput("ExttxtHeader", label = "header",
# value = TRUE),
# selectInput(
# "ExttxtSep", "Choose separater",
# list("Tabulate" = "\t", "Semicolon" = ";",
# "comma" = ",", "Other" = "Other")),
# conditionalPanel(
# condition = "input.ExttxtSep=='Other'",
# textInput(inputId = "ExttxtSepOther",
# "Type in the separator", value = ";"))
# ),
# conditionalPanel(
# condition = "output.showReadMetaMethods=='xls'|| output.showReadMetaMethods=='xlsx'",
# textInput(inputId = "ExtXLSsheet",
# "The sheet you want to read", 1)
# ),
# uiOutput("MetaUploadCelFileNames")
# ), # End sidebarPanel "Upload file containing metadata"
# mainPanel(
# shinyalert("shinyalertUploadMeta", click.hide = FALSE),
# shinyalert("shinyalertUploadMetaData", click.hide = FALSE),
# helpText("The Output below shows how the data is read."),
# dataTableOutput("uploadMetaData"),
# conditionalPanel(
# condition = "output.showReadMetaPrint!=0",
# verbatimTextOutput("showReadMetaPrint"),
# verbatimTextOutput("showReadMetaMethods")
# )
# )
# ) # End tabPanel "Upload metadata"
# ), # End tabPanel "Metadata"
tabPanel(
'Build-in test data',
sidebarLayout(
sidebarPanel(
busyIndicator("Loading data", wait = 1000),
helpText("Select the dataset you want to analyse"),
uiOutput("buildindataselector"),
radioButtons("buildinShowData", "Show",
choices = list("Metadata" = "Metadata",
"Gene Expression" = "GEP"),
selected = "GEP")
),
mainPanel(
conditionalPanel(
condition = "input.buildinShowData=='Metadata'",
dataTableOutput("buildinMetaData")
),
conditionalPanel(
condition = "input.buildinShowData=='GEP'",
dataTableOutput("buildinGEP")
)
)
)
) # End tabPanel "Build-in data"
# tabPanel(
# 'Metadata in use',
# sidebarLayout(
# sidebarPanel(
# helpText("Select the dataset you want to use"),
# uiOutput("metadataselector")
# ),
# mainPanel(
# dataTableOutput("MetaDataInUseOut")
# )
# )
# ) # End tabPanel "Metadata in use"
) # End navbarPage "Type of data"/"Load data"
), # End tabPanel "Load data"
tabPanel(
'Results',
navbarPage(
'Classification results',
tabPanel(
'Estimated probabilities',
sidebarLayout(
sidebarPanel(
condition = "input.conditionedPanels == 'Classification results'",
h3("Classification systems:"),
checkboxGroupInput(
"getClassifications",
label = "Perform classifications:",
choices = c("BAGS",
"ABC / GCB (COO)" = "ABCGCB",
"ABC / GCB / GCB-CC / GCB-CB (Extended COO)" =
"ABCGCB2",
"Rituximab (R)",
"Cyclophosphamide (C)",
"Doxorubicin (H)",
"Vincristine (O)",
# "Dexamethasone",
"Combined (CHO)",
"Melphalan"
),
selected = "BAGS"
),
conditionalPanel(
condition = paste(abc.cond, rtx.cond, cyc.cond, dox.cond,
vin.cond, dex.cond, cho.cond, sep = "|"),
h3("Classification options:")
),
conditionalPanel(
condition = abc.cond,
sliderInput("nc.range",
"ABC/GCB, range of non classified:",
step = 0.01,
min = 0, max = 1, value = c(0.1, 0.9))
),
conditionalPanel(
condition = rtx.cond,
checkboxInput(inputId = "HSCorrected",
label = strong("Rituximap, human serum
corrected"),
value = TRUE),
checkboxInput(inputId = "Lysis",
label = strong("Rituximap, lysis based"),
value = FALSE),
sliderInput("Rituximab.range",
"Rituximab, range of intermediate:",
step = 0.01,
min = 0, max = 1, value = c(0.38, 0.54))
),
conditionalPanel(
condition = cyc.cond,
sliderInput("Cyclophosphamide.range",
"Cyclophosphamide, range of intermediate:",
step = 0.01,
min = 0, max = 1, value = c(0.33,0.55))
),
conditionalPanel(
condition = dox.cond,
sliderInput("Doxorubicin.range",
"Doxorubicin, range of intermediate:",
step = 0.01,
min = 0, max = 1, value = c(0.14, 0.9))
),
conditionalPanel(
condition = vin.cond,
sliderInput("Vincristine.range",
"Vincristine, range of intermediate:",
step = 0.01,
min = 0, max = 1, value = c(0.46, 0.62))
),
conditionalPanel(
condition = dex.cond,
sliderInput("Dexamethasone.range",
"Dexamethasone, range of intermediate:",
step = 0.01,
min = 0, max = 1, value = c(0.25, 0.75))
),
conditionalPanel(
condition = cho.cond,
sliderInput("Combined.range",
"Combined CHO, range of intermediate:",
step = 0.01,
min = 0, max = 1, value = c(0.09, 0.93))
),
br(),
conditionalPanel(
condition = paste(abc.cond, rtx.cond, cyc.cond, dox.cond,
vin.cond, dex.cond, cho.cond, sep = "|"),
helpText("Click to reset ranges to default:"),
actionButton("resetButton",
HTML(paste(icon("repeat", lib = "glyphicon"),
"Reset")))
),
br(),
tags$hr(),
downloadButton('downloadData', 'Download classification results')
), # End sidebarPanel
mainPanel(
shinyalert("shinyalertResults", click.hide = FALSE),
dataTableOutput("results")
) # End mainPanel
) # End sidebarLayout
)#, # End Estimated probabilites tabPanel
# tabPanel(
# 'Patient summaries',
# sidebarLayout(
# sidebarPanel(
# uiOutput("patientSummaryIPI"),
# uiOutput("patientSummarySelect"),
# hr(),
# jscolorInput("jscolorInputPS",
# label =
# strong("Select colours used for the summaries:"),
# value = "#9199D1"),
# br(),
# br(),
# actionButton(inputId = "SelectColourPS",
# HTML(paste(icon("chevron-down", lib = "glyphicon"),
# "Add colour"))),
# br(),
# uiOutput("SelectedColoursPS"),
# hr(),
# sliderInput("surv.read",
# label = "Survival at (years)",
# step = 3/12, min = 0, max = 7, value = 3)
# ),
# mainPanel(
# shinyalert("shinyalertPatientSummaries", click.hide = FALSE),
# uiOutput("patientSummaries"),
# plotOutput("patientSummaryPlot"),
# uiOutput("patientSummariesExplanation")
# )
# )
# )
)
), # End tabPanel "Results"
id = "navbarPanels",
windowTitle = "hemaClass.org",
inverse = TRUE,
fluid = TRUE,
footer = ""
) # End navbarPage
)
oncoclass/hemaClass documentation built on May 24, 2019, 2:19 p.m.
R Package Documentation
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library(shiny)
library(shinysky)
library(RLumShiny)
#title <- "hemaClass" # Old title :)
title <- HTML(paste0('<span class="rand"',
'style="color: #FF6060; text-decoration: none">',
icon("tint", lib = "glyphicon"), ' hemaClass</span>'))
# Conditions using in classification panel
abc.cond <- "input.getClassifications.indexOf('ABCGCB') != -1"
rtx.cond <- "input.getClassifications.indexOf('Rituximab (R)') != -1"
cyc.cond <- "input.getClassifications.indexOf('Cyclophosphamide (C)') != -1"
dox.cond <- "input.getClassifications.indexOf('Doxorubicin (H)') != -1"
vin.cond <- "input.getClassifications.indexOf('Vincristine (O)') != -1"
dex.cond <- "input.getClassifications.indexOf('Dexamethasone') != -1"
cho.cond <- "input.getClassifications.indexOf('Combined (CHO)') != -1"
shinyUI(
navbarPage(
title = title,
theme = "bootstrap.css",
tabPanel(
'Home',
sidebarLayout(
sidebarPanel(
navlistPanel(
"Information:",
tabPanel("Welcome"),
tabPanel("News"),
tabPanel("Help"),
tabPanel("Publications"),
tabPanel("About"),
well = FALSE,
id = "nlp",
widths = c(12,1)),
width = 4),
mainPanel(
htmlOutput("mpContent")
)
)
), # End tabPanel "Home"
tabPanel(
'Load data',
navbarPage(
'Type of data',
tabPanel(
'CEL files',
sidebarLayout(
sidebarPanel(
h3("Upload .CEL files"),
busyIndicator("Pre-processing .CEL files", wait = 1000),
fileInput("usrFiles",
"Please choose your .CEL files to classify:",
accept = "", multiple = TRUE),
tags$hr(),
conditionalPanel(
condition = "output.showNormMethods == 0",
h4("Please click here to download 4 .CEL files available for
test use"),
tags$a(href = 'http://hemaclass.org/celfiles.zip',
class = "btn btn-default shiny-download-link",
target = "_blank", icon("download"),
'Download test data.')
),
conditionalPanel(
condition = "output.showNormMethods!=0",
h3("RMA Pre-processing"),
selectInput(
"ChooseMethod", "Choose method",
list("Please select" = "blah",
"Use build-in reference" = "standardReference",
"Build a new reference" = "build",
"Upload a reference" = "upload",
"Cohort based RMA" = "RMA"
)
),
conditionalPanel(
condition = "input.ChooseMethod == 'build'",
fileInput("refFiles",
label = "To build a laboratory specific
reference, please upload .CEL files:",
accept = "", multiple = TRUE),
conditionalPanel(
condition = "output.showBuildRefButton!=0",
actionButton("buildreferenceButton",
HTML(paste(icon("cog", lib = "glyphicon"),
"Build reference"))),
conditionalPanel(
condition = "output.showDownloadRefButton!=0",
tags$hr(),
helpText("Download reference to save time on next run:"),
downloadButton('downloadReference',
'Download reference for later use.')
)
)
),
tags$hr()
),
conditionalPanel(
condition = "input.ChooseMethod == 'upload'",
fileInput("refUpload",
"Upload the file containing the reference:",
accept = "", multiple = FALSE),
tags$hr()
),
conditionalPanel(
condition = "input.ChooseMethod == 'standardReference'",
selectInput(
"ChooseReference", "Choose a reference",
list("LLMPP CHOP" = "LLMPPCHOP",
"LLMPP R-CHOP" = "LLMPPRCHOP",
"IDRC" = "IDRC",
"MDFCI" = "MDFCI",
"CHEPRETRO" = "CHEPRETRO",
"UAMS" = "UAMS"
)),
tags$hr()
),
conditionalPanel(
condition = "output.showNormButton!=0",
helpText("Normalize the files according to the chosen
reference:"),
actionButton("normalizeButton",
HTML(paste(icon("cog", lib = "glyphicon"),
"Normalize files"))),
tags$br(),
tags$hr(),
sliderInput("rle.iqr.threshold",
"Keep samples with RLE IQR less than:",
step = 0.01,
min = 0, max = 1.5, value = 0.6)
)
),
mainPanel(
shinyalert("shinyalertUploadCel",
click.hide = FALSE),
shinyalert("shinyalertSelectReference",
click.hide = FALSE),
shinyalert("shinyalertUploadCelSucces",
auto.close.after = 10),
shinyalert("shinyalertSelectReferenceSucess",
auto.close.after = 10),
shinyalert("shinyalertNormalizationSuccess",
click.hide = FALSE, auto.close.after = 10),
dataTableOutput("rle.stats"),
conditionalPanel(
condition = "output.showErrorprints!=0",
verbatimTextOutput("start"),
verbatimTextOutput("start2"),
verbatimTextOutput("showBuildRefButton"),
verbatimTextOutput("showNormButton"),
verbatimTextOutput("showDownloadRefButton"),
verbatimTextOutput("showNormMethods"),
verbatimTextOutput("showErrorprints"))
)
)
), # End tabPanel "CEL files"
# navbarMenu(
# 'Metadata',
# tabPanel(
# 'Input manually',
# sidebarLayout(
# sidebarPanel(
# helpText("You may also calculate IPI from clinical features."),
# checkboxInput(inputId = "IPIcalc",
# label = "Calculate IPI", value = FALSE),
# helpText("Additional columns"),
# select2Input("Additionalcolumns",
# "Type in the names.",
# choices = c("Age","LDH"),
# selected = "IPI"),
# conditionalPanel(
# condition = "input.IPIcalc",
# helpText("You may change the settings for the IPI calculation."),
# numericInput(inputId = "AGE.cut", label = "Get point when age > x", 60),
# numericInput(inputId = "ECOG.cut", label = "Get point when ECOG > x", 1),
# numericInput(inputId = "LDH.cut", label = "Get point when LDH > x", 1),
# numericInput(inputId = "N.Extra.Nodal.cut",
# label = "Get point when number of extra nodal sites > x", 1),
# numericInput(inputId = "Stage.cut", label = "Get point when Stage > x", 2)
# ),
# tags$hr(),
# downloadButton('downloadMetadataManual', 'Download metadata')
# ),
# mainPanel(
# shinyalert("shinyalertInputMeta", click.hide = FALSE),
# conditionalPanel(
# condition = "input.IPIcalc",
# helpText("Input the clinical features for each patient below.",
# "The IPI values are calculated automatically.")
# ),
# conditionalPanel(
# condition = "!input.IPIcalc",
# helpText("Input the IPI scores for each patient below.")
# ),
# div(class = "well container-fluid",
# hotable("hotableMetadataManual"))
# )
# )
# ), # End tabPanel "Input manually"
# tabPanel(
# 'Upload metadata',
# sidebarPanel(
# h4("Upload file containing metadata"),
# busyIndicator("Processing the metadata", wait = 1000),
# fileInput("usrMeta",
# "Please upload the file storing the metadata",
# accept = "", multiple = FALSE),
# conditionalPanel(
# condition = "output.showReadMetaMethods=='txt'",
# helpText("Does the file contain a header"),
# checkboxInput("ExttxtHeader", label = "header",
# value = TRUE),
# selectInput(
# "ExttxtSep", "Choose separater",
# list("Tabulate" = "\t", "Semicolon" = ";",
# "comma" = ",", "Other" = "Other")),
# conditionalPanel(
# condition = "input.ExttxtSep=='Other'",
# textInput(inputId = "ExttxtSepOther",
# "Type in the separator", value = ";"))
# ),
# conditionalPanel(
# condition = "output.showReadMetaMethods=='xls'|| output.showReadMetaMethods=='xlsx'",
# textInput(inputId = "ExtXLSsheet",
# "The sheet you want to read", 1)
# ),
# uiOutput("MetaUploadCelFileNames")
# ), # End sidebarPanel "Upload file containing metadata"
# mainPanel(
# shinyalert("shinyalertUploadMeta", click.hide = FALSE),
# shinyalert("shinyalertUploadMetaData", click.hide = FALSE),
# helpText("The Output below shows how the data is read."),
# dataTableOutput("uploadMetaData"),
# conditionalPanel(
# condition = "output.showReadMetaPrint!=0",
# verbatimTextOutput("showReadMetaPrint"),
# verbatimTextOutput("showReadMetaMethods")
# )
# )
# ) # End tabPanel "Upload metadata"
# ), # End tabPanel "Metadata"
tabPanel(
'Build-in test data',
sidebarLayout(
sidebarPanel(
busyIndicator("Loading data", wait = 1000),
helpText("Select the dataset you want to analyse"),
uiOutput("buildindataselector"),
radioButtons("buildinShowData", "Show",
choices = list("Metadata" = "Metadata",
"Gene Expression" = "GEP"),
selected = "GEP")
),
mainPanel(
conditionalPanel(
condition = "input.buildinShowData=='Metadata'",
dataTableOutput("buildinMetaData")
),
conditionalPanel(
condition = "input.buildinShowData=='GEP'",
dataTableOutput("buildinGEP")
)
)
)
) # End tabPanel "Build-in data"
# tabPanel(
# 'Metadata in use',
# sidebarLayout(
# sidebarPanel(
# helpText("Select the dataset you want to use"),
# uiOutput("metadataselector")
# ),
# mainPanel(
# dataTableOutput("MetaDataInUseOut")
# )
# )
# ) # End tabPanel "Metadata in use"
) # End navbarPage "Type of data"/"Load data"
), # End tabPanel "Load data"
tabPanel(
'Results',
navbarPage(
'Classification results',
tabPanel(
'Estimated probabilities',
sidebarLayout(
sidebarPanel(
condition = "input.conditionedPanels == 'Classification results'",
h3("Classification systems:"),
checkboxGroupInput(
"getClassifications",
label = "Perform classifications:",
choices = c("BAGS",
"ABC / GCB (COO)" = "ABCGCB",
"ABC / GCB / GCB-CC / GCB-CB (Extended COO)" =
"ABCGCB2",
"Rituximab (R)",
"Cyclophosphamide (C)",
"Doxorubicin (H)",
"Vincristine (O)",
# "Dexamethasone",
"Combined (CHO)",
"Melphalan"
),
selected = "BAGS"
),
conditionalPanel(
condition = paste(abc.cond, rtx.cond, cyc.cond, dox.cond,
vin.cond, dex.cond, cho.cond, sep = "|"),
h3("Classification options:")
),
conditionalPanel(
condition = abc.cond,
sliderInput("nc.range",
"ABC/GCB, range of non classified:",
step = 0.01,
min = 0, max = 1, value = c(0.1, 0.9))
),
conditionalPanel(
condition = rtx.cond,
checkboxInput(inputId = "HSCorrected",
label = strong("Rituximap, human serum
corrected"),
value = TRUE),
checkboxInput(inputId = "Lysis",
label = strong("Rituximap, lysis based"),
value = FALSE),
sliderInput("Rituximab.range",
"Rituximab, range of intermediate:",
step = 0.01,
min = 0, max = 1, value = c(0.38, 0.54))
),
conditionalPanel(
condition = cyc.cond,
sliderInput("Cyclophosphamide.range",
"Cyclophosphamide, range of intermediate:",
step = 0.01,
min = 0, max = 1, value = c(0.33,0.55))
),
conditionalPanel(
condition = dox.cond,
sliderInput("Doxorubicin.range",
"Doxorubicin, range of intermediate:",
step = 0.01,
min = 0, max = 1, value = c(0.14, 0.9))
),
conditionalPanel(
condition = vin.cond,
sliderInput("Vincristine.range",
"Vincristine, range of intermediate:",
step = 0.01,
min = 0, max = 1, value = c(0.46, 0.62))
),
conditionalPanel(
condition = dex.cond,
sliderInput("Dexamethasone.range",
"Dexamethasone, range of intermediate:",
step = 0.01,
min = 0, max = 1, value = c(0.25, 0.75))
),
conditionalPanel(
condition = cho.cond,
sliderInput("Combined.range",
"Combined CHO, range of intermediate:",
step = 0.01,
min = 0, max = 1, value = c(0.09, 0.93))
),
br(),
conditionalPanel(
condition = paste(abc.cond, rtx.cond, cyc.cond, dox.cond,
vin.cond, dex.cond, cho.cond, sep = "|"),
helpText("Click to reset ranges to default:"),
actionButton("resetButton",
HTML(paste(icon("repeat", lib = "glyphicon"),
"Reset")))
),
br(),
tags$hr(),
downloadButton('downloadData', 'Download classification results')
), # End sidebarPanel
mainPanel(
shinyalert("shinyalertResults", click.hide = FALSE),
dataTableOutput("results")
) # End mainPanel
) # End sidebarLayout
)#, # End Estimated probabilites tabPanel
# tabPanel(
# 'Patient summaries',
# sidebarLayout(
# sidebarPanel(
# uiOutput("patientSummaryIPI"),
# uiOutput("patientSummarySelect"),
# hr(),
# jscolorInput("jscolorInputPS",
# label =
# strong("Select colours used for the summaries:"),
# value = "#9199D1"),
# br(),
# br(),
# actionButton(inputId = "SelectColourPS",
# HTML(paste(icon("chevron-down", lib = "glyphicon"),
# "Add colour"))),
# br(),
# uiOutput("SelectedColoursPS"),
# hr(),
# sliderInput("surv.read",
# label = "Survival at (years)",
# step = 3/12, min = 0, max = 7, value = 3)
# ),
# mainPanel(
# shinyalert("shinyalertPatientSummaries", click.hide = FALSE),
# uiOutput("patientSummaries"),
# plotOutput("patientSummaryPlot"),
# uiOutput("patientSummariesExplanation")
# )
# )
# )
)
), # End tabPanel "Results"
id = "navbarPanels",
windowTitle = "hemaClass.org",
inverse = TRUE,
fluid = TRUE,
footer = ""
) # End navbarPage
)
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