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app.R
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app.R
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version_id <- paste0("v2.0.20240821")
# User Input -------------------------------------------------------------------
ProjectName <- ''
ExpressionMatrix_file <- ''
MetaData_file <- ''
MetaParam_File <- ''
## Password Settings -----------------------------------------------------------
Password_Protected <- FALSE
PasswordSet <- "teamscience"
## Pre-Selected Inputs ---------------------------------------------------------
# An option from the meta, All, or NULL
PreSelect_SamplyType <- "All"
PreSelect_Feature <- "All"
# An option from the meta or NULL
PreSelect_SubFeature <- NULL
PreSelect_SecondaryFeature <- NULL
## Provided Input --------------------------------------------------------------
## User make sure paths are correct
GeneSet_File <- "Genesets/GeneSet_List_HS_v6.RData"
GeneSetTable_File <- "Genesets/GeneSet_CatTable_v6.txt"
About_MD_File <- "PurposeAndMethods.Rmd"
ExampleExpr_File <- "Example_Data/TCGA_CHOL_Expression_PatientID.txt"
ExampleClin_File <- "Example_Data/TCGA_CHOL_Clinical_PatientID.txt"
ExampleParam_File <- "Example_Data/TCGA_SurvivalApp_Global_Parameters.txt"
## Check if Immune deconvolution package is installed
immudecon <- "immunedeconv"
immudecon_check <- immudecon %in% rownames(installed.packages())
# Input Check ------------------------------------------------------------------
if (!file.exists(ExpressionMatrix_file)) {
FileProvided <- FALSE
} else { FileProvided <- TRUE }
if (!file.exists(MetaParam_File)) {
ParamFileProvided <- FALSE
} else { ParamFileProvided <- TRUE }
if (!isTruthy(ProjectName)) {
ProjectName <- paste("{ Survival Analysis }")
} else {
ProjectName <- paste("{",ProjectName,"Survival Analysis }")
}
if (isTruthy(PreSelect_Feature)) {
if (toupper(PreSelect_Feature) == "ALL") {
PreSelect_Feature <- "Show all Samples"
}
}
gs <- loadRData(GeneSet_File)
# Gene Set Table
GeneSetTable <- as.data.frame(fread(GeneSetTable_File, sep = '\t', header = T))
GeneSetCats <- unique(GeneSetTable[,1])
# Functions --------------------------------------------------------------------
#increase file upload size
options(shiny.maxRequestSize=5000*1024^2)
SurvPlot_Height <- "550px"
SurvPlot_Width <- "850px"
StatCols <- c("MedianCutP","QuartileCutP","OptimalCutP","TopBottomCutP","UserCutP")
# Password Table ---------------------------------------------------------------
# user database for login
if (Password_Protected) {
user_base <- tibble::tibble(
user = "user",
password = PasswordSet,
permissions = "admin",
name = "User"
)
}
# UI Tabs ----------------------------------------------------------------------
## Login Tab -------------------------------------------------------------------
login_tab <- tabPanel(
title = icon("lock"),
value = "login",
loginUI("login")
)
## Data Input Tab --------------------------------------------------------------
#if (!FileProvided) {
DataInput_tab <- tabPanel("Data Input",
fluidPage(
sidebarPanel(
width = 3,
id = "DataInputPanel",
p(),
textInput("UserProjectName","Project Name:", value = "Survival Analysis"),
uiOutput("rendExprFileInput"),
fluidRow(
column(5, style = 'padding-right:2px;margin-top:-30px;',
checkboxInput("LogExprFile","Log2 Expression", value = F)
),
column(7, style = 'padding-left:2px;margin-top:-30px;',
checkboxInput("ScaleNormExprFile","Scale Normalize Expression", value = F)
)
),
uiOutput("rendClinFileInput"),
fluidRow(
column(12, style = 'margin-top:-15px;',
actionButton("UseExpData","Load Example Data"),
tags$a(href="http://shawlab.science/shiny/PATH_SURVEYOR_ExampleData/PATH_SURVEYOR_App/", "Download example data", target='_blank'),
)
),
shiny::hr(),
uiOutput("rendClinParamHeader"),
h4("Clinical Parameters"),
fluidRow(
column(12, style = 'margin-top:-20px;',
radioButtons("ParamChoice","", choices = c("Define Parameters","Upload Parameter File"), inline = T)
)
),
fluidRow(
column(8,
uiOutput("rendClinParamFileInput"),
uiOutput("rendSurvTimeColSelect"),
uiOutput("rendSurvIDColSelect")
),
column(4,
uiOutput("rendSurvTimeUnits")
)
)
),
mainPanel(
uiOutput("rendExprFilePrevHeader"),
div(DT::dataTableOutput("ExprFile_Preview"), style = "font-size:10px"),
uiOutput("rendClinFilePrevHeader"),
div(DT::dataTableOutput("ClinFile_Preview"), style = "font-size:10px"),
uiOutput("rendParamFilePrevHeader"),
div(DT::dataTableOutput("ClinParamFile_Preview"), style = "font-size:10px")
),
tagList(
tags$head(
tags$style(
HTML("
.info_box {
width: auto;
height: auto;
color: #000000;
background-color: #f5f5f5;
padding: 3px 8px;
font-size: 12px;
z-index : 9999;
}",
glue::glue("#{'AppVersion'} {{
position: {'fixed'};
top: 0;
right: 0;
}}")
)
)
),
div(id = "AppVersion", class = "info_box", version_id)
)
)
)
#}
## Survival Tab ----------------------------------------------------------------
Survival_tab <- tabPanel("Survival Analysis",
fluidPage(
sidebarLayout(
### Sidebar Panel ---------------------------------
sidebarPanel(
conditionalPanel(condition = "input.SurvPanels == '1' | input.SurvPanels == '2' | input.SurvPanels == '3' | input.SurvPanels == '4'",
tabsetPanel(
id = "survside",
tabPanel("Sample Parameters",
p(),
uiOutput("rendSampleTypeSelection"),
selectizeInput("FeatureSelection","Select Feature to Subset Samples:",choices = NULL, selected = 1),
uiOutput("rendSubFeatureSelection"),
fluidRow(
column(4,
selectizeInput("SurvivalType_time","Survival Time Data:",choices = NULL, selected = 1),
),
column(4,
selectizeInput("SurvivalType_id","Survival ID Data:",choices = NULL, selected = 1),
),
column(4,
selectInput("ScoreMethod","Scoring Method",choices = c("ssgsea","gsva","zscore","plage"))
)
),
tabsetPanel(
id = "GeneSetTabs",
tabPanel("Gene Sets",
p(),
selectInput("GeneSetCat_Select","Select Geneset Category:", choices = GeneSetCats),
div(DT::dataTableOutput("GeneSetTable"), style = "font-size:10px"),
value = 1
),
tabPanel("Single Genes",
p(),
div(DT::dataTableOutput("GeneGeneSetTable"), style = "font-size:10px"),
value = 2
),
tabPanel("User Gene Set",
p(),
radioButtons("UserGSoption","",choices = c("Gene Set Upload","Text Box Input"), inline = T),
conditionalPanel(condition = "input.UserGSoption == 'Gene Set Upload'",
fileInput("userGeneSet","Gene Set Upload", accept = c(".gmt",".tsv",".txt",".RData")),
div(DT::dataTableOutput("userGeneSetTable"), style = "font-size:10px")
),
conditionalPanel(condition = "input.UserGSoption == 'Text Box Input'",
textInput("userGeneSetTextName","Custom Gene Set Name", value = "Custom_Geneset"),
textInput("userGeneSetText","Gene Symbols", placeholder = "Comma, space, or tab delimited")
),
value = 3
)
),
checkboxInput("ViewGeneSetGenes","View Genes in Selected Gene Set", value = F),
uiOutput("rendGenesInGeneSetTab")
),
tabPanel("Figure Parameters",
p(),
conditionalPanel(condition = "input.SurvPanels == '1' | input.SurvPanels == '2' | input.SurvPanels == '3'",
h3("Survival Plot Parameters"),
fluidRow(
column(6,
numericInput("SurvXaxis","Survival Age Limit (years)", value = NA),
#uiOutput("rendSurvXaxis"),
numericInput("SurvXaxisBreaks","Survival X-Axis Breaks (Years):",value = 1, min = 0, step = 0.25),
selectInput("SurvLegendPos","Legend Position",choices = c("right","left","top","bottom","none"))
),
column(6, style = "margin-top:15px",
radioButtons("SurvYearOrMonth","Survival X-Axis Units:",choices = c("Years","Months"), inline = T),
checkboxInput("ShowPval","Show P.Value",value = T),
checkboxInput("ShowConfInt","Show Confidence Interval",value = F),
checkboxInput("ShowMedSurvLine","Show Median Survival Line",value = F)
)
)
),
conditionalPanel(condition = "input.SurvPanels == '2' | input.SurvPanels == '3'",
shiny::hr(),
h3("Forest Plot Parameters"),
numericInput("ForestFontSize","Font Size",value = 1),
shiny::hr(),
h3("Linearity Plot Parameters"),
fluidRow(
column(4,
numericInput("linAxisFont","X/Y Axis Font Size",value = 14, step = 1)
),
column(4,
numericInput("linTickFont","Axis Tick Font Size",value = 10, step = 1)
),
column(4,
numericInput("linMainFont","Title Font Size",value = 16, step = 1)
)
)
),
conditionalPanel(condition = "input.SurvPanels == '4'",
p(),
h3("Boxplot Parameters"),
fluidRow(
column(4,
numericInput("boxplotFont","Font Size:", value = 15, step = 1)
),
column(4,
numericInput("boxplotDot", "Dot Size:", value = 0.75, step = 0.25)
),
column(4,
selectInput("boxplotTextAngle","X-Axis Text:",
choices = c("Horizontal (0 degrees)" = 0,"Angled (45 degrees)" = 45,"Vertical (90 degrees)" = 90))
)
),
hr(),
h3("Heatmap Parameters"),
fluidRow(
column(6,
numericInput("heatmapFontR", "Row Font Size:", value = 9, step = 1)
),
column(6,
numericInput("heatmapFontC", "Column Font Size:", value = 10, step = 1)
)
)
),
hr(),
h3("Plot Download Parameters"),
fluidRow(
column(4,
numericInput("PlotDnldHight","Plot Height",value = 8, min = 0, step = 1)
),
column(4,
numericInput("PlotDnldWidth","Plot Width",value = 8, min = 0, step = 1)
),
column(4,
selectInput("PlotDnldUnits","Units",choices = c("in","cm","mm","px"))
)
)
)
)
)
#conditionalPanel(condition = "input.SurvPanels == '5'",
# tabsetPanel(
# tabPanel("Input Parameters",
# p(),
# h4("Sample Selection"),
# uiOutput("rendSampleTypeSelection_lasso"),
# selectizeInput("FeatureSelection_lasso","Select Feature:", choices = NULL, selected = 1),
# uiOutput("rendSubFeatureSelection_lasso"),
# h4("Feature Selection"),
# textInput("LassoModelName","Lasso Model Name:",value = "Custom_Lasso_Model"),
# selectizeInput("LassoFeatureSelection_lasso","Select or Paste Features to Generate Lasso Model:", choices = NULL, selected = 1, multiple = T),
# h4("Lasso Parameters"),
# fluidRow(
# column(6,
# selectizeInput("SurvTimeSelec_lasso","Survival Time Data:", choices = NULL, selected = 1),
# ),
# column(6,
# selectizeInput("SurvIDSelect_lasso","Survival ID Data:", choices = NULL, selected = 1),
# )
# ),
# fluidRow(
# column(5,
# numericInput("LassoTrainProp","Training Sample Proportion:",value = 50, step = 1, max = 100,min = 1)
# ),
# column(4,
# numericInput("LassoAlpha","Set Lasso Alpha:", value = 1, min = 0, step = 0.1)
# ),
# column(3,
# numericInput("LassoSeedSelection","Set Seed:", value = 100, min = 1, step = 1)
# )
# ),
# p(),
# fluidRow(
# column(8,
# radioButtons("viewLassoMinOrSE","Select Lambda to Generate Risk Score:", inline = T,choices = c("Lambda Min","Lambda SE","Custom")),
# ),
# column(4,
# uiOutput("rendCustomLambda")
# )
# ),
# uiOutput("rednLassoCoefTable"),
# #,
# fluidRow(
# column(6,
# dnld_ui("dnldLassoModel","Download Lasso Model")
# ),
# column(6,
# dnld_ui("dnldLassoRunData","Download Lasso Run Data")
# )
# )
# ),
# tabPanel("Figure Parameters",
# p(),
# h4("Survival Plot Parameters"),
# radioButtons("LassoPlotCutP","Plot Cut-Point", choices = c("Median","Quartile","Optimal","Quantile","User Specified"),
# inline = T),
# uiOutput("rendCutPinput"),
# fluidRow(
# column(4,
# uiOutput("rendSurvXaxis_lasso")
# ),
# column(8,
# textInput("SurvPlotTitle_lasso","Survival Plot Title:",value = "")
# )
# ),
# fluidRow(
# column(3,
# selectInput("SurvLegendPos_lasso","Legend Position",choices = c("top","right","left","bottom","none"))
# ),
# column(3,
# checkboxInput("ShowPval_lasso","Show P.Value",value = T)
# ),
# column(3,
# checkboxInput("ShowConfInt_lasso","Show Confidence Interval",value = F)
# ),
# column(3,
# checkboxInput("ShowMedSurvLine_lasso","Show Median Survival Line",value = F)
# )
# )
# )
# )
#)
),
### Main Panel ------------------------------------
mainPanel(
tabsetPanel(
id = "SurvPanels",
#### Main Surv --------------------------------
tabPanel("Pathway Level Survival Analysis",
tabsetPanel(
id = "SurvPanelsMain",
tabPanel("Median Cut-Point Survival",
p(),
tableOutput("ssgseaCheck"),
htmlOutput("BINSurvDescrip", style = "font-size:14px;"),
shiny::hr(),
shinycssloaders::withSpinner(shinyjqui::jqui_resizable(plotOutput("SplotBIN", height = SurvPlot_Height, width = SurvPlot_Width)), type = 6),
dnld_ui("dnldSplotBIN_SVG","SVG"),
shiny::hr(),
shinycssloaders::withSpinner(shinyjqui::jqui_resizable(plotOutput("ssgseaBINDensity", width = "650px", height = "400px")), type = 6),
dnld_ui("dnldssgseaBINDensity_SVG","SVG"),
shiny::hr(),
h4("Cox Hazard Regression Analysis Summary"),
fluidRow(
column(6,
div(shinycssloaders::withSpinner(tableOutput("SBinaryHRtab"), type = 7, size = 0.5), style = "font-size:12px"),
style = 'border-right: 0.5px solid lightgray',
),
column(6,
verbatimTextOutput("MedianCutPSumm")
)
),
value = 1),
tabPanel("Quartile Survival",
p(),
htmlOutput("QuartSurvDescrip", style = "font-size:14px;"),
shiny::hr(),
shinycssloaders::withSpinner(shinyjqui::jqui_resizable(plotOutput("Splot", height = SurvPlot_Height, width = SurvPlot_Width)), type = 6),
dnld_ui("dnldSplot_SVG","SVG"),
shiny::hr(),
shinycssloaders::withSpinner(shinyjqui::jqui_resizable(plotOutput("ssgseaQuartDensity", width = "650px", height = "400px")), type = 6),
dnld_ui("dnldssgseaQuartDensity_SVG","SVG"),
shiny::hr(),
h4("Cox Hazard Regression Analysis Summary"),
fluidRow(
column(6,
div(shinycssloaders::withSpinner(tableOutput("SQuartileHRtab"), type = 7, size = 0.5), style = "font-size:12px"),
style = 'border-right: 0.5px solid lightgray',
),
column(6,
verbatimTextOutput("QuartileCutPSumm")
)
),
value = 2),
tabPanel("Optimal Cut-Point Survival",
p(),
htmlOutput("CutPSurvDescrip", style = "font-size:14px;"),
shiny::hr(),
shinycssloaders::withSpinner(shinyjqui::jqui_resizable(plotOutput("ScutPointPlot", height = SurvPlot_Height, width = SurvPlot_Width)), type = 6),
dnld_ui("dnldScutPointPlot_SVG","SVG"),
shiny::hr(),
shinycssloaders::withSpinner(shinyjqui::jqui_resizable(plotOutput("ssgseaCutPDensity", width = "650px", height = "400px")), type = 6),
dnld_ui("dnldssgseaCutPDensity_SVG","SVG"),
shiny::hr(),
h4("Cox Hazard Regression Analysis Summary"),
fluidRow(
column(6,
div(shinycssloaders::withSpinner(tableOutput("CutPointHRtab"), type = 7, size = 0.5), style = "font-size:12px"),
#uiOutput("rendCutPointHRtab"),
style = 'border-right: 0.5px solid lightgray',
),
column(6,
verbatimTextOutput("OptimalCutPSumm")
)
),
value = 3),
tabPanel("Top/Bottom Cut-Point Survival",
p(),
htmlOutput("QuantSurvDescrip", style = "font-size:14px;"),
shiny::hr(),
shinycssloaders::withSpinner(shinyjqui::jqui_resizable(plotOutput("SquantPlot", height = SurvPlot_Height, width = SurvPlot_Width)), type = 6),
numericInput("QuantPercent","Top/Bottom Cut-Point Quantile Cutoff (%)", value = 25, min = 0, max = 100),
dnld_ui("dnldSquantPlot_SVG","SVG"),
shiny::hr(),
shinycssloaders::withSpinner(shinyjqui::jqui_resizable(plotOutput("ssgseaQuantDensity", width = "650px", height = "400px")), type = 6),
dnld_ui("dnldssgseaQuantDensity_SVG","SVG"),
shiny::hr(),
h4("Cox Hazard Regression Analysis Summary"),
fluidRow(
column(6,
div(shinycssloaders::withSpinner(tableOutput("SQuantileHRtab"), type = 7, size = 0.5), style = "font-size:12px"),
#uiOutput("rendQuantHRtab"),
style = 'border-right: 0.5px solid lightgray',
),
column(6,
verbatimTextOutput("QuantileCutPSumm")
)
),
value = 4),
tabPanel("User Cut-Point Survival",
p(),
htmlOutput("Quant2SurvDescrip", style = "font-size:14px;"),
shiny::hr(),
shinycssloaders::withSpinner(shinyjqui::jqui_resizable(plotOutput("SquantPlot2", height = SurvPlot_Height, width = SurvPlot_Width)), type = 6),
numericInput("QuantPercent2","Above/Below User Quantile Cut-Point (%)", value = 25, min = 0, max = 100),
dnld_ui("dnldSquantPlot2_SVG","SVG"),
shiny::hr(),
shinycssloaders::withSpinner(shinyjqui::jqui_resizable(plotOutput("ssgseaQuant2Density", width = "650px", height = "400px")), type = 6),
dnld_ui("dnldssgseaQuant2Density_SVG","SVG"),
shiny::hr(),
h4("Cox Hazard Regression Analysis Summary"),
fluidRow(
column(6,
div(shinycssloaders::withSpinner(tableOutput("SQuantileHR2tab"), type = 7, size = 0.5), style = "font-size:12px"),
style = 'border-right: 0.5px solid lightgray',
),
column(6,
verbatimTextOutput("UserCutPSumm")
)
),
value = 5)
),
value = 1),
#### Univar Surv ------------------------------
tabPanel("Univariate Survival Analysis",
p(),
fluidRow(
column(6,
selectizeInput("SingleSurvivalFeature","Select Feature:",choices = NULL, selected = 1, width = "80%"),
# Allows all select inputs to be wide enough to read the contents
tags$head(
tags$style(HTML('
.selectize-dropdown {
width: 500px !important;
}'
)
)
),
fluidRow(
column(3,
checkboxInput("UniVarNAcheck","Remove NA/Unknown/Inf",value = T)
),
column(3,
checkboxInput("UniVarContCheck","Continuous Feature",value = F)
),
column(3,
conditionalPanel(condition = "input.UniVarContCheck == true",
checkboxInput("UniVarContHiLoCheck","Continuous Feature as Median Cut-Point",value = T)
)
)
),
uiOutput("rendSurvFeatVariableUni"),
)
),
tabsetPanel(
id = "UniVarPlots",
tabPanel("Survival Plot",
p(),
shinycssloaders::withSpinner(shinyjqui::jqui_resizable(plotOutput("featSplot", width = SurvPlot_Width, height = SurvPlot_Height)), type = 6),
dnld_ui("dnldfeatSplot_SVG","SVG")
),
tabPanel("Coxh Table",
p(),
fluidRow(
column(6,
div(shinycssloaders::withSpinner(tableOutput("SSingleFeatureHRtab"), type = 7, size = 0.5), style = "font-size:12px; width:500px; overflow-X: scroll")
),
column(6,
verbatimTextOutput("UnivarSummary")
)
)
),
tabPanel("Forest Plot",
p(),
shinycssloaders::withSpinner(shinyjqui::jqui_resizable(plotOutput("SinglevarForestPlot", width = "100%", height = "800px")), type = 6),
downloadButton("dnldUniVarForestplot_SVG","SVG")
),
tabPanel("Multi-Feature Forest Plot",
p(),
fluidRow(
column(6,
selectizeInput("MultiFeatUnivarSelect","Select Features for Forest Plot",
choices = NULL, multiple = T, selected = 1, width = "100%")
),
column(2,
textInput("UnivarForestPlotXlim","X-Limits (Low,High)",value = "0,5",
placeholder = "Low,High", width = "150px")
),
column(2,
selectInput("UnivarForestPlotXtrans","X-Axis Transform",
choices = c("none", "log", "log2", "log10"))
)
),
uiOutput("rendMultiFeatUnivarForestPlot"),
fluidRow(
dnld_ui("dnldMultiFeatUnivarForestPlot_SVG","SVG"),
dnld_ui("dnldMultiFeatUnivarForestPlot_table","Download as Table")
),
p(),
div(DT::dataTableOutput("univarForestPlotTable"), style = "font-size:12px"),
dnld_ui("dnldunivarForestPlotTable","Download Table")
),
tabPanel("Linearity Check",
p(),
fluidRow(
column(3,
selectInput("ResidualTypeUni","Select Residual Type",
choices = c("deviance", "martingale", "score", "schoenfeld", "dfbeta", "dfbetas", "scaledsch", "partial"))
),
column(3,
selectInput("linPredict1", "X-axis Scale:",
choices = c("linear.predictions","observation.id","time"))
)
),
uiOutput("timewarnmessage1"),
shinycssloaders::withSpinner(shinyjqui::jqui_resizable(plotOutput("UnivarLinearityPlot", width = "100%", height = "500px")), type = 6),
dnld_ui("dnldUniVarLinplot_SVG","SVG")
)
),
value = 2),
#### Multivar Surv ----------------------------
tabPanel("Multivariate Coxh Analysis",
tabsetPanel(
id = "multivariate",
##### Multivar Add Surv ----------------------------
tabPanel("Bivariate Additive Survival Analysis",
p(),
fluidRow(
column(6,
selectizeInput("SurvivalFeatureBi1","Select Feature 1:",choices = NULL, selected = 1, width = "80%"),
#uiOutput("rendSurvivalFeatureBi1"),
fluidRow(
column(4,
checkboxInput("BiVarAddNAcheck1","Remove NA/Unknown/Inf",value = T)
),
column(4,
checkboxInput("BiVarAddContCheck1","Continuous Feature",value = F)
),
column(4,
conditionalPanel(condition = "input.BiVarAddContCheck1 == true",
checkboxInput("BiVarAddContHiLoCheck1","Continuous Feature as Median Cut-Point",value = T)
)
#uiOutput("rendBiVarAddContHiLoCheck1")
)
),
uiOutput("rendSurvFeatVariableBi1")
),
column(6,
selectizeInput("SurvivalFeatureBi2","Select Feature 2:",choices = NULL, selected = 1, width = "80%"),
#uiOutput("rendSurvivalFeatureBi2"),
fluidRow(
column(4,
checkboxInput("BiVarAddNAcheck2","Remove NA/Unknown/Inf",value = T)
),
column(4,
checkboxInput("BiVarAddContCheck2","Continuous Feature",value = F)
),
column(4,
conditionalPanel(condition = "input.BiVarAddContCheck2 == true",
checkboxInput("BiVarAddContHiLoCheck2","Continuous Feature as Median Cut-Point",value = T)
)
#uiOutput("rendBiVarAddContHiLoCheck2")
)
),
uiOutput("rendSurvFeatVariableBi2")
),
#column(4,
# htmlOutput("BivarAddSummExpl", style = "font-size:14px;")
#)
),
tabsetPanel(
id = "BiVarPlots",
tabPanel("Cox HR Table",
p(),
fluidRow(
column(6,
div(shinycssloaders::withSpinner(tableOutput("BiFeatureHRtab"), type = 7, size = 0.5), style = "font-size:12px; width:500px; overflow-X: scroll")
),
column(6,
verbatimTextOutput("bivarSummary"),
fluidRow(
column(6,
verbatimTextOutput("bivarAnova1")
),
column(6,
verbatimTextOutput("bivarAnova2")
)
)
)
)
),
tabPanel("Forest Plot",
p(),
shinycssloaders::withSpinner(shinyjqui::jqui_resizable(plotOutput("BivarForestPlot", width = "100%", height = "800px")), type = 6),
downloadButton("dnldBiVarAddForest_SVG","SVG")
#dnld_ui("dnldBiVarAddForest_SVG","SVG")
),
tabPanel("Linearity Check",
p(),
fluidRow(
column(3,
selectInput("ResidualTypeBi","Select Residual Type",
choices = c("deviance", "martingale", "score", "schoenfeld", "dfbeta", "dfbetas", "scaledsch", "partial"))
),
column(3,
selectInput("linPredict2", "X-axis Scale:",
choices = c("linear.predictions","observation.id","time"))
)
),
uiOutput("timewarnmessage2"),
shinycssloaders::withSpinner(shinyjqui::jqui_resizable(plotOutput("BivarLinearityPlot", width = "100%", height = "500px")), type = 6),
dnld_ui("dnldBiVarAddLinplot_SVG","SVG")
)
)
),
##### Multivar Int Surv ----------------------------
tabPanel("Bivariate Interaction Survival Analysis",
p(),
fluidRow(
column(6,
selectizeInput("SurvivalFeatureBi1Inter","Select Feature 1:",choices = NULL, selected = 1, width = "80%"),
fluidRow(
column(4,
checkboxInput("BiVarIntNAcheck1","Remove NA/Unknown/Inf",value = T)
),
column(4,
checkboxInput("BiVarIntContCheck1","Continuous Feature",value = F)
),
column(4,
conditionalPanel(condition = "input.BiVarIntContCheck1 == true",
checkboxInput("BiVarIntContHiLoCheck1","Continuous Feature as Median Cut-Point",value = T)
)
)
),
uiOutput("rendSurvFeatVariableBi1Inter")
),
column(6,
selectizeInput("SurvivalFeatureBi2Inter","Select Feature 1:",choices = NULL, selected = 1, width = "80%"),
fluidRow(
column(4,
checkboxInput("BiVarIntNAcheck2","Remove NA/Unknown/Inf",value = T)
),
column(4,
checkboxInput("BiVarIntContCheck2","Continuous Feature",value = F)
),
column(4,
conditionalPanel(condition = "input.BiVarIntContCheck2 == true",
checkboxInput("BiVarIntContHiLoCheck2","Continuous Feature as Median Cut-Point",value = T)
)
)
),
uiOutput("rendSurvFeatVariableBi2Inter")
),
column(4,
verbatimTextOutput("BivarIntSummExpl")
)
),
tabsetPanel(
id = "BiVarInterTabs",
tabPanel("Survival Plot",
p(),
shinycssloaders::withSpinner(shinyjqui::jqui_resizable(plotOutput("featSplotBi", width = SurvPlot_Width, height = SurvPlot_Height)), type = 6),
dnld_ui("dnldfeatSplotBi_SVG","SVG")
),
tabPanel("Cox HR Table",
p(),
fluidRow(
column(6,
div(shinycssloaders::withSpinner(tableOutput("BiFeatureHRtabInter"), type = 7, size = 0.5), style = "font-size:12px; width:500px; overflow-X: scroll")
),
column(6,
verbatimTextOutput("bivarSummaryInter"),
verbatimTextOutput("bivarAnovaInter1")
)
)
),
tabPanel("Linearity Check",
p(),
fluidRow(
column(3,
selectInput("ResidualTypeInter","Select Residual Type",
choices = c("deviance", "martingale", "score", "schoenfeld", "dfbeta", "dfbetas", "scaledsch", "partial"))
),
column(3,
selectInput("linPredict3", "X-axis Scale:",
choices = c("linear.predictions","observation.id","time"))
)
),
uiOutput("timewarnmessage3"),
shinycssloaders::withSpinner(shinyjqui::jqui_resizable(plotOutput("BivarLinearityPlotInter", width = "100%", height = "500px")), type = 6),
dnld_ui("dnldBiVarIntLinplot_SVG","SVG")
)
)
),
##### Multivar Surv ----------------------------
tabPanel("Multivariate Coxh Analysis",
p(),
fluidRow(
column(6,
selectizeInput("SurvivalFeature","Select Feature(s):",choices = NULL, selected = 1, multiple = T, width = "100%"),
#uiOutput("rendSurvivalFeature"),
checkboxInput("MultiVarNAcheck","Remove NA/Unknown",value = T)
)
),
tabsetPanel(
id = "multivartabstwo",
tabPanel("Coxh Tables",
fluidRow(
column(6,
h4("Coxh Hazard Ratio (Categorical)"),
verbatimTextOutput("multivarSummaryCat"),
div(shinycssloaders::withSpinner(tableOutput("SFeatureHRtabCat"), type = 7, size = 0.5), style = "font-size:12px; width:500px; overflow-X: scroll")
),
column(6,
h4("Coxh Hazard Ratio (Continuous)"),
verbatimTextOutput("multivarSummaryCont"),
div(shinycssloaders::withSpinner(tableOutput("SFeatureHRtabCont"), type = 7, size = 0.5), style = "font-size:12px; width:500px; overflow-X: scroll")
)
)
),
tabPanel("Forest Plot",
p(),
shinycssloaders::withSpinner(shinyjqui::jqui_resizable(plotOutput("MultivarForestPlot", width = "100%", height = "800px")), type = 6),
downloadButton("dnldMultiVarForest_SVG","SVG")
)
)
),
##### Multivar Forest -----------------
tabPanel("Multivariate Forest Plot",
p(),
fluidRow(
column(4,
selectizeInput("MultiFeatMultivarSelect","Select Main Forest Feature",
choices = NULL, multiple = F, selected = 1, width = "100%"),
#uiOutput("rendMultiFeatMultivarSelect"),
uiOutput("rendMultiFeatMultivarRefSelect")
),
column(3,
selectizeInput("MultiFeatMultivarSubSelect","Select and Add Features to Forest Plot:",
choices = NULL, multiple = T, selected = 1, width = "100%")
),
column(2,
textInput("MultivarForestPlotXlim","X-Limits (Low,High)",value = "0,5",
placeholder = "Low,High")
),
column(2,
selectInput("MultivarForestPlotXtrans","X-Axis Transform",
choices = c("none", "log", "log2", "log10"))
)
),
uiOutput("rendMultiFeatMultivarForestPlot"),
fluidRow(
dnld_ui("dnldMultiFeatMultivarForestPlot_SVG","SVG"),
dnld_ui("dnldMultiFeatMultivarForestPlot_table","Download as Table")
),
p(),
div(DT::dataTableOutput("multiForestPlotTable"), style = "font-size:12px"),
dnld_ui("dnldmultiForestPlotTable","Download Table")
)
),
value = 3),
#### Lasso
#tabPanel("Lasso Cox Model",
# p(),
# fluidRow(
# column(2,
# br(),
# actionButton("RunLassoModelGen","Generate Lasso Model")
# ),
# column(3,
# uiOutput("rendSurvTimeSelecView_lasso")
# ),
# column(3,
# uiOutput("rendSurvIDSelecView_lasso")
# )
# ),
# fluidRow(
# column(6,
# shinycssloaders::withSpinner(shinyjqui::jqui_resizable(plotOutput("Lasso_Train_Splot", width = "100%", height = "500px")),type = 6),
# dnld_ui("dnldSplotLassoTrain_SVG","SVG"),
# shiny::hr(),
# h4("Path of Coefficients"),
# shinyjqui::jqui_resizable(plotOutput("Lasso_CoeffPlot", width = "100%", height = "400px")),
# shiny::hr(),
# h4("Training Cox Hazard Regression Analysis Summary"),
# uiOutput("rendLassoTrainHRtab"),
# verbatimTextOutput("LassoTrainCoxSumm")
# ),
# column(6,
# shinycssloaders::withSpinner(shinyjqui::jqui_resizable(plotOutput("Lasso_Test_Splot", width = "100%", height = "500px")),type = 6),
# dnld_ui("dnldSplotLassoTest_SVG","SVG"),
# shiny::hr(),
# h4("Lambda Cross-Validation"),
# shinyjqui::jqui_resizable(plotOutput("Lasso_LambdaPlot", width = "100%", height = "400px")),
# shiny::hr(),
# h4("Testing Cox Hazard Regression Analysis Summary"),
# uiOutput("rendLassoTestHRtab"),
# verbatimTextOutput("LassoTestCoxSumm")
# )
# ),
# value = 5),
#### Data Explor ------------------------------
tabPanel("Data Exploration",
tabsetPanel(
id = "DataExploration",
##### Surv Data ---------------------------------
tabPanel("Download Survival Data",
p(),
selectizeInput("MetaTableCols","Select Meta Columns to View:",multiple = T, choices = NULL, selected = ""),
div(DT::dataTableOutput("MetaTable"), style = "font-size:12px"),
fluidRow(
column(2,
dnld_ui("DnldClin","Download Clinical Data")
),
column(2,
dnld_ui("DnldExpr","Download Expression Data")
)
),
value = 5),
##### Density ---------------------------------
tabPanel("Score Density",
p(),
fluidRow(
numericInput("densityPercent","User Defined Percentile (Red)",value = 15, width = "200px"),
checkboxInput("QuartileLinesCheck","Show Quartile Lines (Blue)",value = T)
),
shinycssloaders::withSpinner(shinyjqui::jqui_resizable(plotOutput("ssgseaDensity", width = "100%", height = "500px")), type = 6),
dnld_ui("dnldssgseaDensity_SVG","SVG"),
p(),
div(DT::dataTableOutput("ssgseaDensityTable"), style = "font-size:12px"),
dnld_ui("dnldssgseaDensityTable","Download Table"),
value = 6),
##### Feat Comp ---------------------------------
tabPanel("Feature Comparison",
p(),
fluidRow(
column(3,
selectizeInput("ScatterFeature","Select Feature:",multiple = F, choices = NULL, selected = 1)
),
column(2,
radioButtons("ColorScatterChoice","Color Plot by:",choices = c("Feature","Single Color"))
),
column(3,
conditionalPanel(condition = "input.ColorScatterChoice == 'Feature'",
selectizeInput("ScatterColor","Color By:",multiple = F, choices = NULL, selected = 1)
),
conditionalPanel(condition = "input.ColorScatterChoice == 'Single Color'",
selectInput("ScatterColor2","Color:",choices = colors(), selected = "cadetblue"))
),
column(1, style = "padding-right:2px",
checkboxGroupInput("ScatterLog","", choices = c("Log x-axis","Log y-axis"))
),
column(2, style = "margin-top:12px",
checkboxInput("RegressionLine","Add Regression Line", value = T)
)
),
shinycssloaders::withSpinner(shinyjqui::jqui_resizable(plotlyOutput("FeatCompScatterPlot", width = "100%", height = "500px")), type = 6),
p(),
div(DT::dataTableOutput("FeatCompScatterTable"), style = "font-size:12px"),
dnld_ui("dnldFeatCompScatterTable","Download Table"),
value = 7),
##### Risk Strat ---------------------------------
tabPanel("Risk Stratification",
p(),
fluidRow(
column(4,
numericInput("cutoffTime1","High-Risk Survival Time Cutoff:", value = 364, min = 0, step = 1),
selectInput("survStatus1","Survival Status Below Cutoff:", choices = c("1","0","0/1"), selected = "1")
),
column(4,
numericInput("cutoffTime0","Low-Risk Survival Time Cutoff:", value = 365, min = 0, step = 1),
selectInput("survStatus0","Survival Status Above Cutoff:", choices = c("1","0","0/1"), selected = "0")
),
column(4,
conditionalPanel(condition = "input.riskstrat == 'box'",
selectInput("boxoptselecRisk","Stat Compare Method:", choices = c("none","wilcox.test","t.test")),
checkboxInput("SBoxLog", "Log Transform Score", value = T)
),
conditionalPanel(condition = "input.riskstrat == 'heat'",
selectizeInput("riskHeatAnno","Add Annotation:", choices = NULL, selected = 1, multiple = T),
selectInput("ClusterMethod", "Select Cluster Method:",
choices = c("ward.D", "ward.D2", "complete", "single", "average", "mcquitty", "median", "centroid"))
)
)