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ui.R
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ui.R
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#ui.R
sidebar <- dashboardSidebar(
sidebarMenu(id="tabs",
menuItem("Summary", tabName = "summary", icon=icon("table"), selected = TRUE),
menuItem("Clinical Ratio", tabName = 'Plot_ratio', icon=icon("bar-chart-o")),
menuItem("Sankey Plot", tabName="sankey_plot", icon = icon("line-chart")),
menuItem("Survival Rate", tabName="sur_rate_plot", icon = icon("line-chart")),
menuItem("KM Analysis", tabName="km", icon = icon("line-chart")),
menuItem("Cox Analysis", tabName="cox", icon = icon("table")),
menuItem("Nomogram", tabName="nomogram", icon = icon("align-center")),
menuItem("Map", icon=icon("map"),
menuSubItem('Data Explorer', tabName = 'explorer'),
menuSubItem('Interactive Map', tabName = "map")),
menuItem("README", tabName = "readme", icon = icon("mortar-board"))))
body <- dashboardBody(
tags$head(
tags$link(rel = "stylesheet", type = "text/css", href = "custom.css")
),
tabItems(
#summary
tabItem(tabName = "summary",
box(width = NULL, status = "primary", solidHeader = TRUE, title = "Summary",
h4(style = "text-align: center", "The Esophageal Cancer Clinical Data Interactive Analysis (ECCDIA)"),
p(style = "text-align: justify", "ECCDIA: an interactive web tool for comprehensive clinical and survival data analysis of esophageal cancer (r version). The Esophageal Cancer Clinical Data Interactive Analysis (ECCDIA, <http://webapps.3steps.cn/ECCDIA/>) was developed to provide basic data analysis, survival analysis, and nomogram of the overall group and subgroup of 77,273 EC patients. The basic data analysis contained clinical factor ratio distribution analysis, Sankey plot analysis for relationships between clinical factors, and a map of clinical factors’ distribution. The survival analysis included Kaplan-Meier (K-M) analysis and Cox analysis for different subgroups of EC patients. The nomogram module enabled clinicians to precisely predict different subgroups of EC patients’ survival probability."),
br(),
downloadButton("downloadSummaryData", "Download"),
DTOutput('summary'))),
#map
tabItem(tabName = "explorer",
box(width = NULL, status = "primary", solidHeader = TRUE, title = "Data Map",
downloadButton("downloadDataMap", "Download"),
div(style = 'overflow-x: scroll', withSpinner(DTOutput('data_map'))))),
tabItem(
tabName = "map",
fluidRow(
column(width = 3,
tabBox(width = NULL,
tabPanel(h4("Parameters"),
selectInput(inputId = "var_map",
label = "Clinical Factors",
choices = c('Num_Patients','Average_age', 'Average_tumor_size',
'year_SR_1', 'year_SR_2', 'year_SR_3', 'year_SR_4', 'year_SR_5'),
selected = 'Num_Patients'),
width = 3))),
column(width = 9,
box(width = NULL, withSpinner(plotlyOutput("mapplot", height = "800px")), collapsible = TRUE,
title = "Map", status = "primary", solidHeader = TRUE)))),
#clinical ratio
tabItem(tabName = "ratio",
box(width = NULL, status = "primary", solidHeader = TRUE, title = "Clinical Parameter Ratio",
br(),br(),
div(style = 'overflow-x: scroll', DTOutput('ratio')))),
tabItem(
tabName = "Plot_ratio",
fluidRow(
column(width = 3,
tabBox(width = NULL,
tabPanel(h4("Parameters"),
materialSwitch(inputId = "RF_switch", label = 'Ratio/Num', status = 'success'),
selectInput(inputId = "CF",
label = "Clinical Factors",
choices = CF,
selected = CF[2]),
fluidRow(
column(12, strong('Choose Subgroup of Data'),
fluidRow(
column(width = 12, selectInput(inputId = "ratio_subgroup",
label = NULL,
c('all', CF),
selected = 'all')),
column(width = 12, selectInput(inputId = "ratio_group_name", label = NULL,
c('all')))))),
selectInput("barplot_r_legend_pos",
label = "Legend Position:",
choices = c('v', 'h'),
selected = "v"),
selectInput("color_name",
label = "Color Change:",
choices = c('Set1', 'Set2', 'Set3', 'Paired', 'YlOrRd'),
selected = "Set1"),
sliderInput("bar_plot_xy_tickfont", "X&Y Tick Size :",
min = 11, max = 30, value = 15, step = 1),
sliderInput("bar_plot_titlefont", "X&Y Title Font :",
min = 11, max = 30, value = 15, step = 1),
sliderInput("bar_plot_legend_labelsize", "Legend Labels Size :",
min = 11, max = 30, value = 15, step = 1),
sliderInput("bar_plot_margin", "Margin:",
min = 80, max = 200, value = 80, step = 5)))),
column(width = 9,
box(width = NULL, withSpinner(plotlyOutput("ratio_bar", height = "600px")), collapsible = TRUE,
title = "Frequency Distribution", status = "primary", solidHeader = TRUE)))),
#sankey plot
tabItem(
tabName = "sankey_plot",
fluidRow(
column(width = 3,
tabBox(width = NULL,
tabPanel(h4("Parameters"),
radioButtons("san_orientation", "Horizontal or Vertical", choiceNames = list('horizontal', 'vertical'), choiceValues = list('h', 'v')),
selectizeInput("san_var",
label = "Clinical Factors",
choices = CF,
multiple = T,
options = list(maxItems = 3, placeholder = 'Select a name'),
selected = c(CF[1], CF[3])),
fluidRow(
column(12, strong('Choose Subgroup of Data'),
fluidRow(
column(width = 12, selectInput(inputId = "san_subgroup",
label = NULL,
c('all', 'Year', CF),
selected = 'all')),
column(width = 12, selectizeInput(inputId = "san_group_name", label = NULL,
c('all')))))),
sliderInput("san_label_tickfont", "Label Size:",
min = 10, max = 40, value = 20, step = 1)))),
column(width = 9,
box(width = NULL, withSpinner(plotlyOutput("sankey_plot", height = "600px")), collapsible = TRUE,
title = "Frequency Distribution", status = "primary", solidHeader = TRUE)))),
#survival rate
tabItem(
tabName = "sur_rate_plot",
fluidRow(
column(width = 3,
tabBox(width = NULL,
tabPanel(h4("Parameters"),
radioButtons("SR_OC_switch", "OS or CSS", choiceNames = list('OS', 'CSS'), choiceValues = list("OS", "CSS")),
numericInput(inputId = "cho_rate", label = 'Survival Rate (0-10 year)',
min = 0, max = 10, value = 1, step = 0.1),
fluidRow(
column(12, strong('Choose Clinical Factor'),
fluidRow(
column(width = 12, selectInput(inputId = "srate_var",
label = NULL,
choices = CF[-which(CF == 'State')],
selected = CF[1])),
column(width = 12, selectizeInput("sur_rate_group_name", label = NULL,
multiple = T, c('all')))))),
selectInput("lineplot_r_legend_pos",
label = "Legend Position:",
choices = c('v', 'h'),
selected = 'v'),
sliderInput("line_size", "Line Size:",
min = 1, max = 10, value = 2, step = 1),
sliderInput("line_plot_xy_tickfont", "X&Y Tick Font:",
min = 11, max = 30, value = 15, step = 1),
sliderInput("line_plot_titlefont", "X&Y Title Font:",
min = 11, max = 30, value = 20, step = 1),
sliderInput("line_plot_legend_labelsize", "Legend Labels Size:",
min = 11, max = 30, value = 15, step = 1),
sliderInput("line_plot_margin", "Margin:",
min = 80, max = 200, value = 80, step = 5)))),
column(width = 9,
box(width = NULL, withSpinner(plotlyOutput("sur_rate_plot", height = "600px")), collapsible = TRUE,
title = "Survival Rate", status = "primary", solidHeader = TRUE),
box(width = NULL, status = "primary", solidHeader = TRUE, title = "Survival Rate Table",
downloadButton("downloadSurvivalData", "Download"),
div(style = 'overflow-x: scroll', DTOutput('pop_rate_tab')))))),
#km analysis
tabItem(
tabName = "km",
fluidRow(
column(width = 3,
tabBox(width = 12,
tabPanel(h4("Common Parameters"),
radioButtons("km_OC_switch", "OS or CSS", choiceNames = list('OS', 'CSS'), choiceValues = list("OS", "CSS")),
selectInput(inputId = "sur_var",
label = "Clinical Factors",
choices = CF,
selected = CF[1]),
fluidRow(
column(12, strong('Choose Subgroup of Data'),
fluidRow(
column(width = 12, selectInput(inputId = "subgroup",
label = NULL,
c('all', CF),
selected = 'all')),
column(width = 12, selectInput(inputId = "group_name", label = NULL,
c('all')))))))),
tabBox(width = 12,
tabPanel(h4("Static Parameters"),
selectInput(inputId = "sur_med_line",
label = "Survival Median Line",
choices = c("none", "hv", "h", "v"),
selected = "none"),
checkboxInput("risk_table", "Risk Table?",
value = TRUE),
checkboxInput("ncensor_plot", "Ncensor Plot?",
value = FALSE),
sliderInput("main_fontsize", "Main Fontsize (Title/X/Y/Ticks)",
min = 15, max = 40, value = 25, step = 1),
sliderInput("tab_fontsize", "Table Fontsize",
min = 5, max = 30, value = 10, step = 1),
sliderInput("table_height", "Table Height",
min = 0.1, max = 1, value = 0.25, step = 0.1),
sliderInput("ncensor_height", "Ncensor Plot Height",
min = 0.1, max = 1, value = 0.35, step = 0.1),
sliderInput("line_size", "Line Size",
min = 1, max = 10, value = 3, step = 1),
width = 2)),
tabBox(width = 12,
tabPanel(h4("Dynamic Parameters"),
radioButtons("dyn_risk_table", "Risk Table", choiceNames = list('Yes', 'No'), choiceValues = list("Yes", "No")),
sliderInput("dyn_main_fontsize", "Main Fontsize (Title/X/Y/Ticks)",
min = 15, max = 40, value = 20, step = 1),
sliderInput("dyn_tab_fontsize", "Table Fontsize",
min = 5, max = 30, value = 12, step = 1),
sliderInput("dyn_table_height", "Table Height",
min = 0.1, max = 1, value = 0.3, step = 0.1),
sliderInput("dyn_line_size", "Line Width",
min = 0, max = 10, value = 1, step = 1),
width = 2))),
column(width = 9,
box(width = NULL, withSpinner(plotOutput("OS_plot", height = "1000px")), collapsible = TRUE,
title = "Static Survival Analysis", status = "primary", solidHeader = TRUE)),
column(width = 9,
box(width = NULL, withSpinner(plotlyOutput("OS_plotly", height = "1000px")), collapsible = TRUE,
title = "Dynamic Survival Analysis", status = "primary", solidHeader = TRUE)))),
#cox analysis
tabItem(
tabName = "cox",
fluidRow(
column(width = 3,
tabBox(width = NULL,
tabPanel(h4("Parameters"),
radioButtons(inputId = "Cox_OC_switch", "OS or CSS", choiceNames = list('OS', 'CSS'),
choiceValues = list("OS", "CSS"), selected = 'OS'),
radioButtons("UM_switch", "Univariate or Multivariate", choiceNames = list('uvm', 'mvm'),
choiceValues = list("uvm", "mvm"), selected = 'mvm'),
selectInput(inputId = "COX_subgroup",
label = "Cox Subgroup",
choices = c('ALL', 'SCC', 'AD', 'stage_I_II', 'stage_III_IV', 'Surg_Rad_Che', 'Almost_no_therapy',
'mets_brain', 'mets_liver', 'mets_lung'),
selected = 'ALL')))),
column(width = 9,
box(width = NULL, status = "primary", solidHeader = TRUE, title = "Train",
downloadButton("downloadTrainCoxData", "Download"),
div(style = 'overflow-x: scroll', DTOutput('cox_os_train', width = "100%"))
),
box(width = NULL, status = "primary", solidHeader = TRUE, title = "Test",
downloadButton("downloadTestCoxData", "Download"),
div(style = 'overflow-x: scroll', DTOutput('cox_os_test', width = "100%"))
),
box(width = NULL, status = "primary", solidHeader = TRUE, title = "All",
downloadButton("downloadAllCoxData", "Download"),
div(style = 'overflow-x: scroll', DTOutput('cox_os_all', width = "100%")))))),
#nomogram
tabItem(
tabName = "nomogram",
fluidRow(
column(width = 3,
tabBox(width = NULL,
tabPanel(h4("Parameters"),
radioButtons(inputId = "nom_OC_switch", "OS or CSS", choiceNames = list('OS', 'CSS'),
choiceValues = list("OS", "CSS"), selected = 'OS'),
selectInput(inputId = "nom_os_subgroup",
label = "Nomogram Subgroup",
choices = c('ALL', 'SCC', 'AD', 'stage_I_II', 'stage_III_IV', 'Surg_Rad_Che'),
selected = 'ALL')))),
column(width = 9,
conditionalPanel(condition = "input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'ALL'||
input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'AD'||
input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'stage_I_II'||
input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'stage_III_IV'||
input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'Surg_Rad_Che'||
input.nom_OC_switch == 'CSS' && input.nom_os_subgroup == 'ALL'||
input.nom_OC_switch == 'CSS' && input.nom_os_subgroup == 'AD'",
box(sliderInput(inputId = "age_s", label = 'Age',
min = 20, max = 85, value = 20, step = 1), width = 10, height = 100, solidHeader = TRUE)),
conditionalPanel(condition = "input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'ALL'||
input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'AD'||
input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'stage_I_II'||
input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'stage_III_IV'||
input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'Surg_Rad_Che'||
input.nom_OC_switch == 'CSS' && input.nom_os_subgroup == 'ALL'||
input.nom_OC_switch == 'CSS' && input.nom_os_subgroup == 'AD'",
box(numericInput(inputId = "age_n", label = 'Age', min = 20, max = 85, value = 20, step = 1),
width = 2, height = 100, solidHeader = TRUE)),
conditionalPanel(condition = "input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'stage_I_II'",
box(sliderInput(inputId = "tumor_size_s", label = "Tumor Size(mm)", value = 200, step = 10, min = 0, max = 1000),
height = 100, width = 10, solidHeader = TRUE)),
conditionalPanel(condition = "input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'stage_I_II'",
box(numericInput(inputId = "tumor_size_n", label = 'Tumor Size(mm)', value = 200, step = 10, min = 0, max = 1000),
height = 100, width = 2, solidHeader = TRUE)),
conditionalPanel(condition = "input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'ALL'||
input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'SCC'||
input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'AD'||
input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'stage_III_IV'||
input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'Surg_Rad_Che'||
input.nom_OC_switch == 'CSS' && input.nom_os_subgroup == 'ALL'||
input.nom_OC_switch == 'CSS' && input.nom_os_subgroup == 'SCC'||
input.nom_OC_switch == 'CSS' && input.nom_os_subgroup == 'AD'",
box(sliderInput(inputId = "RNP_s", label = 'Regional Nodes Positive', value = 3, step = 1, min = 0, max = 26),
height = 100, width = 10, solidHeader = TRUE)),
conditionalPanel(condition = "input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'ALL'||
input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'SCC'||
input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'AD'||
input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'stage_III_IV'||
input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'Surg_Rad_Che'||
input.nom_OC_switch == 'CSS' && input.nom_os_subgroup == 'ALL'||
input.nom_OC_switch == 'CSS' && input.nom_os_subgroup == 'SCC'||
input.nom_OC_switch == 'CSS' && input.nom_os_subgroup == 'AD'",
box(numericInput(inputId = "RNP_n", label = "Regional Nodes Positive", value = 3, step = 1, min = 0, max = 26),
height = 100, width = 2, solidHeader = TRUE)),
conditionalPanel(condition = "input.nom_OC_switch == 'stop'",
box(sliderInput(inputId = "TNSM_s", label = 'Total Num Situ or Malignant', value = 1, step = 1, min = 1, max = 7),
height = 100, width = 10, solidHeader = TRUE)),
conditionalPanel(condition = "input.nom_OC_switch == 'stop'",
box(numericInput(inputId = "TNSM_n", label = "Total Num Situ or Malignant", value = 1, step = 1, min = 1, max = 7),
height = 100, width = 2, solidHeader = TRUE)),
conditionalPanel(condition = "input.nom_OC_switch == 'CSS'&&input.nom_os_subgroup == 'ALL'||
input.nom_OC_switch == 'OS'&&input.nom_os_subgroup == 'SCC'||
input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'stage_III_IV'||
input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'stage_I_II'||
input.nom_OC_switch == 'CSS'&&input.nom_os_subgroup == 'ALL'||
input.nom_OC_switch == 'CSS' && input.nom_os_subgroup == 'AD'||
input.nom_OC_switch == 'CSS' && input.nom_os_subgroup == 'Surg_Rad_Che'",
box(selectInput(inputId = "sex", label = "Gender", choices=c('Female', 'Male'), selected = "Female"),
width = 3, solidHeader = TRUE)),
conditionalPanel(condition = "input.nom_OC_switch == 'CSS'&&input.nom_os_subgroup == 'ALL'",
box(selectInput(inputId = "Primary_Site", label = "Primary Site",
choices=c("LTE", "MTE", "TE", "UTE", "NOS_E", "CE", "OLE", "AE"), selected = "LTE"),
width = 3, solidHeader = TRUE)),
conditionalPanel(condition="input.nom_OC_switch == 'OS'&&input.nom_os_subgroup =='ALL'||
input.nom_OC_switch == 'OS'&&input.nom_os_subgroup == 'SCC'||
input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'stage_I_II'||
input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'Surg_Rad_Che'||
input.nom_OC_switch == 'CSS'&&input.nom_os_subgroup == 'ALL'||
input.nom_OC_switch == 'CSS' && input.nom_os_subgroup == 'AD'||
input.nom_OC_switch == 'CSS' && input.nom_os_subgroup == 'stage_I_II'",
box(selectInput(inputId = "grade", label = "Grade", choices=c("I", "II", "III", "IV"),
selected = "I"), width = 3, solidHeader = TRUE)),
conditionalPanel(condition="input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'stage_I_II'",
box(selectInput(inputId = "Histologic_type", label = "Histologic Type",
choices=c("SCC", "AD"), selected = "SCC"),
width = 3, solidHeader = TRUE)),
conditionalPanel(condition="input.nom_OC_switch == 'OS'&&input.nom_os_subgroup =='ALL'||
input.nom_OC_switch == 'OS'&&input.nom_os_subgroup == 'AD'||
input.nom_OC_switch == 'CSS'&&input.nom_os_subgroup == 'ALL'||
input.nom_OC_switch == 'CSS'&&input.nom_os_subgroup == 'SCC'||
input.nom_OC_switch == 'CSS' && input.nom_os_subgroup == 'AD'||
input.nom_OC_switch == 'CSS' && input.nom_os_subgroup == 'Surg_Rad_Che'",
box(selectInput(inputId = "stage", label = "Stage",
choices=c("I", "II", "III", "IV"), selected = "I"),
width = 3, solidHeader = TRUE)),
conditionalPanel(condition="input.nom_OC_switch == 'CSS' && input.nom_os_subgroup == 'stage_I_II'",
box(selectInput(inputId = "T", label = "T",
choices=c("T0", "T1", "T2", "T3", "T4"), selected = "T1"),
width = 3, solidHeader = TRUE)),
conditionalPanel(condition="input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'stage_I_II'",
box(selectInput(inputId = "N", label = "N", choices=c('N0', 'N1_3'), selected = "N0"),
width = 3, solidHeader = TRUE)),
conditionalPanel(condition="input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'stage_III_IV'",
box(selectInput(inputId = "M", label = "M", choices=c('M0', 'M1'), selected = "M0"), width = 3, solidHeader = TRUE)),
conditionalPanel(condition= "input.nom_OC_switch == 'stop'",
box(selectInput(inputId = "Race", label = "Race",
choices=c("White", "Black", "API", "AI/AN "), selected = "White"),
width = 3, solidHeader = TRUE)),
conditionalPanel(condition= "input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'SCC'||
input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'stage_I_II'||
input.nom_OC_switch == 'CSS' && input.nom_os_subgroup == 'AD'||
input.nom_OC_switch == 'CSS' && input.nom_os_subgroup == 'stage_I_II'||
input.nom_OC_switch == 'CSS' && input.nom_os_subgroup == 'Surg_Rad_Che'",
box(selectInput(inputId = "Insurance", label = "Insurance",
choices=c("Medicaid", "Insured", "Uninsured"), selected = "Insured"),
width = 3, solidHeader = TRUE)),
conditionalPanel(condition = "input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'SCC'||
input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'stage_I_II'||
input.nom_OC_switch == 'OS' && input.nom_os_subgroup == 'stage_III_IV'",
box(selectInput(inputId = "marital_status", label = "Marital Status", choices=c('Unmarried', 'Married', 'DSW'),
selected = "Married"), width = 3, solidHeader = TRUE))),
column(width = 12,
box(width = NULL, height = "145px",
h4(
withSpinner(textOutput("surv_text1")),
withSpinner(textOutput("surv_text3")),
withSpinner(textOutput("surv_text5"))
),
collapsible = TRUE, color = "purple",
title = "Output", status = "primary", solidHeader = TRUE)),
column(width = 12,
box(width = NULL, withSpinner(plotOutput("OS_nom", height = "800px")), collapsible = TRUE,
title = "Nomogram", status = "primary", solidHeader = TRUE)),
column(width = 12,
box(width = 4, withSpinner(plotOutput("OS_cal_train", height = "600px")), collapsible = TRUE,
title = "Train", status = "primary", solidHeader = TRUE),
box(width = 4, withSpinner(plotOutput("OS_cal_test", height = "600px")), collapsible = TRUE,
title = "Test", status = "primary", solidHeader = TRUE),
box(width = 4, withSpinner(plotOutput("OS_cal_all", height = "600px")), collapsible = TRUE,
title = "All", status = "primary", solidHeader = TRUE)))),
#readme
tabItem(
tabName = "readme",
withMathJax(),
includeMarkdown("README.md"))))
dashboardPage(
dashboardHeader(title = "ECCDIA"),
sidebar,
body,
title = "ECCDIA | The Esophageal Cancer Clinical Data Interactive Analysis",
skin = "blue")