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ui.R
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executable file
·174 lines (154 loc) · 12.4 KB
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library(shiny)
library(ggplot2)
library(markdown)
library(shinythemes)
shinyUI(fluidPage(theme = shinythemes::shinytheme("united"),
tags$head(includeScript("google-analytics.js")),
navbarPage("Prospective Lynch Syndrome Database (PLSD) - cumulative risk for cancer by age, genetic variant, and gender",
tabPanel("Any cancer",
sidebarLayout(
sidebarPanel(
HTML("<p><b>Calculation of cumulative risk for cancer in selected organ(s) irrespective of cancer(s) in any other organ</b></p><br>"),
selectInput("ctype3", label = em("Organ"),
list("Any organ" = "PANCANCER", "Colon" = "153","Stomach" = "151","Duodenum" = "152","Sigmoid/rectum" = "154","Bile duct/gall bladder" = "156","Pancreas" = "157","Breast" = "174","Endometrium" = "182","Ovaries" = "183","Prostate" = "185","Urinary bladder" = "188","Ureter/kidney" = "189","Brain" = "191","Stomach/duodenum/bile duct/gall bladder/pancreas" = "151_152_156_157","Urine bladder/ureter/kidney" = "188_189","Endometrium/ovaries" = "182_183", "Colon/sigmoid/rectum" = "153_154")
),
sliderInput("Age3", label = em("Current age"),min = 25, max = 70, value = 25),
conditionalPanel(
condition = "input.ctype3 == '182' || input.ctype3 == '174' || input.ctype3 == '183' || input.ctype3 == '182_183'",
selectInput("Sex3", label=em("Gender"),list("Female" = "FEMALE"))
),
conditionalPanel(
condition = "input.ctype3 == '185'",
selectInput("Sex4", label=em("Gender"),list("Male" = "MALE"))
),
conditionalPanel(
condition = "input.ctype3 == '153' || input.ctype3 == '154'",
selectInput("Sex5", label=em("Gender"),list("Female" = "FEMALE", "Male" = "MALE"))
),
conditionalPanel(
condition = "input.ctype3 == 'PANCANCER' || input.ctype3 == '151' || input.ctype3 == '152' || input.ctype3 == '156' || input.ctype3 == '157' || input.ctype3 == '188' || input.ctype3 == '189' || input.ctype3 == '191' || input.ctype3 == '151_152_156_157' || input.ctype3 == '188_189' || input.ctype3 == '153_154'",
selectInput("Sex6", label=em("Gender"),list("Both genders combined" = "BOTH"))
),
HTML('<i>'),
selectInput("genecarrier3", label = "Genetic variant",
list("path_MLH1" = "MLH1", "path_MSH2" = "MSH2", "path_MSH6" = "MSH6", "path_PMS2" = 'PMS2')
),
HTML('</i>')
),
mainPanel(
plotOutput("plot_incidence_gene_organ_cancer", height = "500px"),
HTML('<div style=\"position:relative; left:6em\">'),
#htmlOutput('text1'),
HTML('<br>'),
#DT::dataTableOutput('table_ALL3'),
tableOutput('table_ALL3'),
HTML('</div>'),
HTML('<br>'),
conditionalPanel(
condition = "input.genecarrier3 == 'PMS2'",
HTML('<br><div style=\"position:relative; left:7em\">'),
HTML("Warning: PMS2 results unreliable - "),
actionLink("seeAbout", "see About"),
HTML('</div>')
),
HTML('<br><br>')
)
)
),
#navbarPage("Prospective Lynch Syndrome Database (PLSD)",
tabPanel("Carrier without previous cancer",
sidebarLayout(
sidebarPanel(
HTML("<p><b>Calculation of cumulative risk for first cancer</b></p><br>"),
selectInput("ctype", label = em("Cancer type"),
list("Any cancer type" = "PANCANCER", "Colorectal cancer" = "CRC", "Ovarian cancer" = "OVARIAN", "Endometrial cancer" = "END","Urine bladder/kidney/ureter cancer" = "URO", "Gastric/small intestine/biliary tract/pancreas cancer" = "UGI")
),
sliderInput("Age", label = em("Current age"),
min = 25, max = 70, value = 25),
selectInput("Sex", label=em("Gender"),
list("Female" = "FEMALE", "Male" = "MALE")
),
HTML('<i>'),
selectInput("genecarrier", label = "Genetic variant",
list("path_MLH1" = "MLH1", "path_MSH2" = "MSH2", "path_MSH6" = "MSH6", "path_PMS2"="PMS2")
),
HTML('</i>')
),
mainPanel(
#tags$head(HTML("<script type='text/javascript' src='js/google.js'></script>")),
#tabsetPanel(
#HTML('<br><br>'),
#tabPanel("Plot", plotOutput("plot_incidence_gene")),
#tabPanel("Table",tableOutput("table_ALL")), type="tabs"
#),
plotOutput("plot_incidence_gene", height = "500px"),
HTML('<div style=\"position:relative; left:7em\">'),
htmlOutput('text1'),
HTML('<br>'),
tableOutput('table_ALL'),
HTML('</div>'),
#HTML('<br><br>'),
conditionalPanel(
condition = "input.genecarrier == 'PMS2'",
HTML('<br><div style=\"position:relative; left:7em\">'),
HTML("Warning: PMS2 results unreliable - "),
actionLink("seeAbout", "see About"),
HTML('</div>')
),
HTML('<br><br><br>')
)
)
),
#tabPanel("|"),
#shinythemes::themeSelector(),
tabPanel("Carrier with previous cancer",
sidebarLayout(
sidebarPanel(
HTML("<p><b>Calculation of cumulative risk for subsequent cancer</b></p><br>"),
selectInput("ctype2", label = em("Cancer type"),
list("Any cancer type" = "PANCANCER", "Colorectal cancer" = "CRC")
),
sliderInput("Age2", label = em("Current age"),
min = 25, max = 70, value = 25),
HTML('<i>'),
selectInput("genecarrier2", label = "Genetic variant",
list("path_MLH1" = "MLH1", "path_MSH2" = "MSH2", "path_MSH6" = "MSH6")
),
HTML('</i>')
),
mainPanel(
plotOutput("plot_incidence_gene_subsequent_cancer", height = "500px"),
HTML('<div style=\"position:relative; left:7em\">'),
#htmlOutput('text1'),
HTML('<br>'),
tableOutput('table_ALL2'),
HTML('</div>'),
HTML('<br>'),
conditionalPanel(
condition = "input.genecarrier2 == 'PMS2'",
HTML('<br><div style=\"position:relative; left:7em\">'),
HTML("Warning: PMS2 results unreliable - "),
actionLink("seeAbout", "see About"),
HTML('</div>')
),
HTML('<br><br>')
)
)
),
#tabPanel('|'),
#shinythemes::themeSelector(),
tabPanel("About",
sidebarLayout(
sidebarPanel(
HTML("<p>"),
strong("Recent news"),
HTML("</p><br>[ Dec-08-2015 ] <i>LScarisk.org launched</i>"),
HTML("<br>[ Jun-03-2016 ] <i>Risk estimates for subsequent cancers have been added</i>"),
HTML("<br>[ Jul-31-2017 ] <i>Risk estimates up to 75 years for any cancer have been added</i>")
),
mainPanel(
includeMarkdown('about.md')
)
)
)
,id="mainNavbar",fluid=F,collapsible=T,position="static-top", windowTitle="PLSD")))