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inst/app/tools/bioCancer/Circomics_ui.R
In bioCancer: Interactive Multi-Omics Cancers Data Visualization and Analysis
# output$LegendCircos <- renderPlot({
# #my.colors = colorRampPalette(c("blue3","cyan","white","yellow", "red","black"))
# my.colors = colorRampPalette(c("blue3", "white", "red"))
# z=matrix(1:100,nrow=1)
# x=1
# y=seq(3,2345,len=100) # supposing 3 and 2345 are the range of your data
# image(x,y,z,col=my.colors(100),axes=FALSE,xlab="",ylab="")
# #axis(2)
# #mtext(text=c("Min","Low","middle","High","Max","NA"), line=1.8, las=2, side=4, at=c(50,500,900, 1400,1900,2300),adj = 1)
# #mtext(text=c("Down","Low","0","High","Up","NA"), line=0.5, las=2, side=2, outer = FALSE, at=c(50,500,900, 1400,1900,2300),adj = 1)
# mtext(text=c("Min","Medium","Max"), line=1.8, las=2, side=4, at=c(50,1150, 2300),adj = 1)
# mtext(text=c("Down","0","Up"), line=0.5, las=2, side=2, outer = FALSE, at=c(50,1150, 2300),adj = 1)
# })
output$CircosLegend <- renderImage({
# When input$n is 3, filename is ./images/image3.jpeg
filename <- paste(path.package('bioCancer'),"/extdata/imgs/CircosLegend.png", sep="")
# Return a list containing the filename and alt text
list(src = filename,
contentType = 'image/png',
width = 200,
height = 250,
alt = paste("Image number"))
}, deleteFile = FALSE)
# pull user data to r_data$ListProfData
output$uiPullUserDataCNA <- renderUI({
selectInput(inputId = "UserData_CNA_id", label='CNA:',
choices= r_info$datasetlist, selected= "", multiple=FALSE,
selectize = FALSE
)
})
output$uiPullUserDatamRNA <- renderUI({
selectInput(inputId = "UserData_mRNA_id", label='mRNA:',
choices= r_info$datasetlist, selected= "", multiple=FALSE,
selectize = FALSE
)
})
output$uiPullUserDataMetHM27 <- renderUI({
selectInput(inputId = "UserData_MetHM27_id", label='Methylation HM27',
choices= r_info$datasetlist, selected= NULL, multiple=FALSE,
selectize = FALSE
)
})
output$uiPullUserDataMetHM450 <- renderUI({
selectInput(inputId = "UserData_MetHM450_id", label='Methylation HM450',
choices= r_info$datasetlist, selected= NULL, multiple=FALSE,
selectize = FALSE
)
})
output$uiPullUserDataFreqMut <- renderUI({
selectInput(inputId = "UserData_FreqMut_id", label='Mutation Frequency',
choices= r_info$datasetlist, selected= NULL, multiple=FALSE,
selectize = FALSE
)
})
output$uiPullUserDatamiRNA <- renderUI({
selectInput(inputId = "UserData_miRNA_id", label='miRNA',
choices= r_info$datasetlist, selected= NULL, multiple=FALSE,
selectize = FALSE
)
})
output$uiPullUserDataRPPA <- renderUI({
selectInput(inputId = "UserData_RPPA_id", label='RPPA',
choices= r_info$datasetlist, selected= NULL, multiple=FALSE,
selectize = FALSE
)
})
output$ui_CircosDimension <- renderUI({
Dimension <- c("CNA","Methylation", "mRNA","Mutation","miRNA","RPPA", "All" )
selectizeInput("CircosDimensionID", label= "Select Dimension:", choices= Dimension,
selected = "", multiple=TRUE)
})
output$StrListProfDataCircos <- renderPrint({
withProgress(message = 'loading Profiles Data from cgdsr server... ', value = 1, {
getListProfData(panel='Circomics',input$GeneListID)
#print("Start getting Frequency of Mutation ...")
r_info[['Freq_DfMutData']] <- getFreqMutData(list = r_info$ListMutData, geneListLabel = input$GeneListID)
#print("End getting Mutation Frequency...")
})
## don't use r_data$ListProfData => cause réinitiate wheel
# if(is.null(r_data$ListProfData)){
# c("Gene List is empty. copy and paste genes from text file (Gene/line) or use gene list from examples.")
# }else{
#
c("STUDIES:", input$StudiesIDCircos,
"Genetic Profiles: mRNA, Methylation, CNA, miRNA, Mutation, RPPA",
"Gene List:", input$GeneListID
)
# }
})
output$ui_userDataMergeDimension <- renderUI({
tagList(
if('CNA' %in% input$userDataID){
uiOutput("uiPullUserDataCNA")
},
if('mRNA' %in% input$userDataID){
uiOutput("uiPullUserDatamRNA")
},
if('Mutation' %in% input$userDataID){
uiOutput("uiPullUserDataFreqMut")
},
if('MetHM27' %in% input$userDataID){
uiOutput("uiPullUserDataMetHM27")
},
if('MetHM450' %in% input$userDataID2){
uiOutput("uiPullUserDataMetHM450")
},
if('miRNA' %in% input$userDataID2){
uiOutput("uiPullUserDatamiRNA")
},
if('RPPA' %in% input$userDataID2){
uiOutput("uiPullUserDataRPPA")
}
)
# conditionalPanel(condition="input.userDataID== 'mRNA'",
# uiOutput("uiPullUserDatamRNA")
# )
# conditionalPanel(condition="input.userDataID== 'MetHM27'",
# uiOutput("uiPullUserDataMetHM27")
# )
# conditionalPanel(condition="input.userDataID== 'MetHM450'",
# uiOutput("uiPullUserDataMetHM450")
# )
# conditionalPanel(condition="input.userDataID2== 'Mutation'",
# uiOutput("uiPullUserDataFreqMut")
# )
# conditionalPanel(condition="input.userDataID2== 'miRNA'",
# uiOutput("uiPullUserDatamiRNA")
# )
# conditionalPanel(condition="input.userDataID2== 'RPPA'",
# uiOutput("uiPullUserDataRPPA")
# )
})
output$ui_userDataMergeSwithButton <- renderUI({
if(!is.null(input$userDataID) || !is.null(input$userDataID2)){
div(class="row",
div(class="col-xs-8",
conditionalPanel(condition = "input.StudiesIDCircos != null && input.pullUserDataButtonId ==false",
h5('Merge user data to wheel')),
conditionalPanel(condition = "input.StudiesIDCircos != null && input.pullUserDataButtonId ==true",
h5('Merge User data to wheel', style = "color:#428bca"))
),
div(class="col-xs-4",
conditionalPanel(condition = "input.StudiesIDCircos != null",
switchButton(inputId = "pullUserDataButtonId",
value = FALSE, col = "GB", type = "OO")
)
)
)
}
})
output$ui_bad_userData_message <- renderUI({
# if user data is in ListProfData
if(any(grepl('UserData', lapply(r_info$ListProfData, function(x) names(x)))) || any(grepl('UserData', names(r_info$ListMutData)))){
h5("+ User data",align="center", style = "color:#428bca;font-size:100%")
}else{
h5(" select correct User data",align="center", style = "color:red;font-size:100%")
}
})
output$ui_Circomics <- renderUI({
## get Studies for Circomics
updateSelectizeInput(session, 'StudiesIDCircos', choices = Studies[,1],
selected = c("luad_tcga_pub","blca_tcga_pub"))
#,"prad_tcga_pub","ucec_tcga_pub"
conditionalPanel("input.tabs_Enrichment == 'Circomics'",
wellPanel(
selectizeInput('StudiesIDCircos', 'Studies in Wheel', choices= Studies[,1],
selected = c("luad_tcga_pub","blca_tcga_pub"), multiple = TRUE),
conditionalPanel(condition = "input.StudiesIDCircos == null",
h5("Select at less two studies",align="center",style = "color:red")
),
# if(length(input$StudiesIDCircos)==1){
div(class="row",
div(class="col-xs-8",
conditionalPanel(condition = "input.StudiesIDCircos != null && input.ViewProfDataCircosID==false",
h5('Check for availability')),
conditionalPanel(condition = "input.StudiesIDCircos != null && input.ViewProfDataCircosID==true",
h5('Check for availability', style = "color:#428bca")
)
),
div(class="col-xs-4",
conditionalPanel(condition = "input.StudiesIDCircos != null",
switchButton(inputId = "ViewProfDataCircosID",
value = FALSE, col = "GB", type = "OO"))
)
),
div(class="row",
div(class="col-xs-8",
conditionalPanel(condition = "input.StudiesIDCircos != null && input.loadListProfDataCircosId ==false",
h5('Load genetic profiles')),
conditionalPanel(condition = "input.StudiesIDCircos != null && input.loadListProfDataCircosId ==true",
h5('Load genetic profiles', style = "color:#428bca"))
),
div(class="col-xs-4",
conditionalPanel(condition = "input.StudiesIDCircos != null",
switchButton(inputId = "loadListProfDataCircosId",
value = FALSE, col = "GB", type = "OO")
)
)
),
div(class="row",
div(class="col-xs-8",
conditionalPanel(condition= 'input.loadListProfDataCircosId == true && input.pushListProfData == false',
h5('Import data to Workspace')),
conditionalPanel(condition= 'input.loadListProfDataCircosId == true && input.pushListProfData == true',
h5('Import data to Workspace', style = "color:#428bca"))
),
div(class='col-xs-4',
conditionalPanel(condition = 'input.loadListProfDataCircosId == true',
switchButton(inputId = "pushListProfData",
value = FALSE, col = "GB", type = "OO")
)
)
),
conditionalPanel(condition = "input.pushListProfData==true",
h5("The data sets are loaded to Workspace.",align="center", style = "color:#428bca")
),
conditionalPanel(condition = "input.pullUserDataButtonId==true",
#
uiOutput("ui_bad_userData_message")
#
),
#}
conditionalPanel("input.loadListProfDataCircosId == true",
wellPanel(
################
# radioButtons("CircosDimensionID", "Choose Dimensions:", #checkboxGroupInput
# choiceNames =
# list("Copy Number Alteration","Methylation HM27 HM450","mRNA expression",
# "Mutation","miRNA expression", "RPPA", "ALL"),
# choiceValues =
# list("CNA","Met", "mRNA", "Mutation", "miRNA", "RPPA", "All")
# ,selected = character(0)
# )
uiOutput("ui_CircosDimension")
#
)
),
conditionalPanel("input.CircosDimensionID != null",
wellPanel(
h4("Merge user data to wheel:"),
div(class="row",
div(class="col-xs-6",
checkboxGroupInput("userDataID", label = NULL,
choices =
list("CNA", "mRNA","Mutation","MetHM27")
)
),
div(class="col-xs-6",
checkboxGroupInput("userDataID2", label= NULL,
choices =
list("MetHM450", "miRNA", "RPPA")
)
)
),
# div(class="row",
# div(class="col-xs-3",
# checkboxInput('UserDataCNAID', 'CNA', FALSE)),
# div(class="col-xs-3",
# checkboxInput('UserDatamRNAID', 'mRNA', FALSE)),
# div(class="col-xs-2",
# checkboxInput('UserDataFreqMutID', 'Mut', FALSE)),
# div(class="col-xs-2",
# checkboxInput('UserDataMet27ID', 'Met27', FALSE))
# ),
# div(class="row",
# div(class="col-xs-4",
# checkboxInput('UserDataMet450ID', 'Met450', FALSE)),
# div(class="col-xs-4",
# checkboxInput('UserDatamiRNAID', 'miRNA', FALSE)),
# div(class="col-xs-4",
# checkboxInput('UserDataRPPAID', 'RPPA', FALSE))
# ),
uiOutput("ui_userDataMergeDimension"),
uiOutput("ui_userDataMergeSwithButton")
# div(class="row",
# div(class="col-xs-6",
# actionButton('pullUserDataButtonId', 'Add to wheel', icon('arrow-down'),style='padding:4px; font-size:80%')),
# div(class="col-xs-6",
# #checkboxInput("getlistProfDataCircosID", "Load", value = FALSE))
# actionButton('UnpullUserDataButtonId', 'Remove',style='padding:4px; font-size:80%')
# )
# #checkboxInput('confirmPullUserDataID', 'Confirm Pull', FALSE)
# )
# }
)
),
#################
# conditionalPanel("input.CircosDimensionID == 'All'",
# #plot_downloader("SaveMetabologram_All", pre = ""),
# downloadButton('Save_Metabologram_All', 'All')
#
# ),
checkboxInput("CircosLegendID", "Legend", value=FALSE),
# radioButtons(inputId = "WheelID", label = "Wheel Style:",
# c("Summary"="init" ,"Zoom" = "Zoom", "Static" = "Static"),
# selected = "", inline = TRUE),
# radioButtons(inputId = "saveWheelID", label = "Save Wheel:",
# c("SVG" = "SVG", "Gif" = "Gif"),
# selected = "SVG", inline = TRUE),
#
# conditionalPanel(condition = "input.saveWheelID == 'SVG'",
# downloadButton('SaveSVG', 'SVG')),
#
# conditionalPanel(condition = "input.saveWheelID == 'Gif'",
# downloadButton("SaveGif")),
conditionalPanel("input.CircosLegendID==true",
# wellPanel(
#plotOutput("LegendCircos")
imageOutput("CircosLegend")
# )
# h4("Wheel Legend"),
# p(span("Black", style="color:black"),": Non available data."),
# p(span("White", style="color:black"),": Non significant rate."),
# p(span("Cyan", style="color:deepskyblue"),": Middle Negative significant rate."),
# p(span("Blue", style="color:blue"),": Negative significant rate."),
# p(span("Yellow", style="color:gold"),": Middle Positive significant rate."),
# p(span("Red", style="color:red"),": Positive significant rate.")
),
help_and_report(modal_title = "Circomics", fun_name = "CircomicsHelp",
author = "Karim Mezhoud",
help_file = inclRmd(file.path(
getOption("radiant.path.bioCancer"),"app/tools/help/Circomics.md")))
)
)
})
## Load Profile data in datasets to Processing panel
observe({
if (not_pressed(input$pushListProfData)) return()
isolate({
loadInDatasets(fname="xCNA", header=TRUE)
loadInDatasets(fname="xmRNA", header=TRUE)
loadInDatasets(fname="xMetHM450", header=TRUE)
loadInDatasets(fname="xMetHM27", header=TRUE)
loadInDatasets(fname="xMut", header=TRUE)
loadInDatasets(fname="xFreqMut", header=TRUE)
loadInDatasets(fname="xmiRNA", header=TRUE)
loadInDatasets(fname="xRPPA", header=TRUE)
#### Updating datasets generate error with vars view tab
# sorting files alphabetically
#r_data[['datasetlist']] <- sort(r_data[['datasetlist']])
#updateSelectInput(session, "dataset", label = "Datasets:",
# choices = r_data$datasetlist,
# selected = "")
})
})
observe({
if (not_pressed(input$pushListProfData)) #return()
isolate({
r_data[['xCNA']] <- NULL
r_data[['xmRNA']] <- NULL
r_data[['xMetHM27']] <- NULL
#r_data$ListMetData[['xMetHM27']] <- NULL
r_data[['xMetHM450']] <- NULL
#r_data$ListMetData[['xMetHM450']] <- NULL
r_data[['xmiRNA']] <- NULL
r_data[['xRPPA']] <- NULL
r_data[['xMut']] <- NULL
r_data[['xFreqMut']] <- NULL
})
})
# observe({
#
# if (not_pressed(input$SaveSVG)) return()
# isolate({
# library(metabologram)
# CoffeewheelTreeData <- reStrDimension(r_data$ListProfData)
# metabologram(CoffeewheelTreeData, width=500, height=500, main="metabologram", showLegend = TRUE, fontSize = 12, legendBreaks=c("NA","Min","Negative", "0", "Positive", "Max"), legendColors=c("black","blue","cyan","white","yellow","red") , legendText="Legend")
#
# })
# })
#
# output$SaveGif = downloadHandler(
# filename = function(){'random.png'},
# content = function(file){
# CoffeewheelTreeData <- reStrDimension(r_data$ListProfData)
# ggsave(file,metabologram(CoffeewheelTreeData, width=500, height=500, main="metabologram", showLegend = TRUE, fontSize = 12, legendBreaks=c("NA","Min","Negative", "0", "Positive", "Max"), legendColors=c("black","blue","cyan","white","yellow","red") , legendText="Legend"))
# #file.rename('random.gif', file)
# }
# )
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# output$LegendCircos <- renderPlot({
# #my.colors = colorRampPalette(c("blue3","cyan","white","yellow", "red","black"))
# my.colors = colorRampPalette(c("blue3", "white", "red"))
# z=matrix(1:100,nrow=1)
# x=1
# y=seq(3,2345,len=100) # supposing 3 and 2345 are the range of your data
# image(x,y,z,col=my.colors(100),axes=FALSE,xlab="",ylab="")
# #axis(2)
# #mtext(text=c("Min","Low","middle","High","Max","NA"), line=1.8, las=2, side=4, at=c(50,500,900, 1400,1900,2300),adj = 1)
# #mtext(text=c("Down","Low","0","High","Up","NA"), line=0.5, las=2, side=2, outer = FALSE, at=c(50,500,900, 1400,1900,2300),adj = 1)
# mtext(text=c("Min","Medium","Max"), line=1.8, las=2, side=4, at=c(50,1150, 2300),adj = 1)
# mtext(text=c("Down","0","Up"), line=0.5, las=2, side=2, outer = FALSE, at=c(50,1150, 2300),adj = 1)
# })
output$CircosLegend <- renderImage({
# When input$n is 3, filename is ./images/image3.jpeg
filename <- paste(path.package('bioCancer'),"/extdata/imgs/CircosLegend.png", sep="")
# Return a list containing the filename and alt text
list(src = filename,
contentType = 'image/png',
width = 200,
height = 250,
alt = paste("Image number"))
}, deleteFile = FALSE)
# pull user data to r_data$ListProfData
output$uiPullUserDataCNA <- renderUI({
selectInput(inputId = "UserData_CNA_id", label='CNA:',
choices= r_info$datasetlist, selected= "", multiple=FALSE,
selectize = FALSE
)
})
output$uiPullUserDatamRNA <- renderUI({
selectInput(inputId = "UserData_mRNA_id", label='mRNA:',
choices= r_info$datasetlist, selected= "", multiple=FALSE,
selectize = FALSE
)
})
output$uiPullUserDataMetHM27 <- renderUI({
selectInput(inputId = "UserData_MetHM27_id", label='Methylation HM27',
choices= r_info$datasetlist, selected= NULL, multiple=FALSE,
selectize = FALSE
)
})
output$uiPullUserDataMetHM450 <- renderUI({
selectInput(inputId = "UserData_MetHM450_id", label='Methylation HM450',
choices= r_info$datasetlist, selected= NULL, multiple=FALSE,
selectize = FALSE
)
})
output$uiPullUserDataFreqMut <- renderUI({
selectInput(inputId = "UserData_FreqMut_id", label='Mutation Frequency',
choices= r_info$datasetlist, selected= NULL, multiple=FALSE,
selectize = FALSE
)
})
output$uiPullUserDatamiRNA <- renderUI({
selectInput(inputId = "UserData_miRNA_id", label='miRNA',
choices= r_info$datasetlist, selected= NULL, multiple=FALSE,
selectize = FALSE
)
})
output$uiPullUserDataRPPA <- renderUI({
selectInput(inputId = "UserData_RPPA_id", label='RPPA',
choices= r_info$datasetlist, selected= NULL, multiple=FALSE,
selectize = FALSE
)
})
output$ui_CircosDimension <- renderUI({
Dimension <- c("CNA","Methylation", "mRNA","Mutation","miRNA","RPPA", "All" )
selectizeInput("CircosDimensionID", label= "Select Dimension:", choices= Dimension,
selected = "", multiple=TRUE)
})
output$StrListProfDataCircos <- renderPrint({
withProgress(message = 'loading Profiles Data from cgdsr server... ', value = 1, {
getListProfData(panel='Circomics',input$GeneListID)
#print("Start getting Frequency of Mutation ...")
r_info[['Freq_DfMutData']] <- getFreqMutData(list = r_info$ListMutData, geneListLabel = input$GeneListID)
#print("End getting Mutation Frequency...")
})
## don't use r_data$ListProfData => cause réinitiate wheel
# if(is.null(r_data$ListProfData)){
# c("Gene List is empty. copy and paste genes from text file (Gene/line) or use gene list from examples.")
# }else{
#
c("STUDIES:", input$StudiesIDCircos,
"Genetic Profiles: mRNA, Methylation, CNA, miRNA, Mutation, RPPA",
"Gene List:", input$GeneListID
)
# }
})
output$ui_userDataMergeDimension <- renderUI({
tagList(
if('CNA' %in% input$userDataID){
uiOutput("uiPullUserDataCNA")
},
if('mRNA' %in% input$userDataID){
uiOutput("uiPullUserDatamRNA")
},
if('Mutation' %in% input$userDataID){
uiOutput("uiPullUserDataFreqMut")
},
if('MetHM27' %in% input$userDataID){
uiOutput("uiPullUserDataMetHM27")
},
if('MetHM450' %in% input$userDataID2){
uiOutput("uiPullUserDataMetHM450")
},
if('miRNA' %in% input$userDataID2){
uiOutput("uiPullUserDatamiRNA")
},
if('RPPA' %in% input$userDataID2){
uiOutput("uiPullUserDataRPPA")
}
)
# conditionalPanel(condition="input.userDataID== 'mRNA'",
# uiOutput("uiPullUserDatamRNA")
# )
# conditionalPanel(condition="input.userDataID== 'MetHM27'",
# uiOutput("uiPullUserDataMetHM27")
# )
# conditionalPanel(condition="input.userDataID== 'MetHM450'",
# uiOutput("uiPullUserDataMetHM450")
# )
# conditionalPanel(condition="input.userDataID2== 'Mutation'",
# uiOutput("uiPullUserDataFreqMut")
# )
# conditionalPanel(condition="input.userDataID2== 'miRNA'",
# uiOutput("uiPullUserDatamiRNA")
# )
# conditionalPanel(condition="input.userDataID2== 'RPPA'",
# uiOutput("uiPullUserDataRPPA")
# )
})
output$ui_userDataMergeSwithButton <- renderUI({
if(!is.null(input$userDataID) || !is.null(input$userDataID2)){
div(class="row",
div(class="col-xs-8",
conditionalPanel(condition = "input.StudiesIDCircos != null && input.pullUserDataButtonId ==false",
h5('Merge user data to wheel')),
conditionalPanel(condition = "input.StudiesIDCircos != null && input.pullUserDataButtonId ==true",
h5('Merge User data to wheel', style = "color:#428bca"))
),
div(class="col-xs-4",
conditionalPanel(condition = "input.StudiesIDCircos != null",
switchButton(inputId = "pullUserDataButtonId",
value = FALSE, col = "GB", type = "OO")
)
)
)
}
})
output$ui_bad_userData_message <- renderUI({
# if user data is in ListProfData
if(any(grepl('UserData', lapply(r_info$ListProfData, function(x) names(x)))) || any(grepl('UserData', names(r_info$ListMutData)))){
h5("+ User data",align="center", style = "color:#428bca;font-size:100%")
}else{
h5(" select correct User data",align="center", style = "color:red;font-size:100%")
}
})
output$ui_Circomics <- renderUI({
## get Studies for Circomics
updateSelectizeInput(session, 'StudiesIDCircos', choices = Studies[,1],
selected = c("luad_tcga_pub","blca_tcga_pub"))
#,"prad_tcga_pub","ucec_tcga_pub"
conditionalPanel("input.tabs_Enrichment == 'Circomics'",
wellPanel(
selectizeInput('StudiesIDCircos', 'Studies in Wheel', choices= Studies[,1],
selected = c("luad_tcga_pub","blca_tcga_pub"), multiple = TRUE),
conditionalPanel(condition = "input.StudiesIDCircos == null",
h5("Select at less two studies",align="center",style = "color:red")
),
# if(length(input$StudiesIDCircos)==1){
div(class="row",
div(class="col-xs-8",
conditionalPanel(condition = "input.StudiesIDCircos != null && input.ViewProfDataCircosID==false",
h5('Check for availability')),
conditionalPanel(condition = "input.StudiesIDCircos != null && input.ViewProfDataCircosID==true",
h5('Check for availability', style = "color:#428bca")
)
),
div(class="col-xs-4",
conditionalPanel(condition = "input.StudiesIDCircos != null",
switchButton(inputId = "ViewProfDataCircosID",
value = FALSE, col = "GB", type = "OO"))
)
),
div(class="row",
div(class="col-xs-8",
conditionalPanel(condition = "input.StudiesIDCircos != null && input.loadListProfDataCircosId ==false",
h5('Load genetic profiles')),
conditionalPanel(condition = "input.StudiesIDCircos != null && input.loadListProfDataCircosId ==true",
h5('Load genetic profiles', style = "color:#428bca"))
),
div(class="col-xs-4",
conditionalPanel(condition = "input.StudiesIDCircos != null",
switchButton(inputId = "loadListProfDataCircosId",
value = FALSE, col = "GB", type = "OO")
)
)
),
div(class="row",
div(class="col-xs-8",
conditionalPanel(condition= 'input.loadListProfDataCircosId == true && input.pushListProfData == false',
h5('Import data to Workspace')),
conditionalPanel(condition= 'input.loadListProfDataCircosId == true && input.pushListProfData == true',
h5('Import data to Workspace', style = "color:#428bca"))
),
div(class='col-xs-4',
conditionalPanel(condition = 'input.loadListProfDataCircosId == true',
switchButton(inputId = "pushListProfData",
value = FALSE, col = "GB", type = "OO")
)
)
),
conditionalPanel(condition = "input.pushListProfData==true",
h5("The data sets are loaded to Workspace.",align="center", style = "color:#428bca")
),
conditionalPanel(condition = "input.pullUserDataButtonId==true",
#
uiOutput("ui_bad_userData_message")
#
),
#}
conditionalPanel("input.loadListProfDataCircosId == true",
wellPanel(
################
# radioButtons("CircosDimensionID", "Choose Dimensions:", #checkboxGroupInput
# choiceNames =
# list("Copy Number Alteration","Methylation HM27 HM450","mRNA expression",
# "Mutation","miRNA expression", "RPPA", "ALL"),
# choiceValues =
# list("CNA","Met", "mRNA", "Mutation", "miRNA", "RPPA", "All")
# ,selected = character(0)
# )
uiOutput("ui_CircosDimension")
#
)
),
conditionalPanel("input.CircosDimensionID != null",
wellPanel(
h4("Merge user data to wheel:"),
div(class="row",
div(class="col-xs-6",
checkboxGroupInput("userDataID", label = NULL,
choices =
list("CNA", "mRNA","Mutation","MetHM27")
)
),
div(class="col-xs-6",
checkboxGroupInput("userDataID2", label= NULL,
choices =
list("MetHM450", "miRNA", "RPPA")
)
)
),
# div(class="row",
# div(class="col-xs-3",
# checkboxInput('UserDataCNAID', 'CNA', FALSE)),
# div(class="col-xs-3",
# checkboxInput('UserDatamRNAID', 'mRNA', FALSE)),
# div(class="col-xs-2",
# checkboxInput('UserDataFreqMutID', 'Mut', FALSE)),
# div(class="col-xs-2",
# checkboxInput('UserDataMet27ID', 'Met27', FALSE))
# ),
# div(class="row",
# div(class="col-xs-4",
# checkboxInput('UserDataMet450ID', 'Met450', FALSE)),
# div(class="col-xs-4",
# checkboxInput('UserDatamiRNAID', 'miRNA', FALSE)),
# div(class="col-xs-4",
# checkboxInput('UserDataRPPAID', 'RPPA', FALSE))
# ),
uiOutput("ui_userDataMergeDimension"),
uiOutput("ui_userDataMergeSwithButton")
# div(class="row",
# div(class="col-xs-6",
# actionButton('pullUserDataButtonId', 'Add to wheel', icon('arrow-down'),style='padding:4px; font-size:80%')),
# div(class="col-xs-6",
# #checkboxInput("getlistProfDataCircosID", "Load", value = FALSE))
# actionButton('UnpullUserDataButtonId', 'Remove',style='padding:4px; font-size:80%')
# )
# #checkboxInput('confirmPullUserDataID', 'Confirm Pull', FALSE)
# )
# }
)
),
#################
# conditionalPanel("input.CircosDimensionID == 'All'",
# #plot_downloader("SaveMetabologram_All", pre = ""),
# downloadButton('Save_Metabologram_All', 'All')
#
# ),
checkboxInput("CircosLegendID", "Legend", value=FALSE),
# radioButtons(inputId = "WheelID", label = "Wheel Style:",
# c("Summary"="init" ,"Zoom" = "Zoom", "Static" = "Static"),
# selected = "", inline = TRUE),
# radioButtons(inputId = "saveWheelID", label = "Save Wheel:",
# c("SVG" = "SVG", "Gif" = "Gif"),
# selected = "SVG", inline = TRUE),
#
# conditionalPanel(condition = "input.saveWheelID == 'SVG'",
# downloadButton('SaveSVG', 'SVG')),
#
# conditionalPanel(condition = "input.saveWheelID == 'Gif'",
# downloadButton("SaveGif")),
conditionalPanel("input.CircosLegendID==true",
# wellPanel(
#plotOutput("LegendCircos")
imageOutput("CircosLegend")
# )
# h4("Wheel Legend"),
# p(span("Black", style="color:black"),": Non available data."),
# p(span("White", style="color:black"),": Non significant rate."),
# p(span("Cyan", style="color:deepskyblue"),": Middle Negative significant rate."),
# p(span("Blue", style="color:blue"),": Negative significant rate."),
# p(span("Yellow", style="color:gold"),": Middle Positive significant rate."),
# p(span("Red", style="color:red"),": Positive significant rate.")
),
help_and_report(modal_title = "Circomics", fun_name = "CircomicsHelp",
author = "Karim Mezhoud",
help_file = inclRmd(file.path(
getOption("radiant.path.bioCancer"),"app/tools/help/Circomics.md")))
)
)
})
## Load Profile data in datasets to Processing panel
observe({
if (not_pressed(input$pushListProfData)) return()
isolate({
loadInDatasets(fname="xCNA", header=TRUE)
loadInDatasets(fname="xmRNA", header=TRUE)
loadInDatasets(fname="xMetHM450", header=TRUE)
loadInDatasets(fname="xMetHM27", header=TRUE)
loadInDatasets(fname="xMut", header=TRUE)
loadInDatasets(fname="xFreqMut", header=TRUE)
loadInDatasets(fname="xmiRNA", header=TRUE)
loadInDatasets(fname="xRPPA", header=TRUE)
#### Updating datasets generate error with vars view tab
# sorting files alphabetically
#r_data[['datasetlist']] <- sort(r_data[['datasetlist']])
#updateSelectInput(session, "dataset", label = "Datasets:",
# choices = r_data$datasetlist,
# selected = "")
})
})
observe({
if (not_pressed(input$pushListProfData)) #return()
isolate({
r_data[['xCNA']] <- NULL
r_data[['xmRNA']] <- NULL
r_data[['xMetHM27']] <- NULL
#r_data$ListMetData[['xMetHM27']] <- NULL
r_data[['xMetHM450']] <- NULL
#r_data$ListMetData[['xMetHM450']] <- NULL
r_data[['xmiRNA']] <- NULL
r_data[['xRPPA']] <- NULL
r_data[['xMut']] <- NULL
r_data[['xFreqMut']] <- NULL
})
})
# observe({
#
# if (not_pressed(input$SaveSVG)) return()
# isolate({
# library(metabologram)
# CoffeewheelTreeData <- reStrDimension(r_data$ListProfData)
# metabologram(CoffeewheelTreeData, width=500, height=500, main="metabologram", showLegend = TRUE, fontSize = 12, legendBreaks=c("NA","Min","Negative", "0", "Positive", "Max"), legendColors=c("black","blue","cyan","white","yellow","red") , legendText="Legend")
#
# })
# })
#
# output$SaveGif = downloadHandler(
# filename = function(){'random.png'},
# content = function(file){
# CoffeewheelTreeData <- reStrDimension(r_data$ListProfData)
# ggsave(file,metabologram(CoffeewheelTreeData, width=500, height=500, main="metabologram", showLegend = TRUE, fontSize = 12, legendBreaks=c("NA","Min","Negative", "0", "Positive", "Max"), legendColors=c("black","blue","cyan","white","yellow","red") , legendText="Legend"))
# #file.rename('random.gif', file)
# }
# )
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