gui-old/ui.R
In manlius/muxViz: MuxViz - Visualization and Analysis of Multilayer Networks
library(shiny)
library(ShinyDash)
library(markdown)
library(shinydashboard)
library(rCharts)
#library(shinyIncubator)
library(digest)
library(shinyjs)
library(colourpicker)
library(d3heatmap)
library(networkD3)
source("version.R")
source("language.R")
#library("shinythemes")
#RGB colors table
#http://www.javascripter.net/faq/rgbtohex.htm
paletteWeb <- "<a href='http://www.colorschemer.com/online.html' target='_blank'>Online Color Palette</a>, <a href='http://colorbrewer2.org'>Online Color Scheme</a>"
myBoxCnt <- 0
#http://getbootstrap.com/components/#glyphicons
#http://fontawesome.io/icons/
#http://rstudio.github.io/shinydashboard/appearance.html#icons
#interactive heatmaps
#http://www.statsblogs.com/2013/12/15/visualization-of-2012-crime-rates-of-different-states-in-the-us-using-rcharts/
paletteChoiceArray <- sort(row.names(brewer.pal.info[1]))
buildPath <- function(folder,objname){
folder <- gsub("\"","", folder )
objname <- gsub("\"","", objname )
if( Sys.info()["sysname"]=="Windows" ){
#return( paste(getwd(),folder,objname,sep="\\") )
return( paste0("\"",paste(getwd(),folder,objname,sep="\\"),"\"") )
}else{
#return( paste(getwd(),folder,objname,sep="/") )
return( paste(getwd(),folder,objname,sep="/") )
}
}
buildTmpPath <- function(objname){
return( buildPath("tmp",objname) )
}
concatenatePath <- function(folder,objname){
folder <- gsub("\"","", folder )
objname <- gsub("\"","", objname )
if( Sys.info()["sysname"]=="Windows" ){
return( paste0("\"",paste(folder, paste0(objname, collapse="\\"), sep="\\"),"\"") )
}else{
return( paste(folder, paste0(objname, collapse="/"), sep="/") )
}
}
getExecutablePath <- function(exec_name){
path <- ""
if( Sys.info()["sysname"]=="Windows" ){
path <- buildPath("bin",paste0(exec_name,"_windows.exe"))
}else if( Sys.info()["sysname"]=="Linux" ){
path <- buildPath("bin",paste0(exec_name,"_linux"))
}else{
path <- buildPath("bin",paste0(exec_name,"_macosx"))
}
return(path)
}
fanmodCheck <- function(){
res <- system(getExecutablePath("fanmod"), ignore.stdout = F, ignore.stderr = F, intern=F)
if(res==255){
return(paste0("<i class='fa fa-check'></i> ",getText("txtFanmodCheck"),"<br>"))
}else{
return(paste0("<i class='fa fa-warning'></i> ",getText("txtFanmodCheckWarning"),"<br>"))
}
}
multimapCheck <- function(){
res <- system(getExecutablePath("multiplex-infomap"), ignore.stdout = F, ignore.stderr = F, intern=F)
if(res==255){
return(paste0("<i class='fa fa-check'></i> ",getText("txtMultimapCheck"),"<br>"))
}else{
return(paste0("<i class='fa fa-warning'></i> ",getText("txtMultimapCheckWarning"),"<br>"))
}
}
muxbenchCheck <- function(){
res1 <- system(getExecutablePath("muxbench1"), ignore.stdout = F, ignore.stderr = F, intern=F)
res2 <- system(getExecutablePath("muxbench2"), ignore.stdout = F, ignore.stderr = F, intern=F)
res3 <- system(getExecutablePath("muxbench3"), ignore.stdout = F, ignore.stderr = F, intern=F)
if(res1==0 && res2==0 && res3==0){
return(paste0("<i class='fa fa-check'></i> ",getText("txtMuxbenchCheck"),"<br>"))
}else{
return(paste0("<i class='fa fa-warning'></i> ",getText("txtMuxbenchCheck"),"<br>"))
}
}
myBox <- function(id, Title, Type="basic", ...){
myBoxCnt <<- myBoxCnt + 1
if(Type=="basic"){
return(
div(style="background-color: #FFFFFF; border-width: 1px; border-style: solid; border-color: #3286AD; margin: 10px 5px 10px 5px; -moz-border-radius: 15px; border-radius: 15px;",
div(style="background-color: #3286AD; color: #FFFFFF; -moz-border-top-right-radius: 15px; -moz-border-top-left-radius: 15px; border-top-left-radius: 15px; border-top-right-radius: 15px; text-align: center; font-family: 'Arial';", HTML(paste0("<font size='+1'><strong>",Title,"</strong></font> <i id=\"btnRollBox",myBoxCnt,"\" class=\"fa fa-caret-square-o-up\" onclick=\"rollBox(",paste0("btnRollBox",myBoxCnt,", RollBox",myBoxCnt),")\"></i>"))),
div(style="padding: 5px 5px 5px 5px;", id=paste0("RollBox",myBoxCnt),
list(...)
)
)
)
}
if(Type=="info"){
return(
div(style="background-color: #FFFFFF; border-width: 1px; border-style: solid; border-color: #165400; margin: 10px 5px 10px 5px; -moz-border-radius: 15px; border-radius: 15px;",
div(style="background-color: #165400; color: #FFFFFF; -moz-border-top-right-radius: 15px; -moz-border-top-left-radius: 15px; border-top-left-radius: 15px; border-top-right-radius: 15px; text-align: center; font-family: 'Arial';", HTML(paste0("<font size='+1'><strong>",Title,"</strong></font>"))),
div(style="padding: 5px 5px 5px 5px;",
list(...)
)
)
)
}
}
textInputRow <- function (inputId, label, value = "", width=NULL) {
div(style="display:inline-block",
tags$label(label, `for` = inputId),
tags$input(id = inputId, type = "text", value = value,class="input-small", width=width))
}
checkboxInputRow <- function (inputId, label, value = "") {
div(style="display:inline-block",
tags$label(label, `for` = inputId),
tags$input(id = inputId, type = "checkbox", value = value, class="input-small"))
}
placeHelp <- function(){
HTML(paste("<div style=\"float: right;\">", icon("question-circle"), "Help", "</div>"))
}
placeInfo <- function(){
HTML(paste(icon("info-circle"), "Info"))
}
placeWarn <- function(){
HTML(paste("<font color=\"red\">",icon("exclamation-circle"), "Re-apply layout", "</font>"))
}
shinyUI(function(request) {
bootstrapPage(
#shinyUI(fluidPage(shinythemes::themeSelector(),
tags$head(tags$link(rel='stylesheet', type='text/css', href='styles.css')),
# Load D3.js
tags$head(tags$script(src = 'http://d3js.org/d3.v3.min.js')),
tags$head(tags$script(src = "muxviz.js")),
tags$head(tags$title("muxViz")),
#headerPanel("muxViz Graphical User Interface"),
navbarPage("",
tabPanel(icon("home"),
sidebarLayout(position = "right",
sidebarPanel(
helpText(HTML(paste(getText("muxVizVersion"),muxVizVersion))),
helpText(HTML(paste(getText("muxVizUpdate"),muxVizUpdate))),
hr(),
helpText(HTML(paste(getText("muxVizSystem"),Sys.info()["sysname"]))),
helpText(HTML(paste(Sys.info()["version"]))),
hr(),
helpText(HTML(paste(version["version.string"][[1]]))),
hr(),
HTML(multimapCheck()),
HTML(fanmodCheck())
#HTML(muxbenchCheck())
),
mainPanel(
HTML("<img src='img/home.png' height='550' style='{margin-left: auto; margin-right: auto;}'>")
)
)
),
navbarMenu(getText("navBarFile"),
tabPanel("Import",
actionLink("btnImportHelp", placeHelp() ),
tabsetPanel(
tabPanel("Import Networks",
fluidRow(
column(width = 9,
myBox("boxNetworkModel", getText("NetworkModel"), "basic",
HTML("<img src='img/network_type.png' width='100%' alt=''/>"),
radioButtons('radMultiplexModel', '',
c(Edge_Colored='MULTIPLEX_IS_EDGECOLORED',
Interconnected_Multiplex='MULTIPLEX_IS_INTERCONNECTED',
Interdependent_Multiplex='MULTIPLEX_IS_INTERDEPENDENT',
General_Multilayer='MULTIPLEX_IS_MULTILAYER'
),
selected='MULTIPLEX_IS_EDGECOLORED',
inline=T
)
)
),
column(width = 3,
conditionalPanel(condition="input.radMultiplexModel=='MULTIPLEX_IS_EDGECOLORED'",
myBox("boxMultiplexType", getText("boxMultiplexType"), "basic",
radioButtons('radMultiplexType', '',
c(Ordinal='MULTIPLEX_IS_ORDERED',
Categorical='MULTIPLEX_IS_CATEGORICAL'),
selected='MULTIPLEX_IS_CATEGORICAL'
),
actionLink("btnMultiplexTypeInfo", placeInfo() ),
tags$br(),
tags$br(),
textInputRow("txtOmega", label=HTML(getText("txtOmega")), "1"),
helpText(getText("helpParameters"))
)
),
conditionalPanel(condition="input.radMultiplexModel!='MULTIPLEX_IS_EDGECOLORED'",
helpText(getText("txtNoParameters"))
)
)
),
fluidRow(
column(width = 3,
myBox("boxProjectID", getText("ProjectID"), "basic",
textInput("txtProjectName", label=HTML(paste0("<strong>",getText("txtProjectName"),"</strong>")), paste0("muxViz_",as.character(format(Sys.time(), "%d-%m-%Y_%H%M%S")))
)
),
myBox("boxConfiguration", getText("Configuration"), "basic",
#helpText(HTML("<h4>Open Configuration File</h4>")),
#helpText(HTML(paste0("<strong><font color='#262626'>",getText("ConfigurationFileFormat"),"</font></strong>"))),
checkboxInput('chkConfigFileHeader', getText("chkConfigFileHeader"), FALSE),
textInputRow("txtConfigFileSep", label=HTML(getText("txtConfigFileSep")), ";"),
fileInput('project_file', "",
accept=c('text/csv', 'text/comma-separated-values,text/plain', '.csv')
)
#HTML(paste0("<strong>",getText("ConfigurationFile"),"</strong>"))
)
),
#todo: here conditional panel depending on project_file
column(width = 3,
myBox("boxInputFormat", getText("InputFormat"), "basic",
checkboxInput('chkEdgeListFileHeader', getText("chkEdgeListFileHeader"), FALSE),
textInput("txtEdgeListFileSep", label=getText("txtEdgeListFileSep"), " "),
helpText(getText("txtEdgeListFileSepHelp2")),
checkboxInput("chkEdgeListLabel", getText("chkEdgeListLabel"), FALSE),
conditionalPanel("input.chkEdgeListLabel",
checkboxInput("chkEdgeListLabel2", getText("chkEdgeListLabel2"), FALSE)
),
actionLink("btnEdgeListFileSepInfo", placeInfo() )
)
),
column(width = 3,
myBox("boxNetworkFormat", getText("NetworkFormat"), "basic",
selectInput("selEdgeListType", HTML(paste0("<strong>",getText("selEdgeListType"),"</strong>")),
choices = c(getText("Undirected"), getText("Directed"))),
checkboxInput("chkEdgeListWeighted", getText("chkEdgeListWeighted"), FALSE),
checkboxInput("chkEdgeListUndirectedBoth", getText("chkEdgeListUndirectedBoth"), FALSE),
checkboxInput("chkRESCALE_WEIGHT",getText("chkRESCALE_WEIGHT"),FALSE),
checkboxInput('chkOutputEdgelistTable',HTML(getText("chkOutputEdgelistTable")),FALSE)
),
HTML("<center>"),
actionButton("btnImportNetworks", getText("btnImportNetworks")),
HTML("</center>")
)
),
tags$hr(),
helpText(HTML(paste0("<h4>",getText("ConfigurationFileSummary"),"</h4>"))),
tableOutput("layersTable"),
tags$hr(),
conditionalPanel(condition="input.btnImportNetworks>0",
myBox("boxNetworkSummary", getText("NetworkSummary"),"info",
#helpText(HTML("<h4>Summary for the multilayer network</h4>")),
htmlWidgetOutput(
outputId = 'projectSummaryHTML',
HTML("Layers: <span id=\"sumLayers\"></span><br>Type of layer: <span id=\"sumLayerType\"></span><br><br>Number of nodes: <span id=\"sumNodes\"></span><br> Minimum ID: <span id=\"sumMinNodeID\"></span><br> Maximum ID: <span id=\"sumMaxNodeID\"></span><br>Number of edges: <span id=\"sumEdges\"></span><br><br>External layout: <span id=\"sumIsLayoutExternal\"></span><br>Is geographical: <span id=\"sumIsLayoutGeographic\"></span><br>")
#seems that I cant use the getText here, it does not load the HTML..
)
),
tags$hr(),
HTML("<h4>Matrix Explorer</h4>"),
checkboxInput("chkShowMatrixExplorer", HTML(getText("chkShowMatrixExplorer"))),
tabPanel("",
selectInput("selMatrixEplorerHeatmapColorPalette", HTML(getText("ColorPalette")), choices = paletteChoiceArray),
actionLink("btnMatrixExplorerPaletteInfo", placeInfo() ),
checkboxInput("chkMatrixEplorerHeatmapShowDendrogram", getText("ApplyClustering")),
tabsetPanel(id="tabsetMatrixEplorerMultilayer",
tabPanel("Multilayer",
uiOutput("matrixExplorerHeatmapMultilayerUI")
),
tabPanel("Aggregate",
uiOutput("matrixExplorerHeatmapAggregateUI")
)
)
)
)
),
tabPanel("Edges Tables",
helpText(HTML(paste0("<h4>",getText("ImportedEdgeLists"),"</h4>"))),
conditionalPanel(condition="input.btnImportNetworks>0",
checkboxInput(inputId = "edgelistTablePageable", label = getText("Pageable"), TRUE),
conditionalPanel("input.edgelistTablePageable==true",
numericInput(inputId = "edgelistTablePageSize",label = getText("EdgesPerPage"),100)
),
htmlOutput("edgelistTable")
)
)
),
tags$hr(),
value=1
),
tabPanel("Console",
actionLink("btnConsoleHelp", placeHelp() ),
tags$textarea(id="Console", rows=20, cols=145, ""),
HTML("<center>"),
actionButton("btnRunConsole" ,getText("Run")),
HTML("</center>")
),
tabPanel("Load/Save session",
actionLink("btnSessionManagerHelp", placeHelp() ),
HTML(paste("<font color=\"red\">",icon("exclamation-circle"), getText("WarningMessage1"), "</font>")),
fluidRow(
column(width = 5,
myBox("boxLoadSession", "Session Manager", "basic",
uiOutput("selOutputSavedSessionsList"),
checkboxInput('chkConfirmDeleteSavedSession', getText("chkConfirmDeleteSavedSession"), FALSE),
actionButton("btnLoadSession", HTML(paste(icon("upload"), getText("btnLoadSession")))),
actionButton("btnDeleteSavedSession", HTML(paste(icon("trash"), getText("btnDeleteSavedSession")))),
bookmarkButton(getText("btnSaveSession"))
)
)
)
)
# tabPanel("Generate report",
# HTML("<center>"),
# downloadButton("btnGenerateReport", getText("btnGenerateReport")),
# HTML("</center>")
# )
# tabPanel("Open",
# HTML("<center>"),
# fileInput('session_file', HTML(paste0("<strong>",getText("SessionFile"),"</strong>")),
# accept=c('.mux')),
# actionButton("btnOpenSession" ,getText("btnOpenSession")),
# HTML("</center>")
# ),
# tabPanel("Save",
# HTML("<center>"),
# actionButton("btnSaveSession" ,getText("btnSaveSession")),
# HTML("</center>")
# )
),
tabPanel("Query",
actionLink("btnQueryHelp", placeHelp() ),
conditionalPanel(condition="input.btnImportNetworks>0",
fluidRow(
column(width = 3,
myBox("boxQuerySetUp", getText("QuerySetUp"), "basic",
selectInput("selQueryType", HTML(getText("selQueryType")), choices = c(getText("Nodes"), getText("Edges"))),
conditionalPanel(condition="input.selQueryType=='Nodes'",
uiOutput("selQueryNodesOutputID"),
uiOutput("selQueryNodesLayersOutputID")
),
conditionalPanel(condition="input.selQueryType=='Edges'",
uiOutput("selQueryEdgesNodesFromOutputID"),
uiOutput("selQueryEdgesNodesToOutputID"),
uiOutput("selQueryEdgesLayersOutputID")
),
checkboxInput("chkQueryShowLabels", getText("chkQueryShowLabels"), F),
HTML("<center>"),
actionButton("btnQuery", getText("Query")),
HTML("</center>")
)
)
),
htmlOutput("queryNodesTable"),
downloadButton('downQueryNodesTable', getText("downQueryNodesTable"))
)
),
tabPanel("Diagnostics",
tabsetPanel(id="tabsetDiagnostics",
tabPanel("Statistics",
tabsetPanel(id="tabsetStatistics",
tabPanel("Nodes",
fluidRow(
column(width = 3,
myBox("boxNodes", getText("Nodes"), "basic",
helpText(getText("txtNumbNonIsolated")),
checkboxInput(inputId = "nodeStatisticsLogy", label = "Log y", F),
HTML("<center>"),
actionButton("btnNodeStatistics", getText("Plot")),
HTML("</center>")
)
),
column(width=6,
showOutput("nodeStatisticsPlot","nvd3")
)
)
),
tabPanel("Edges",
fluidRow(
column(width = 3,
myBox("boxEdges", getText("Edges"), "basic",
helpText(getText("txtNumbEdgesPerLayer")),
checkboxInput(inputId = "edgeStatisticsLogy", label = "Log y", F),
HTML("<center>"),
actionButton("btnEdgeStatistics", getText("Plot")),
HTML("</center>")
)
),
column(width=6,
showOutput("edgeStatisticsPlot","nvd3")
)
)
),
tabPanel("Density",
fluidRow(
column(width = 3,
myBox("boxDensity", getText("Density"), "basic",
helpText(getText("txtDensityPerLayer")),
checkboxInput(inputId = "densityStatisticsLogy", label = "Log y", F),
HTML("<center>"),
actionButton("btnDensityStatistics", getText("Plot")),
HTML("</center>")
)
),
column(width=6,
showOutput("densityStatisticsPlot","nvd3")
)
)
),
tabPanel("Components",
fluidRow(
column(width = 3,
myBox("boxComponents", getText("Components"), "basic",
helpText(getText("txtComponentsPerLayer")),
checkboxInput(inputId = "componentsStatisticsLogy", label = "Log y", F),
HTML("<center>"),
actionButton("btnComponentsStatistics", getText("Plot")),
HTML("</center>")
)
),
column(width=6,
showOutput("componentsStatisticsPlot","nvd3")
)
)
),
tabPanel("Diameter",
fluidRow(
column(width = 3,
myBox("boxDiameter", getText("Diameter"), "basic",
helpText(getText("txtDiameterPerLayer")),
checkboxInput(inputId = "diameterStatisticsLogy", label = "Log y", F),
HTML("<center>"),
actionButton("btnDiameterStatistics", getText("Plot")),
HTML("</center>")
)
),
column(width=6,
showOutput("diameterStatisticsPlot","nvd3")
)
)
),
tabPanel("Mean Path Length",
fluidRow(
column(width = 3,
myBox("boxMeanPathLength", getText("MeanPathLength"), "basic",
helpText(getText("txtMPLPerLayer")),
checkboxInput(inputId = "meanPathLengthStatisticsLogy", label = "Log y", F),
HTML("<center>"),
actionButton("btnMeanPathLengthStatistics", getText("Plot")),
HTML("</center>")
)
),
column(width=6,
showOutput("meanPathLengthStatisticsPlot","nvd3")
)
)
)
)
),
tabPanel("Correlation",
actionLink("btnGlobalDiagnosticsCorrelationHelp", placeHelp() ),
conditionalPanel(condition="input.radMultiplexModel=='MULTIPLEX_IS_INTERDEPENDENT'",
helpText(getText("txtNoParametersInterdependent"))
),
conditionalPanel(condition="input.radMultiplexModel!='MULTIPLEX_IS_INTERDEPENDENT'",
fluidRow(
column(width = 3,
myBox("boxInterLayerCorrelation", getText("txtInterLayerCorrelation"), "basic",
#HTML('<h4>General diagnostics</h4>'),
checkboxInput('chkMULTIPLEX_NODEOVERLAPPING', getText("chkMULTIPLEX_NODEOVERLAPPING"), TRUE),
checkboxInput('chkMULTIPLEX_OVERLAPPING', getText("chkMULTIPLEX_OVERLAPPING"), TRUE),
checkboxInput('chkMULTIPLEX_INTERASSORTATIVITY_PEARSON', getText("chkMULTIPLEX_INTERASSORTATIVITY_PEARSON"), TRUE),
checkboxInput('chkMULTIPLEX_INTERASSORTATIVITY_SPEARMAN', getText("chkMULTIPLEX_INTERASSORTATIVITY_SPEARMAN"), TRUE),
checkboxInput('chkMULTIPLEX_SHORTESTPATH', getText("chkMULTIPLEX_SHORTESTPATH"), TRUE),
selectInput("selAssortativityType", HTML(getText("selAssortativityType")),
choices = c("TT", "II", "OO", "IO", "OI"))
)
),
column(width = 3,
myBox("boxCorrelationGraphicalOptions", getText("txtGraphicalOptions"),"basic",
checkboxInput('chkEXPORT_MATRIX_PLOT', HTML(getText("chkEXPORT_MATRIX_PLOT")), FALSE),
selectInput("selAssortativityTypeColorPalette", HTML(getText("ColorPalette")),
choices = paletteChoiceArray),
actionLink("btnAssortativityPaletteInfo", placeInfo() )
),
HTML("<center>"),
actionButton("btnCalculateCorrelationDiagnostics", getText("btnCalculateCorrelationDiagnostics")),
HTML("</center>")
)
),
tags$hr(),
HTML(paste0('<h4>',getText("txtGlobalDiagnostics"),'</h4>')),
tabsetPanel(
tabPanel("Node Overlapping",
conditionalPanel(condition="input.btnCalculateCorrelationDiagnostics>0 && input.chkMULTIPLEX_NODEOVERLAPPING",
HTML(paste0('<h5>',getText("txtNodeOverlapping"),'</h5>')),
checkboxInput("chkOverlappingNodeHeatmapShowDendrogram", getText("ApplyClustering"), F),
uiOutput("overlappingNodeHeatmapUI"),
tags$br(),
htmlOutput("overlappingNodeSummaryTable"),
downloadButton('downOverlappingNodeSummaryTable', getText("downOverlappingNodeSummaryTable")),
tags$hr()
)
),
tabPanel("Edge Overlapping",
conditionalPanel(condition="input.btnCalculateCorrelationDiagnostics>0 && input.chkMULTIPLEX_OVERLAPPING",
htmlWidgetOutput(
outputId = 'globalDiagnosticsOverlapping',
HTML(paste(
'<h5>Edge Overlapping</h5>',
'Mean Global Overlapping: <span id="sumAvgGlobalOverlapping"></span><br>',
'<br>'
))
),
checkboxInput("chkOverlappingEdgeHeatmapShowDendrogram", getText("ApplyClustering"), F),
uiOutput("overlappingEdgeHeatmapUI"),
tags$br(),
htmlOutput("overlappingSummaryTable"),
downloadButton('downOverlappingSummaryTable', getText("downOverlappingSummaryTable")),
tags$hr()
)
),
tabPanel("Deg. Pearson",
conditionalPanel(condition="input.btnCalculateCorrelationDiagnostics>0 && input.chkMULTIPLEX_INTERASSORTATIVITY_PEARSON",
helpText(HTML(paste0("<h5>",getText("txtInterlayerAssortativityPearson"),"</h5>"))),
checkboxInput("chkInterPearsonHeatmapShowDendrogram", getText("ApplyClustering"), F),
uiOutput("interPearsonHeatmapUI"),
tags$br(),
htmlOutput("interPearsonSummaryTable"),
downloadButton('downInterPearsonSummaryTable', getText("downInterPearsonSummaryTable")),
tags$hr()
)
),
tabPanel("Deg. Spearman",
conditionalPanel(condition="input.btnCalculateCorrelationDiagnostics>0 && input.chkMULTIPLEX_INTERASSORTATIVITY_SPEARMAN",
helpText(HTML(paste0("<h5>",getText("txtInterlayerAssortativitySpearman"),"</h5>"))),
checkboxInput("chkInterSpearmanHeatmapShowDendrogram", getText("ApplyClustering"), F),
uiOutput("interSpearmanHeatmapUI"),
tags$br(),
htmlOutput("interSpearmanSummaryTable"),
downloadButton('downInterSpearmanSummaryTable', getText("downInterSpearmanSummaryTable"))
)
),
tabPanel("SP Distance",
conditionalPanel(condition="input.btnCalculateCorrelationDiagnostics>0 && input.chkMULTIPLEX_SHORTESTPATH",
helpText(HTML(paste0("<h5>",getText("ShortestPathDistanceSimilarity"),"</h5>"))),
checkboxInput("chkDistanceSimilarityHeatmapShowDendrogram", getText("ApplyClustering"), F),
uiOutput("distanceSimilarityHeatmapUI"),
tags$br(),
htmlOutput("distanceSimilaritySummaryTable"),
downloadButton('downDistanceSimilaritySummaryTable', getText("downDistanceSimilaritySummaryTable"))
)
)
)
)
),
tabPanel("Centrality",
actionLink("btnCentralityHelp", placeHelp() ),
fluidRow(
column(width = 3,
myBox("boxCentrality", "Centrality", "basic",
radioButtons('radCentralityAlgorithm', '',
c(Multilayer='CENTRALITY_MULTILAYER',
Single_Layer='CENTRALITY_SINGLELAYER'),
selected='CENTRALITY_MULTILAYER'
)
#checkboxInput("chkNODE_CENTRALITY_MULTIPLEX",getText("chkNODE_CENTRALITY_MULTIPLEX"),TRUE)
),
HTML("<center>"),
actionButton("btnCalculateCentralityDiagnostics", getText("btnCalculateCentralityDiagnostics")),
HTML("</center>")
),
column(width = 3,
myBox("boxDescriptors", "Descriptors", "basic",
#HTML('<h4>Centrality</h4>'),
checkboxInput("chkNODE_CENTRALITY_DEGREE","Degree (in-, out- & tot)",TRUE),
checkboxInput("chkNODE_CENTRALITY_STRENGTH","Strength (in-, out- & tot)",F),
checkboxInput("chkNODE_CENTRALITY_PAGERANK","PageRank",F),
checkboxInput("chkNODE_CENTRALITY_EIGENVECTOR","Eigenvector",F),
checkboxInput("chkNODE_CENTRALITY_HUB","Hub",F),
checkboxInput("chkNODE_CENTRALITY_AUTHORITY","Authority",F),
checkboxInput("chkNODE_CENTRALITY_KATZ","Katz",F),
checkboxInput("chkNODE_CENTRALITY_KCORE","K-core",F),
checkboxInput("chkNODE_CENTRALITY_MULTIPLEXITY","Multiplexity",F)
)
)
),
tags$hr(),
HTML(paste0('<h4>',getText("txtCentralityDiagnostics"),'</h4>')),
conditionalPanel(condition="input.btnCalculateCentralityDiagnostics>0",
checkboxInput(inputId = "centralityTablePageable", label = getText("Pageable"), TRUE),
conditionalPanel("input.centralityTablePageable==true",
uiOutput("numOutputCentralityTableNodesPerPage")
),
tabsetPanel(
tabPanel("Multilayer",
htmlOutput("centralityTable"),
downloadButton('downCentralityTable', getText("downCentralityTable"))
),
tabPanel("Single layer",
htmlOutput("centralityTableSingleLayer"),
downloadButton('downCentralityTableSingleLayer', getText("downCentralityTableSingleLayer"))
)
),
tags$hr(),
fluidRow(
column(width = 3,
myBox("boxDiagnosticsAnalysis", getText("txtDiagnosticsAnalysis"), "basic",
uiOutput("selDiagnosticsCentralityVizOutputID"),
radioButtons('radDiagnosticsCentralityType', getText("Analysis"),
c(TopRanked='DIAGNOSTICS_ANALYSIS_TOPRANKED',
Distribution='DIAGNOSTICS_ANALYSIS_DISTRIBUTION',
Scatter='DIAGNOSTICS_ANALYSIS_SCATTER'),
selected='DIAGNOSTICS_ANALYSIS_TOPRANKED'
),
HTML(paste0("<strong>",getText("txtNetworksToInclude"),"</strong>:")),
checkboxInput(inputId = "chkCentralityAnalysisStructureMultiplex", label = "Multilayer", T),
checkboxInput(inputId = "chkCentralityAnalysisStructureLayer", label = "Layer(s)", F),
conditionalPanel(condition="input.chkCentralityAnalysisStructureLayer",
textInput("txtDiagnosticsCentralityStructureLayer", label=HTML(paste0("<strong>",getText("txtDiagnosticsCentralityStructureLayer"),"</strong>")), "1")
),
checkboxInput(inputId = "chkCentralityAnalysisStructureAggregate", label = "Aggregate", T),
conditionalPanel(condition="input.radDiagnosticsCentralityType == 'DIAGNOSTICS_ANALYSIS_DISTRIBUTION'",
textInput("txtDiagnosticsCentralityDistributionBins", label=HTML(paste0("<strong>",getText("txtDiagnosticsCentralityDistributionBins"),"</strong>")), "30"),
checkboxInput(inputId = "centralityAnalysisDistributionLogx", label = "Log x", F),
checkboxInput(inputId = "centralityAnalysisDistributionLogy", label = "Log y", F)
),
conditionalPanel(condition="input.radDiagnosticsCentralityType == 'DIAGNOSTICS_ANALYSIS_TOPRANKED'",
textInput("txtDiagnosticsCentralityTopRankedBins", label=HTML(paste0("<strong>",getText("txtDiagnosticsCentralityTopRankedBins"),"</strong>")), "20"),
checkboxInput(inputId = "centralityAnalysisTopRankedLog", label = "Log", F)
),
conditionalPanel(condition="input.radDiagnosticsCentralityType == 'DIAGNOSTICS_ANALYSIS_SCATTER'",
uiOutput("selDiagnosticsCentralityVizScatterOutputID"),
textInput('txtDiagnosticsCentralityVizScatterColorTransparency', label=getText("txtDiagnosticsCentralityVizScatterColorTransparency"), "0.7"),
uiOutput("selDiagnosticsCentralityVizScatterSizeOutputID"),
checkboxInput(inputId = "centralityAnalysisScatterLogx", label = "Log x", F),
checkboxInput(inputId = "centralityAnalysisScatterLogy", label = "Log y", F),
checkboxInput(inputId = "centralityAnalysisScatterLogRadius", label = "Log Radius", F)
),
HTML("<center>"),
actionButton("btnCentralityDiagnosticsAnalysis", getText("Plot")),
HTML("</center>")
)
),
column(width=6,
showOutput("centralityAnalysisPlot","nvd3")
)
),
tags$hr()
)
),
tabPanel("Triads",
actionLink("btnTriadsHelp", placeHelp() ),
fluidRow(
column(width = 3,
myBox("boxTriads", "Triadic closure", "basic",
#helpText("Note that directed networks will be transformed to undirected before calculation."),
radioButtons('radTriadicClosureAlgorithm', '',
c(Multilayer='TRIADIC_CLOSURE_MULTILAYER',
Single_Layer='TRIADIC_CLOSURE_SINGLELAYER'),
selected='TRIADIC_CLOSURE_MULTILAYER'
),
conditionalPanel(condition="input.radTriadicClosureAlgorithm=='TRIADIC_CLOSURE_MULTILAYER'"
)
),
HTML("<center>"),
actionButton("btnCalculateTriadsDiagnostics", "Calculate Triadic Closure"),
conditionalPanel(condition="input.btnCalculateTriadsDiagnostics>0",
actionButton("btnRefreshTriadsDiagnostics", HTML(paste(icon("refresh"), getText("RefreshResults"))))
),
HTML("</center>")
)
),
tags$hr(),
HTML('<h4>Triadic Closure</h4>'),
conditionalPanel(condition="input.btnCalculateTriadsDiagnostics>0",
selectInput("selTriadsHeatmapColorPalette", HTML(getText("ColorPalette")), choices = paletteChoiceArray),
actionLink("btnTriadsPaletteInfo", placeInfo() ),
checkboxInput("chkTriadsHeatmapShowDendrogram", getText("ApplyClustering")),
checkboxInput(inputId = "triadsTablePageable", label = getText("Pageable"), TRUE),
checkboxInput(inputId = "triadsHeatmapShowLabels", label = getText("ShowNodeLabels"), TRUE),
conditionalPanel("input.triadsTablePageable==true",
uiOutput("numOutputTriadsTableNodesPerPage")
),
tabsetPanel(
tabPanel("Multilayer",
uiOutput("triadsHeatmapUI"),
tags$br(),
HTML(paste0('<h5>',getText("triadsHeatmapUI"),'</h5>')),
showOutput("triadsDistributionPlot","nvd3"),
HTML('<h5>Tables</h5>'),
htmlOutput("triadsSummaryTable"),
downloadButton('downTriadsSummaryTable', getText("downTriadsSummaryTable")),
tags$hr(),
htmlOutput("triadsTable"),
downloadButton('downTriadsTable', getText("downTriadsTable"))
),
tabPanel("Single layer",
uiOutput("triadsHeatmapSingleLayerUI"),
tags$br(),
HTML(paste0('<h5>',getText("triadsHeatmapSingleLayerUI"),'</h5>')),
showOutput("triadsDistributionPlotSingleLayer","nvd3"),
HTML('<h5>Tables</h5>'),
htmlOutput("triadsSummaryTableSingleLayer"),
downloadButton('downTriadsSummaryTableSingleLayer', getText("downTriadsSummaryTableSingleLayer")),
tags$hr(),
htmlOutput("triadsTableSingleLayer"),
downloadButton('downTriadsTableSingleLayer', getText("downTriadsTableSingleLayer"))
)
)
)
),
tabPanel("Motifs",
actionLink("btnMotifsHelp", placeHelp() ),
fluidRow(
column(width = 3,
myBox("boxMotifs", "Algorithm options","basic",
selectInput("selMotifSize", HTML(paste0("<strong>",getText("selMotifSize"),"</strong>")), choices = as.character(3:4)),
textInput("txtMotifSamples", HTML(paste0("<strong>",getText("txtMotifSamples"),"</strong>")), "100000"),
selectInput("selMotifNullModel", HTML(paste0("<strong>",getText("selMotifNullModel"),"</strong>")),
choices = c("Local const", "Global const", "No regard")),
textInput("txtMotifRandomNetworks", HTML(paste0("<strong>",getText("txtMotifRandomNetworks"),"</strong>")), "1000"),
textInputRow("txtMotifRandomExchangePerEdges", HTML("<strong>Exchanges per edge:</strong>"), "3"),
textInputRow("txtMotifRandomExchangeAttempts", HTML("<strong>Exchange attempts:</strong>"), "3", width="10px")
)
),
column(width = 3,
myBox("boxMotifs2", "Statistical cuts","basic",
checkboxInputRow('chkMotifAbsZscore', HTML("<strong>|Z-score| ></strong>"), FALSE),
textInputRow("txtMotifAbsZscore", "", "3"),
checkboxInputRow('chkMotifPvalue', HTML("<strong>p-value <</strong>"), FALSE),
textInputRow("txtMotifPvalue", "", "0.05"),
checkboxInputRow('chkMotifFrequency', HTML("<strong>Frequency ></strong>"), FALSE),
textInputRow("txtMotifFrequency", "", "0.01")
),
myBox("boxMotifs3", "Graphical options", "basic",
selectInput("selMotifResultsSortBy", HTML(paste0("<strong>",getText("SortBy"),"</strong>")),
choices = c("Frequency", "Z-score", "p-value")),
selectInput("selMotifColorPalette", HTML(getText("ColorPalette")),
choices = append(as.vector(paletteChoiceArray),"random")),
actionLink("btnMotifsPaletteInfo", placeInfo() ),
helpText(getText("selMotifColorPalette"))
),
HTML("<center>"),
actionButton("btnCalculateMotifs", getText("btnCalculateMotifs")),
HTML("</center>")
)
),
tags$hr(),
HTML('<h4>Multilayer motifs</h4>'),
conditionalPanel(condition="input.btnCalculateMotifs>0",
#imageOutput("jsdMatrixSummaryImage",width = "100%", height = "700px"),
#imageOutput("reducibilityDendrogramSummaryImage",width = "100%", height = "700px"),
#HTML('<center><h5>Quality function</h5></center>'),
#showOutput("reducibilityQualityFunction","nvd3"),
#dataTableOutput('motifsTable'),
plotOutput("motifsColorLegend"),
htmlOutput('motifsGvisTable'),
downloadButton('downMotifsTable', getText("downMotifsTable")),
tags$hr()
)
),
tabPanel("Conn. Components",
actionLink("btnComponentsHelp", placeHelp() ),
fluidRow(
column(width = 3,
myBox("boxConnectedComponents", "Connected Components", "basic",
helpText(getText("helpBoxConnectedComponents")),
radioButtons('radConnectedComponentsAlgorithm', '',
c(Multilayer='CONNECTED_COMPONENTS_MULTILAYER',
Single_Layer='CONNECTED_COMPONENTS_SINGLELAYER'),
selected='CONNECTED_COMPONENTS_MULTILAYER'
),
conditionalPanel(condition="input.radConnectedComponentsAlgorithm=='CONNECTED_COMPONENTS_MULTILAYER'"
#selectInput("selConnectedComponentsMuxType", "Method:",
# choices = c("Simple", "Extended")),
# conditionalPanel(condition="input.radMultiplexModel=='MULTIPLEX_IS_EDGECOLORED'",
# helpText("Hint: for Multilayer, the inter-layer strength must be set > 0 from the 'Mux Set Up' tab")
# )
)
#conditionalPanel(condition="input.radConnectedComponentsAlgorithm==''CONNECTED_COMPONENTS_SINGLELAYER",
# selectInput("selConnectedComponentsSingleLayerType", HTML("Components type:"),
# choices = c("Weak", "Strong"))
# ),
),
HTML("<center>"),
actionButton("btnCalculateComponentsDiagnostics", getText("btnCalculateComponentsDiagnostics")),
conditionalPanel(condition="input.btnCalculateComponentsDiagnostics>0",
actionButton("btnRefreshComponentsDiagnostics", HTML(paste(icon("refresh"), getText("RefreshResults"))))
),
HTML("</center>")
)
),
tags$hr(),
HTML('<h4>Connected Components</h4>'),
conditionalPanel(condition="input.btnCalculateComponentsDiagnostics>0",
selectInput("selComponentsHeatmapColorPalette", HTML(getText("ColorPalette")), choices = paletteChoiceArray),
actionLink("btnComponentsPaletteInfo", placeInfo() ),
checkboxInput("chkComponentsHeatmapShowDendrogram", getText("ApplyClustering")),
checkboxInput(inputId = "componentsTablePageable", label = getText("Pageable"), TRUE),
checkboxInput(inputId = "componentsHeatmapShowLabels", label = getText("ShowNodeLabels"), TRUE),
conditionalPanel("input.componentsTablePageable==true",
uiOutput("numOutputComponentsTableNodesPerPage")
),
tabsetPanel(
tabPanel("Multilayer",
uiOutput("componentsHeatmapUI"),
tags$br(),
HTML(paste0('<h5>',getText("componentsHeatmapUI"),'</h5>')),
showOutput("componentsDistributionPlot","nvd3"),
HTML('<h5>Tables</h5>'),
htmlOutput("componentsSummaryTable"),
downloadButton('downComponentsSummaryTable', getText("downComponentsSummaryTable")),
tags$hr(),
htmlOutput("componentsTable"),
downloadButton('downComponentsTable', getText("downComponentsTable"))
),
tabPanel("Single layer",
uiOutput("componentsHeatmapSingleLayerUI"),
tags$br(),
HTML(paste0('<h5>',getText("componentsHeatmapSingleLayerUI"),'</h5>')),
showOutput("componentsDistributionPlotSingleLayer","nvd3"),
HTML('<h5>Tables</h5>'),
htmlOutput("componentsSummaryTableSingleLayer"),
downloadButton('downComponentsSummaryTableSingleLayer', getText("downComponentsSummaryTableSingleLayer")),
tags$hr(),
htmlOutput("componentsTableSingleLayer"),
downloadButton('downComponentsTableSingleLayer', getText("downComponentsTableSingleLayer"))
)
)
)
),
tabPanel("Community",
actionLink("btnCommunityHelp", placeHelp() ),
fluidRow(
column(width = 3,
myBox("boxCommunity", "Algorithm", "basic",
uiOutput("communityChoices"),
uiOutput("communityParameters")
),
HTML("<center>"),
actionButton("btnCalculateCommunityDiagnostics", getText("btnCalculateCommunityDiagnostics")),
conditionalPanel(condition="input.btnCalculateCommunityDiagnostics>0",
actionButton("btnRefreshCommunityDiagnostics", HTML(paste(icon("refresh"), getText("RefreshResults"))))
),
HTML("</center>")
)
),
tags$hr(),
HTML('<h4>Communities</h4>'),
conditionalPanel(condition="input.btnCalculateCommunityDiagnostics>0",
selectInput("selCommunityHeatmapColorPalette", HTML(getText("ColorPalette")), choices = paletteChoiceArray),
actionLink("btnCommunityPaletteInfo", placeInfo() ),
checkboxInput("chkCommunityHeatmapShowDendrogram", getText("ApplyClustering")),
checkboxInput(inputId = "communityTablePageable", label = getText("Pageable"), TRUE),
checkboxInput(inputId = "communityHeatmapShowLabels", label = getText("ShowNodeLabels"), TRUE),
conditionalPanel("input.communityTablePageable==true",
uiOutput("numOutputCommunityTableNodesPerPage")
),
tabsetPanel(
tabPanel("Multilayer",
uiOutput("communityHeatmapUI"),
tags$br(),
tags$br(),
HTML(paste0('<h5>',getText("communityMultiplexAlternativeViz"),'</h5>')),
fluidRow(
column(3,
HTML("<img src='img/chord.png' height='64' width='64' style='{margin-left: auto; margin-right: auto;}'>"),
actionButton("btnPrintCommunityMultiplexChord",
getText("btnPrintCommunityMultiplexChord"))
)
),
tags$br(),
tags$br(),
conditionalPanel("input.chkMultimapBatchExploration",
HTML(paste0('<h5>',getText("communityMultiplexBatchViz"),'</h5>')),
fluidRow(
column(3,
HTML("<img src='img/sankey.png' height='64' width='64' style='{margin-left: auto; margin-right: auto;}'>"),
actionButton("btnPrintCommunityMultiplexSankey",
getText("btnPrintCommunityMultiplexSankey"))
)
),
tags$br(),
fluidRow(
column(4,
showOutput("batchMultiplexCommunityData1","nvd3")
),
column(4,
showOutput("batchMultiplexCommunityData2","nvd3")
)
)
),
tags$br(),
tags$br(),
HTML(paste0('<h5>',getText("communityHeatmapUI"),'</h5>')),
showOutput("communityDistributionPlot","nvd3"),
HTML('<h5>Tables</h5>'),
htmlOutput("communitySummaryTable"),
downloadButton('downCommunitySummaryTable', getText("downCommunitySummaryTable")),
tags$hr(),
htmlOutput("communityTable"),
downloadButton('downCommunityTable', getText("downCommunityTable")),
tags$hr(),
conditionalPanel("input.chkMultimapBatchExploration",
htmlOutput("communityBatchTable"),
downloadButton('downCommunityBatchTable', getText("downCommunityBatchTable"))
)
),
tabPanel("Single layer",
uiOutput("communityHeatmapSingleLayerUI"),
tags$br(),
HTML(paste0('<h5>',getText("communityHeatmapSingleLayerUI"),'</h5>')),
showOutput("communityDistributionPlotSingleLayer","nvd3"),
HTML('<h5>Tables</h5>'),
htmlOutput("communitySummaryTableSingleLayer"),
downloadButton('downCommunitySummaryTableSingleLayer', getText("downCommunitySummaryTableSingleLayer")),
tags$hr(),
htmlOutput("communityTableSingleLayer"),
downloadButton('downCommunityTableSingleLayer', getText("downCommunityTableSingleLayer"))
)
)
)
),
tabPanel("Network of layers",
actionLink("btnGlobalDiagnosticsNetworkLayersHelp", placeHelp() ),
conditionalPanel(condition="input.radMultiplexModel!='MULTIPLEX_IS_EDGECOLORED'",
HTML("<center>"),
tags$br(),
actionButton("btnRenderNetworkOfLayers", getText("btnRenderNetworkOfLayers")),
HTML("</center>"),
HTML("<center>"),
htmlOutput('networkOfLayersPlot'),
HTML("</center>")
)
),
tabPanel("Annular Viz",
actionLink("btnGlobalDiagnosticsAnnularVizHelp", placeHelp() ),
conditionalPanel(condition="input.radMultiplexModel=='MULTIPLEX_IS_INTERDEPENDENT'",
helpText(getText("panelGlobalDiagnosticsAnnularVizHelp"))
),
conditionalPanel(condition="input.radMultiplexModel!='MULTIPLEX_IS_INTERDEPENDENT'",
fluidRow(
column(width = 3,
myBox("boxAnnular", "Metric", "basic",
radioButtons('radAnularVizCorrelationMethod', getText("radAnularVizCorrelationMethod"),
c(Spearman='ANULAR_VIZ_CORRELATION_SPEARMAN',
Pearson='ANULAR_VIZ_CORRELATION_PEARSON',
Jensen_Shannon_Divergence='ANULAR_VIZ_CORRELATION_JSD'),
selected='ANULAR_VIZ_CORRELATION_SPEARMAN'
),
textInput("txtANULAR_VIZ_BINS",label=getText("txtANULAR_VIZ_BINS"),"50"),
checkboxInput("chkANULAR_VIZ_LOG",getText("chkANULAR_VIZ_LOG"),FALSE)
),
HTML("<center>"),
actionButton("btnAnularViz", getText("btnAnularViz")),
HTML("</center>")
),
column(width = 3,
myBox("boxAnnular2", "Graphical Options","basic",
uiOutput("selAnularVizOutputFeatureID"),
uiOutput("selAnularVizOutputLayerID"),
textInputRow("txtANULAR_VIZ_RCORE",label=getText("txtANULAR_VIZ_RCORE"),"0.3"),
textInputRow("txtANULAR_VIZ_RING_DISPLACEMENT", label=getText("txtANULAR_VIZ_RING_DISPLACEMENT"),"0.01"),
checkboxInput("chkANULAR_VIZ_CELL_BORDER", getText("chkANULAR_VIZ_CELL_BORDER"),FALSE),
checkboxInput("chkANULAR_VIZ_SHOW_NODE_LABEL", getText("chkANULAR_VIZ_SHOW_NODE_LABEL"),FALSE),
textInputRow("txtANULAR_VIZ_FONT_SIZE", label=getText("txtANULAR_VIZ_FONT_SIZE"),"1.5"),
selectInput("selAnularColorPalette", HTML(getText("ColorPalette")),
choices = paletteChoiceArray),
actionLink("btnAnnularPaletteInfo", placeInfo() )
)
)
),
tags$hr(),
conditionalPanel(condition="input.btnAnularViz>0 && input.btnCalculateCentralityDiagnostics>0",
helpText(HTML("<h5>Multiplex</h5>")),
helpText(getText("helpAnularVizSummaryMuxImage")),
imageOutput("anularVizSummaryMuxImage",width = "100%", height = "600px"),
tags$hr(),
helpText(HTML(paste0("<h5>",getText("outputAnularVizImages"),"</h5>"))),
helpText(getText("helpOutputAnularVizImages")),
uiOutput("outputAnularVizImages"),
tags$hr()
),
tags$hr()
)
)
)
),
tabPanel("Visualization",
actionLink("btnVisualizationHelp", placeHelp() ),
HTML(paste("<div style=\"float: right; margin: 10px;\">",
actionButton("btnRenderNetworks", getText("btnRenderNetworks")),
"</div>")),
HTML(paste("<div style=\"float: right; margin: 10px;\">",
actionButton("btnApplyLayout", getText("btnApplyLayout")),
"</div>")),
tabsetPanel(
tabPanel("Layout",
fluidRow(
column(width = 9,
myBox("boxVisualization", "Layout Algorithm (Network of Layers)", "basic",
HTML("<img src='img/layout_type.png' width='100%' alt=''/>"),
radioButtons('radNetworkOfLayersLayoutType', '',
c(One_line='NETWORK_LAYERS_LAYOUT_ONELINE',
Multi_line='NETWORK_LAYERS_LAYOUT_MULTILINE',
Force_directed='NETWORK_LAYERS_LAYOUT_FORCEDIRECTED',
Matrix='NETWORK_LAYERS_LAYOUT_MATRIX'
),
selected='NETWORK_LAYERS_LAYOUT_ONELINE',
inline=T
),
conditionalPanel(condition="input.radNetworkOfLayersLayoutType == 'NETWORK_LAYERS_LAYOUT_MULTILINE'",
textInputRow("txtNetworkLayersMultilineRows", label=getText("txtNetworkLayersMultilineRows"), 2),
textInputRow("txtNetworkLayersMultilineCols", label=getText("txtNetworkLayersMultilineCols"), 2),
helpText(getText("helptxtNetworkLayersMultilineCols"))
),
conditionalPanel(condition="input.radNetworkOfLayersLayoutType == 'NETWORK_LAYERS_LAYOUT_MATRIX'",
textInputRow("txtNetworkLayersMatrixRows", label=getText("txtNetworkLayersMatrixRows"), 2),
textInputRow("txtNetworkLayersMatrixCols", label=getText("txtNetworkLayersMatrixCols"), 2),
helpText(getText("helptxtNetworkLayersMatrixCols"))
),
conditionalPanel(condition="input.radNetworkOfLayersLayoutType == 'NETWORK_LAYERS_LAYOUT_FORCEDIRECTED'",
HTML(paste("<font color=\"red\">",icon("exclamation-circle"), getText("boxVisualization1"), "</font>")),
helpText(getText("boxVisualization1b"))
)
)
)
),
fluidRow(
column(width = 4,
myBox("boxVisualization2", "Layout Algorithm (Layer)", "basic",
#HTML('<h4>Algorithm to be used to visualize nodes in the multiplex network</h4>'),
radioButtons('radLayoutAlgorithm', '',
c(Fruchterman_Reingold='LAYOUT_FRUCHTERMAN_REINGOLD',
LGL='LAYOUT_LGL',
DRL='LAYOUT_DRL',
Spring='LAYOUT_SPRING',
Kamada_Kawai='LAYOUT_KAMADA_KAWAI',
Reingold_Tilford='LAYOUT_REINGOLD_TILFORD',
Combined='LAYOUT_COMBINED'),
selected='LAYOUT_COMBINED'
),
conditionalPanel(condition="input.radNetworkOfLayersLayoutType == 'NETWORK_LAYERS_LAYOUT_ONELINE'",
radioButtons('radLayoutDimension', '',
c(Two_Dimensional='LAYOUT_DIMENSION_2D',
Three_Dimensional='LAYOUT_DIMENSION_3D'),
selected='LAYOUT_DIMENSION_2D', inline=TRUE
),
checkboxInput("chkPLOT_AS_EDGE_COLORED", HTML(getText("chkPLOT_AS_EDGE_COLORED")),FALSE),
checkboxInput("chkPLOT_WITH_RGL",HTML("openGL"),TRUE),
helpText(getText("helpchkPLOT_WITH_RGL"))
),
actionLink("btnWarn1", placeWarn())
)
),
column(width = 4,
myBox("boxVisualization3", "Graphical Options","basic",
#HTML('<h4>Type of visualization</h4>'),
radioButtons('radLayoutType', getText("radLayoutType"),
c(Multiplex='LAYOUT_MULTIPLEX',
By_LayerID='LAYOUT_BY_LAYER_ID',
Independent='LAYOUT_INDEPENDENT'),
selected='LAYOUT_MULTIPLEX', inline=TRUE
),
conditionalPanel(condition="input.radLayoutType=='LAYOUT_MULTIPLEX'",
radioButtons('radLayoutTypeMultiplex', getText("radLayoutTypeMultiplex"),
c(Aggregate='LAYOUT_MULTIPLEX_AGGREGATE',
Union='LAYOUT_MULTIPLEX_UNION',
Intersection='LAYOUT_MULTIPLEX_INTERSECTION'),
selected='LAYOUT_MULTIPLEX_AGGREGATE', inline=FALSE
)
),
conditionalPanel(condition="input.radLayoutType=='LAYOUT_BY_LAYER_ID'",
#this is a dynamic object changing because of input
uiOutput("selOutputLayerID")
),
textInputRow("txtLAYOUT_MAXITER",
label=HTML(getText("txtLAYOUT_MAXITER")),
value="1000", width="20px"
),
tags$br(),
actionLink("btnWarn2", placeWarn())
)
)
)
),
tabPanel("Graphics",
fluidRow(
column(width = 4,
myBox("boxVisualization4", "Plot Options","basic",
#HTML('<h4>Options for the rendering of the multiplex</h4>'),
textInputRow('txtPLOT_TITLE', label=getText("txtPLOT_TITLE"), "", width="70px"),
textInputRow('txtPLOT_SUBTITLE', label=getText("txtPLOT_SUBTITLE"), "", width="50px"),
colourpicker::colourInput("colBACKGROUND_COLOR", getText("colBACKGROUND_COLOR"), "white")
),
conditionalPanel(condition="input.chkPLOT_WITH_RGL",
myBox("boxVisualization5", "Light Options (RGL)","basic",
checkboxInput("chkPLOT_LIGHT", getText("chkPLOT_LIGHT"),FALSE),
textInputRow('txtPLOT_LIGHT_PHI', label=getText("txtPLOT_LIGHT_PHI"), "20", width="30px"),
textInputRow('txtPLOT_LIGHT_THETA', label=getText("txtPLOT_LIGHT_THETA"), "30", width="30px"),
HTML("<center>"),
actionButton("btnResetLights", getText("btnResetLights")),
HTML("</center>"),
helpText(getText("helpbtnResetLights"))
)
),
conditionalPanel(condition="!input.chkPLOT_WITH_RGL",
myBox("boxVisualization6", "Window relative margins","basic",
helpText(getText("helpboxVisualization6")),
textInputRow('txtMARGIN_LEFT', label=getText("txtMARGIN_LEFT"), "1"),
textInputRow('txtMARGIN_RIGHT', label=getText("txtMARGIN_RIGHT"), "1"),
textInputRow('txtMARGIN_TOP', label=getText("txtMARGIN_TOP"), "1"),
textInputRow('txtMARGIN_BOTTOM', label=getText("txtMARGIN_BOTTOM"), "1"),
actionLink("btnWarn3", placeWarn())
)
)
),
column(width = 4,
myBox("boxVisualization7", "3D Options", "basic",
conditionalPanel(condition="input.chkPLOT_WITH_RGL",
checkboxInput('chkPLOT_AXES3D', label=getText("chkPLOT_AXES3D"), F),
checkboxInput("chkPLOT_REMEMBER_ORIENTATION", getText("chkPLOT_REMEMBER_ORIENTATION"),TRUE),
textInputRow('txtPLOT_FOV', label=HTML(getText("txtPLOT_FOV")), "20", width=15)
),
conditionalPanel(condition="!input.chkPLOT_WITH_RGL",
HTML(getText("boxVisualization7a")),
tags$br(),
textInputRow('txtPLOT_ROTX', label=HTML('X-axis:'), "0", width="30"),
textInputRow('txtPLOT_ROTY', label=HTML('Y-axis:'), "60", width="30"),
textInputRow('txtPLOT_ROTZ', label=HTML('Z-axis:'), "0", width="30"),
helpText(getText("boxVisualization7b")),
actionLink("btnWarn4", placeWarn()),
# radioButtons('radPlotNonRGLQuickLayout', 'Quick layout:',
# c(Horizontal='PLOT_NONRGL_QUICK_LAYOUT_HORIZONTAL',
# Vertical='PLOT_NONRGL_QUICK_LAYOUT_VERTICAL',
# Custom='PLOT_NONRGL_QUICK_LAYOUT_NONE'),
# selected='PLOT_NONRGL_QUICK_LAYOUT_HORIZONTAL', inline=TRUE
# ),
helpText("Horizontal layout: x=0°, y=60°, z=0°, shift>0."),
helpText("Vertical layout: x=60°, y=45°, z=-45°, shift=0")
),
tags$hr(),
HTML(getText("boxVisualization7c")),
textInputRow('txtLAYER_SHIFT_X', label=HTML('X-axis:'), "0.8", width="30"),
textInputRow('txtLAYER_SHIFT_Y', label=HTML('Y-axis:'), "0", width="30"),
textInputRow('txtLAYER_SCALE', label=HTML(getText("txtLAYER_SCALE")), "4"),
textInputRow('txtLAYER_SPACE', label=HTML(getText("txtLAYER_SPACE")), "3", width="30"),
tags$br(),
actionLink("btnWarn5", placeWarn())
)
)
)
),
tabPanel("Multiplex",
conditionalPanel(condition="input.radMultiplexModel!='MULTIPLEX_IS_EDGECOLORED'",
fluidRow(
column(width = 4,
myBox("boxVisualization8", "Inter-link Options","basic",
checkboxInput("chkINTERLINK_SHOW",HTML(getText("chkINTERLINK_SHOW")),TRUE),
HTML(paste("<font color=\"red\">",icon("exclamation-circle"), getText("boxVisualization8"), "</font>")),
colourpicker::colourInput("colINTERLINK_COLOR", getText("colINTERLINK_COLOR"), "#D8D8D8"),
selectInput('selINTERLINK_TYPE', getText("selINTERLINK_TYPE"), choices= c("dotted", "solid", "dashed", "dotdash", "longdash", "twodash")),
textInputRow('txtINTERLINK_WIDTH', label=getText("txtINTERLINK_WIDTH"), "0.4"),
textInputRow('txtINTERLINK_TRANSP', label=getText("txtINTERLINK_TRANSP"), "0.2"),
helpText(getText("boxVisualization8b"))
)
)
)
),
conditionalPanel(condition="input.radMultiplexModel=='MULTIPLEX_IS_EDGECOLORED'",
helpText(getText("boxVisualization8c"))
)
),
tabPanel("Layers",
fluidRow(
column(width = 4,
conditionalPanel(condition="input.chkPLOT_WITH_RGL",
myBox("boxVisualization9", "Layer Options", "basic",
checkboxInput("chkLAYER_SHOW","Show layers",TRUE),
textInputRow('txtLAYER_LABEL_PREFIX', label=getText("txtLAYER_LABEL_PREFIX"), "L"),
helpText(getText("helptxtLAYER_LABEL_PREFIX")),
colourpicker::colourInput("colLAYER_COLOR", getText("colLAYER_COLOR"), "grey"),
helpText(getText("helpcolLAYER_COLOR")),
textInputRow('txtLAYER_TRANSP', label=getText("txtLAYER_TRANSP"), "0.08"),
helpText(getText("txtLAYER_TRANSPb")),
helpText(getText("txtLAYER_TRANSPc")),
HTML(paste0("<strong>",getText("boxVisualization9b"),"</strong>")),
checkboxInput("chkLAYER_ID_SHOW_TOPLEFT","top-left",FALSE),
checkboxInput("chkLAYER_ID_SHOW_TOPRIGHT","top-right",FALSE),
checkboxInput("chkLAYER_ID_SHOW_BOTTOMLEFT","bottom-left",TRUE),
checkboxInput("chkLAYER_ID_SHOW_BOTTOMRIGHT","bottom-right",FALSE),
textInputRow('txtLAYER_ID_FONTSIZE', label=getText("txtLAYER_ID_FONTSIZE"), "1.5")
)
)
),
column(width = 4,
conditionalPanel(condition="input.chkPLOT_WITH_RGL",
myBox("boxVisualization10", "Aggregate Options", "basic",
checkboxInput("chkAGGREGATE_SHOW",HTML(getText("chkAGGREGATE_SHOW")),FALSE),
actionLink("btnWarn6", placeWarn()),
tags$hr(),
textInputRow('txtLAYER_AGGREGATE_LABEL_PREFIX', label=getText("txtLAYER_AGGREGATE_LABEL_PREFIX"), "Aggregate"),
colourpicker::colourInput("colLAYER_AGGREGATE_COLOR", getText("colLAYER_AGGREGATE_COLOR"), "blue"),
textInputRow('txtLAYER_AGGREGATE_TRANSP', label=getText("txtLAYER_AGGREGATE_TRANSP"), "0.08"),
helpText(getText("txtLAYER_AGGREGATE_TRANSPb"))
)
),
myBox("boxVisualization11", "Inactive Layers","basic",
textInput("txtLAYERS_ACTIVE", label=getText("txtLAYERS_ACTIVE")),
helpText(getText("txtLAYERS_ACTIVEb"))
)
),
# ),
# fluidRow(
column(width = 4,
conditionalPanel(condition="input.chkPLOT_WITH_RGL",
myBox("boxVisualization12", "Geographical Options", "basic",
helpText(getText("boxVisualization12b")),
checkboxInput("chkGEOGRAPHIC_BOUNDARIES_SHOW", HTML(paste0("<strong>Layer</strong> ",getText("chkGEOGRAPHIC_BOUNDARIES_SHOW"))),TRUE),
checkboxInput("chkGEOGRAPHIC_BOUNDARIES_AGGREGATE_SHOW", HTML(paste0("<strong>Aggregate</strong> ",getText("chkGEOGRAPHIC_BOUNDARIES_AGGREGATE_SHOW"))),TRUE),
selectInput("selOSMType", HTML(getText("selOSMType")),
choices = c("bing","mapbox","mapquest-aerial","osm","osm-bbike-german","osm-transport","stamen-toner","stamen-watercolor")),
actionLink("btnGeographicMap", placeInfo() ),
tags$hr(),
helpText(paste0(HTML("<h5>",getText("boxVisualization12d"),"</h5>"))),
textInputRow('txtGEOGRAPHIC_LAT_MIN', label='Min lat:', ""),
textInputRow('txtGEOGRAPHIC_LAT_MAX', label='Max lat:', ""),
textInputRow('txtGEOGRAPHIC_LONG_MIN', label='Min lon:', ""),
textInputRow('txtGEOGRAPHIC_LONG_MAX', label='Max lon:', ""),
helpText(getText("boxVisualization12c")),
actionLink("btnWarn7", placeWarn())
)
)
)
)
),
tabPanel("Nodes",
fluidRow(
column(width = 3,
myBox("boxVisualization13", "Node Size", "basic",
conditionalPanel(condition="input.btnCalculateCentralityDiagnostics==0",
radioButtons('radNodeSizeType', getText("radNodeSizeType"),
c(Uniform='NODE_SIZE_PROPORTIONAL_TO_UNIFORM',
External='NODE_SIZE_PROPORTIONAL_TO_EXTERNAL'
),
selected='NODE_SIZE_PROPORTIONAL_TO_UNIFORM'
)
),
conditionalPanel(condition="input.btnCalculateCentralityDiagnostics>0",
uiOutput("selVizNodeSizeOutputID")
),
radioButtons('radNodeSizeType2', getText("radNodeSizeType2"),
c(Constant='NODE_SIZE_PROPORTIONAL_TYPE_NORMAL',
Log='NODE_SIZE_PROPORTIONAL_TYPE_LOG',
LogLog='NODE_SIZE_PROPORTIONAL_TYPE_LOGLOG'),
selected='NODE_SIZE_PROPORTIONAL_TYPE_LOGLOG', inline=F
),
textInputRow('txtNODE_DEFAULT_SIZE', label=getText("txtNODE_DEFAULT_SIZE"), "10")
)
),
column(width = 3,
myBox("boxVisualization14", "Node Color", "basic",
radioButtons('radNodeColor', getText("radNodeColor"),
c(Random='NODE_COLOR_RANDOM',
Community='NODE_COLOR_COMMUNITY',
Component='NODE_COLOR_COMPONENT',
Centrality='NODE_COLOR_CENTRALITY',
TopRank='NODE_COLOR_TOPRANK',
Uniform='NODE_COLOR_UNIFORM',
Query='NODE_COLOR_QUERY',
External='NODE_COLOR_EXTERNAL'),
selected='NODE_COLOR_UNIFORM'
),
hr(),
conditionalPanel(condition="input.radNodeColor=='NODE_COLOR_EXTERNAL'",
colourpicker::colourInput("colNodeColorFileDefaultNodesColor", getText("colNodeColorFileDefaultNodesColor"), "#959595")
),
conditionalPanel(condition="input.radNodeColor=='NODE_COLOR_CENTRALITY' && input.btnCalculateCentralityDiagnostics>0",
uiOutput("selVizNodeColorOutputID"),
radioButtons('radNodeColorType2', getText("radNodeColorType2"),
c(Constant='NODE_COLOR_PROPORTIONAL_TYPE_NORMAL',
Log='NODE_COLOR_PROPORTIONAL_TYPE_LOG',
LogLog='NODE_COLOR_PROPORTIONAL_TYPE_LOGLOG'),
selected='NODE_COLOR_PROPORTIONAL_TYPE_NORMAL'
),
selectInput("selCentralityColorPalette", HTML(getText("ColorPalette")),
choices = as.vector(paletteChoiceArray)),
actionLink("btnCentralityColorPaletteInfo", placeInfo() ),
textInputRow("txtNODE_COLOR_CENTRALITY_BINS", label="Bins:", "30")
),
conditionalPanel(condition="input.radNodeColor=='NODE_COLOR_CENTRALITY' && input.btnCalculateCentralityDiagnostics==0",
helpText(getText("helpText1"))
),
conditionalPanel(condition="input.radNodeColor=='NODE_COLOR_RANDOM'",
selectInput("selMultiplexColorPalette", HTML(getText("ColorPalette")),
choices = append(as.vector(paletteChoiceArray),"random")),
actionLink("btnMultiplexColorPaletteInfo", placeInfo() )
),
conditionalPanel(condition="input.radNodeColor=='NODE_COLOR_UNIFORM'",
colourpicker::colourInput("colNODE_COLOR_UNIFORM_COLOR", getText("colNODE_COLOR_UNIFORM_COLOR"), "#F2F2F2")
),
conditionalPanel(condition="input.radNodeColor=='NODE_COLOR_TOPRANK' && input.btnCalculateCentralityDiagnostics>0",
uiOutput("selVizNodeColorTopOutputID"),
textInput('txtNODE_COLOR_TOP', label=getText("txtNODE_COLOR_TOP"), "5"),
colourpicker::colourInput("colNODE_COLOR_TOP_COLOR_TOP", getText("colNODE_COLOR_TOP_COLOR_TOP"), "#FF0000"),
colourpicker::colourInput('colNODE_COLOR_TOP_COLOR_OTHERS', getText("colNODE_COLOR_TOP_COLOR_OTHERS"), "#F2F2F2"),
checkboxInput("chkNODE_LABELS_SHOW_ONLY_TOP", getText("chkNODE_LABELS_SHOW_ONLY_TOP"),TRUE),
colourpicker::colourInput('colNODE_COLOR_TOP_LABELS_FONT_COLOR', getText("colNODE_COLOR_TOP_LABELS_FONT_COLOR"), "#000000")
),
conditionalPanel(condition="input.radNodeColor=='NODE_COLOR_TOPRANK' && input.btnCalculateCentralityDiagnostics==0",
helpText(getText("helpText2"))
),
conditionalPanel(condition="input.radNodeColor=='NODE_COLOR_COMMUNITY' && input.btnCalculateCommunityDiagnostics>0",
#textInput("txtCOMMUNITY_MIN_SIZE",label="Color-code with the same RGB all nodes in communities smaller than (useful for evidencing larger communities, not valid for the multiplex):","1"),
uiOutput("selVizNodeColorCommunityTypeOutputID"),
selectInput("selCommunityColorPalette", HTML(getText("ColorPalette")),
choices = append(as.vector(paletteChoiceArray),"random")),
actionLink("btnCommunityColorPaletteInfo", placeInfo() )
),
conditionalPanel(condition="input.radNodeColor=='NODE_COLOR_QUERY' && input.btnQuery>0",
colourpicker::colourInput('colQUERY_NODES_NODE_COLOR', getText("colQUERY_NODES_NODE_COLOR"), "#FF6246"),
colourpicker::colourInput('colQUERY_NODES_NODE_NEIGH_COLOR', getText("colQUERY_NODES_NODE_NEIGH_COLOR"), "#669DC1"),
colourpicker::colourInput('colQUERY_NODES_NODE_OTHER_COLOR', getText("colQUERY_NODES_NODE_OTHER_COLOR"), "#959595"),
checkboxInput("chkNODE_LABELS_SHOW_ONLY_QUERY", getText("chkNODE_LABELS_SHOW_ONLY_QUERY"),TRUE),
colourpicker::colourInput('colNODE_COLOR_QUERY_LABELS_FONT_COLOR', getText("colNODE_COLOR_QUERY_LABELS_FONT_COLOR"), "#000000")
),
conditionalPanel(condition="input.radNodeColor=='NODE_COLOR_COMMUNITY' && input.btnCalculateCommunityDiagnostics==0",
helpText(getText("helpText3"))
),
conditionalPanel(condition="input.radNodeColor=='NODE_COLOR_COMPONENT' && input.btnCalculateComponentsDiagnostics>0",
uiOutput("selVizNodeColorComponentTypeOutputID"),
selectInput("selComponentColorPalette", HTML(getText("ColorPalette")),
choices = append(as.vector(paletteChoiceArray),"random")),
actionLink("btnComponentColorPaletteInfo", placeInfo() )
),
conditionalPanel(condition="input.radNodeColor=='NODE_COLOR_COMPONENT' && input.btnCalculateComponentsDiagnostics==0",
helpText(getText("helpText4"))
),
conditionalPanel(condition="input.radNodeColor=='NODE_COLOR_QUERY' && input.btnQuery==0",
helpText(getText("helpText5"))
)
)
),
# ),
# fluidRow(
column(width = 4,
myBox("boxVisualization15", "Other Options", "basic",
checkboxInput("chkNODE_ISOLATED_HIDE", getText("chkNODE_ISOLATED_HIDE"),TRUE),
conditionalPanel(condition="input.chkNODE_ISOLATED_HIDE && input.radMultiplexModel!='MULTIPLEX_IS_EDGECOLORED'",
checkboxInput("chkNODE_ISOLATED_HIDE_INTERLINKS", getText("chkNODE_ISOLATED_HIDE_INTERLINKS"),TRUE)
),
textInputRow('txtNODE_TRANSP', label=getText("txtNODE_TRANSP"), "0.8"),
helpText(getText("helpText6")),
textInput("txtNODE_FRAME_COLOR", getText("txtNODE_FRAME_COLOR"),""),
helpText(getText("helpText7")),
checkboxInput("chkNODE_LABELS_SHOW", getText("chkNODE_LABELS_SHOW"),FALSE),
helpText(getText("helpText8")),
conditionalPanel("input.chkNODE_LABELS_SHOW",
checkboxInput("chkNODE_LABELS_SHOW_WRAP", getText("chkNODE_LABELS_SHOW_WRAP"),FALSE),
conditionalPanel(condition="input.chkNODE_LABELS_SHOW_WRAP",
textInputRow('txtNODE_LABELS_WRAP', label=getText("txtNODE_LABELS_WRAP"), "10"),
helpText(getText("helpText9")),
textInputRow('txtNODE_LABELS_WRAP_OFFSET', label=getText("txtNODE_LABELS_WRAP_OFFSET"), "0"),
helpText(getText("helpText10"))
),
textInputRow('txtNODE_LABELS_DISTANCE', label=getText("txtNODE_LABELS_DISTANCE"), "1."),
textInputRow('txtNODE_LABELS_FONT_SIZE', label=getText("txtNODE_LABELS_FONT_SIZE"), "0.5"),
colourpicker::colourInput('colNODE_LABELS_FONT_COLOR', getText("colNODE_LABELS_FONT_COLOR"), "#2F2F2F")
)
)
),
column(width = 3,
conditionalPanel(condition="input.radNodeColor=='NODE_COLOR_EXTERNAL' || input.selVizNodeSizeID=='External' || input.radNodeSizeType=='NODE_SIZE_PROPORTIONAL_TO_EXTERNAL'",
myBox("boxVisualization16", "External color/size", "basic",
helpText(getText("helpText11")),
#checkboxInput('chkNodeColorFileHeader', 'Header', TRUE),
textInput("txtNodeColorFileSep", label=getText("txtNodeColorFileSep"), " "),
fileInput('nodecolor_file', HTML(paste0("<strong>* ",getText("nodecolor_file"),"</strong>")),
accept=c('text/csv', 'text/comma-separated-values,text/plain', '.csv')),
HTML("<center>"),
actionButton("btnImportNodeColor", getText("Import")),
HTML("</center>")
)
)
)
)
),
tabPanel("Edges",
fluidRow(
column(width = 3,
myBox("boxVisualization17", "Edge Size","basic",
radioButtons('radEdgeSizeType', getText("radEdgeSizeType"),
c(Uniform='EDGE_SIZE_PROPORTIONAL_TO_UNIFORM',
External='EDGE_SIZE_PROPORTIONAL_TO_EXTERNAL',
Weight='EDGE_SIZE_PROPORTIONAL_TO_WEIGHT'),
selected='EDGE_SIZE_PROPORTIONAL_TO_WEIGHT', inline=F
),
radioButtons('radEdgeSizeType2', getText("radEdgeSizeType2"),
c(Constant='EDGE_SIZE_PROPORTIONAL_TYPE_NORMAL',
Log='EDGE_SIZE_PROPORTIONAL_TYPE_LOG',
LogLog='EDGE_SIZE_PROPORTIONAL_TYPE_LOGLOG'),
selected='EDGE_SIZE_PROPORTIONAL_TYPE_LOGLOG', inline=F
),
textInputRow('txtEDGE_DEFAULT_SIZE', label=getText("txtEDGE_DEFAULT_SIZE"), "2")
)
),
column(width = 3,
myBox("boxVisualization18", "Edge Color", "basic",
radioButtons('radEdgeColor', getText("radEdgeColor"),
c(Random='EDGE_COLOR_RANDOM',
Uniform='EDGE_COLOR_UNIFORM',
External='EDGE_COLOR_EXTERNAL'),
selected='EDGE_COLOR_UNIFORM'
),
hr(),
conditionalPanel(condition="input.radEdgeColor=='EDGE_COLOR_EXTERNAL'",
colourpicker::colourInput("colEdgeColorFileDefaultEdgesColor", getText("colEdgeColorFileDefaultEdgesColor"), "#F2F2F2")
),
conditionalPanel(condition="input.radEdgeColor=='EDGE_COLOR_RANDOM'",
selectInput("selMultiplexEdgeColorPalette", HTML(getText("ColorPalette")),
choices = append(as.vector(paletteChoiceArray),"random")),
actionLink("btnMultiplexEdgeColorPaletteInfo", placeInfo() )
),
conditionalPanel(condition="input.radEdgeColor=='EDGE_COLOR_UNIFORM'",
colourpicker::colourInput('colEDGE_COLOR', getText("colEDGE_COLOR"), "#F2F2F2")
#helpText(getText("helpText12"))
)
)
),
# ),
# fluidRow(
column(width = 4,
myBox("boxVisualization19", "Other Options", "basic",
textInputRow('txtEDGE_BENDING', label=getText("txtEDGE_BENDING"), "0"),
helpText("0 means straight; max 1"),
textInputRow('txtEDGE_TRANSP', label=getText("txtEDGE_TRANSP"), "0.2"),
helpText(getText("helpText13")),
textInputRow('txtLAYER_ARROW_SIZE', label=getText("txtLAYER_ARROW_SIZE"), "0.2"),
textInputRow('txtLAYER_ARROW_WIDTH', label=getText("txtLAYER_ARROW_WIDTH"), "0.2")
)
),
column(width = 3,
conditionalPanel(condition="input.radEdgeColor=='EDGE_COLOR_EXTERNAL' || input.radEdgeSizeType=='EDGE_SIZE_PROPORTIONAL_TO_EXTERNAL'",
myBox("boxVisualization21", "External color/size", "basic",
helpText(getText("helpText20")),
#checkboxInput('chkEdgeColorFileHeader', 'Header', TRUE),
textInput("txtEdgeColorFileSep", label=getText("txtEdgeColorFileSep"), " "),
fileInput('edgecolor_file', HTML(paste0("<strong>* ",getText("edgecolor_file"),"</strong>")),
accept=c('text/csv', 'text/comma-separated-values,text/plain', '.csv')),
HTML("<center>"),
actionButton("btnImportEdgeColor", getText("Import")),
HTML("</center>")
)
)
)
)
),
tabPanel("Export",
br(),
fluidRow(
column(width = 4,
myBox("boxVisualization20", "Options", "basic",
conditionalPanel(condition="input.chkPLOT_WITH_RGL",
radioButtons('radRGLExport', getText("radRGLExport"),
c(PNG='RGL_EXPORT_PNG',
PDF='RGL_EXPORT_PDF',
SVG='RGL_EXPORT_SVG',
webGL='RGL_EXPORT_WEBGL'),
selected='RGL_EXPORT_PNG', inline=TRUE
),
HTML("<center>"),
conditionalPanel(condition="input.radRGLExport=='RGL_EXPORT_PNG'",
actionButton("btnExportRendering","Export PNG")
),
conditionalPanel(condition="input.radRGLExport=='RGL_EXPORT_PDF'",
actionButton("btnExportRenderingPDF","Export PDF")
),
conditionalPanel(condition="input.radRGLExport=='RGL_EXPORT_SVG'",
actionButton("btnExportRenderingSVG","Export SVG")
),
conditionalPanel(condition="input.radRGLExport=='RGL_EXPORT_WEBGL'",
actionButton("btnExportRenderingWeb","Export webGL")
),
HTML("</center>")
),
conditionalPanel(condition="!input.chkPLOT_WITH_RGL",
radioButtons('radNORGLExport', getText("radNORGLExport"),
c(PNG='NORGL_EXPORT_PNG',
PDF='NORGL_EXPORT_PDF'),
selected='NORGL_EXPORT_PNG', inline=TRUE
),
conditionalPanel(condition="input.radNORGLExport=='NORGL_EXPORT_PNG'",
textInputRow("txtExportRenderingClassicPNGWidth", "Width (px):", "1024"),
textInputRow("txtExportRenderingClassicPNGHeight", "Height (px):", "768"),
textInputRow("txtExportRenderingClassicPNGResolution", "Resolution (dpi):", "300"),
tags$br(),
HTML("<center>"),
actionButton("btnExportRenderingClassicPNG","Export PNG"),
HTML("</center>")
),
conditionalPanel(condition="input.radNORGLExport=='NORGL_EXPORT_PDF'",
textInputRow("txtExportRenderingClassicPDFWidth", "Width (px):", "1024"),
textInputRow("txtExportRenderingClassicPDFHeight", "Height (px):", "768"),
tags$br(),
HTML("<center>"),
actionButton("btnExportRenderingClassicPDF","Export PDF"),
HTML("</center>")
)
)
)
)
)
)
),
value=0
),
tabPanel("Reducibility",
actionLink("btnReducibilityHelp", placeHelp() ),
conditionalPanel(condition="input.radMultiplexModel=='MULTIPLEX_IS_INTERDEPENDENT'",
helpText(getText("helpText14"))
),
conditionalPanel(condition="input.radMultiplexModel!='MULTIPLEX_IS_INTERDEPENDENT'",
fluidRow(
column(width = 3,
myBox("boxReducibility", "Algorithms","basic",
#HTML('<h4>Algorithms to be used to calculate the correlation between layers and clustering</h4>'),
radioButtons('radReducibilityCorrelationMethod', getText("radReducibilityCorrelationMethod"),
c(Jensen_Shannon_Divergence='REDUCIBILITY_METHOD_CORRELATION_JENSEN_SHANNON'),
selected='REDUCIBILITY_METHOD_CORRELATION_JENSEN_SHANNON'),
tags$hr(),
selectInput("selReducibilityClusterMethod", getText("selReducibilityClusterMethod"),
choices = c("ward.D2","single","complete","average","mcquitty","median","centroid"))
)
),
column(width = 3,
myBox("boxReducibility2", "Graphical Options", "basic",
selectInput("selReducibilityColorPalette", HTML(getText("ColorPalette")),
choices = paletteChoiceArray),
actionLink("btnReducibilityPaletteInfo", placeInfo() ),
textInputRow("txtREDUCIBILITY_HEATMAP_FONT_SIZE",label=getText("txtREDUCIBILITY_HEATMAP_FONT_SIZE"),"1.5")
),
HTML("<center>"),
actionButton("btnCalculateReducibility", getText("btnCalculateReducibility")),
HTML("</center>")
#actionButton("btnExportReducibilityRendering","Export PNG"),
)
),
tags$hr(),
HTML('<h4>Structural reducibility</h4>'),
conditionalPanel(condition="input.btnCalculateReducibility>0",
uiOutput("reducibilityHeatmapUI"),
#imageOutput("jsdMatrixSummaryImage",width = "100%", height = "700px"),
#imageOutput("reducibilityDendrogramSummaryImage",width = "100%", height = "700px"),
tags$br(),
HTML('<h5>Reduction Quality</h5>'),
showOutput("reducibilityQualityFunction","nvd3"),
tags$hr()
)
)
),
tabPanel("Dynamics",
actionLink("btnDynamicsHelp", placeHelp() ),
fluidRow(
column(width = 3,
myBox("boxDynamics", "Timeline file","basic",
#helpText(HTML("<h4>Open Timeline File</h4>")),
helpText(HTML(paste0("<strong><font color='#262626'>* ", getText("helpText16"),"</font></strong>"))),
#checkboxInput('chkTimelineFileHeader', 'Header', TRUE),
textInput("txtTimelineFileSep", label=getText("txtTimelineFileSep"), " "),
fileInput('timeline_file', HTML(paste0("<strong>* ", getText("timeline_file"),"</strong>")),
accept=c('text/csv', 'text/comma-separated-values,text/plain', '.csv')
),
HTML("<center>"),
actionButton("btnImportTimeline", getText("btnImportTimeline")),
HTML("</center>")
),
HTML("<center>"),
checkboxInput("chkTIMELINE_RENDER_TO_FILE", getText("chkTIMELINE_RENDER_TO_FILE"),FALSE),
actionButton("btnRenderDynamicsSnapshots", getText("btnRenderDynamicsSnapshots")),
hr(),
actionButton("btnFFMPEGDynamicsSnapshots", getText("btnFFMPEGDynamicsSnapshots")),
HTML("</center>")
),
column(width = 4,
myBox("boxDynamics2", "Graphical Options", "basic",
textInput("txtTimelineDefaultNodesSize", label=getText("txtTimelineDefaultNodesSize"), "10"),
helpText(getText("helpText17")),
colourpicker::colourInput("colTimelineDefaultNodesColor", getText("colTimelineDefaultNodesColor"), "#959595"),
textInput("txtTimelineDefaultEdgesSize", label=getText("txtTimelineDefaultEdgesSize"), "1"),
helpText(getText("helpText18")),
colourpicker::colourInput("colTimelineDefaultEdgesColor", getText("colTimelineDefaultEdgesColor"), "#959595"),
helpText(getText("helpText18"))
#tags$hr(),
#textInput("txtFFMPEG_PATH",label="Full path of your ffmpeg binary to make the video (if not valid, video will not be made):",""),
#textInput("txtFFMPEG_FLAGS",label="Parameters to be passed to ffmpeg (if not valid, video will not be made):",""),
)
)
),
helpText(HTML("<h4>Summary for the timeline</h4>")),
conditionalPanel(condition="input.btnImportTimeline>0 && input.btnRenderNetworks>0",
htmlWidgetOutput(
outputId = 'projectTimelineHTML',
HTML(paste(
'Time steps: <span id="timelineTimesteps"></span><br>',
'Affecting the dynamics of nodes: <span id="timelineAffectNodes"></span><br>',
'Affecting the dynamics of edges: <span id="timelineAffectEdges"></span><br>',
'<br>'
))
)
)
),
tabPanel("Graphics",
mainPanel(
tabsetPanel(
tabPanel("Points",
HTML("<img width='800' src='img/pointtypes.png' alt=''/>")
),
tabPanel("Lines",
HTML("<img width='800' src='img/linetypes.png' alt=''/>")
),
tabPanel("Colors",
HTML("<img width='800' src='img/colorpalettes.png' alt=''/>")
),
tabPanel("Maps",
HTML("<img width='800' src='img/backmaps.png' alt=''/>")
)
)
)
),
tabPanel("Data",
HTML("<center>"),
HTML("<i class='fa fa-flask fa-4x'></i><h1>Available data</h1><br>"),
HTML("</center>"),
fluidRow(
column(width = 5,
showOutput("dataPieChart","nvd3")
),
column(width = 6,
showOutput("dataScatterPlot","nvd3")
)
),
HTML("<center>"),
HTML("<a href='https://comunelab.fbk.eu/data.php' target='_blank'><i class='fa fa-download fa-4x'></i><h1>Go to the download page</h1></a><br>"),
HTML("</center>"),
#tableOutput("dataTable")
dataTableOutput('dataTable')
),
navbarMenu("Help",
tabPanel("Help",
mainPanel(
htmlWidgetOutput(
outputId = 'tabHelp',
HTML("<img src='img/logo_small.jpg' alt=''/>"),
HTML(getText("GlobalHelp"))
),
value=4
)
),
tabPanel("Citation",
mainPanel(
htmlWidgetOutput(
outputId = 'tabCitation',
HTML("<img src='img/logo_small.jpg' alt=''/>"),
HTML("<h3>Citation</h3>"),
HTML("If you use <span>muxViz</span> for your analysis and visualization of multilayer networks, you should cite the following paper:<br>"),
br(),
HTML('<ul><li>M. De Domenico, M. Porter and A. Arenas, <i>MuxViz: a tool for multilayer analysis and visualization of networks</i>, Journal of Complex Networks 3, 159 (2015) [<a href="http://comnet.oxfordjournals.org/content/3/2/159" target="_blank">Open</a>]</li></ul>'),
HTML("<span>muxViz</span> is based on several algorithms. Please, cite the papers corresponding to the algorithms used in your research.")
)
)
),
tabPanel("About",
mainPanel(
htmlWidgetOutput(
outputId = 'tabCredits',
HTML("<img src='img/logo_small.jpg' alt=''/>"),
HTML("<h3>muxViz Project</h3>"),
HTML("Software released under <a href='http://www.gnu.org/licenses/gpl-3.0.html' target='_blank'>GPLv3</a><br>"),
HTML("Developed by <a href='http://deim.urv.cat/~manlio.dedomenico/index.php' target='_blank'>Manlio De Domenico</a><br><a href='http://deim.urv.cat' target='_blank'>School of Computer Science and Mathematics</a>, <a href='http://www.urv.cat' target='_blank'>Universitat Rovira i Virgili</a><br><br>"),
HTML("Visit the <a href='http://deim.urv.cat/~manlio.dedomenico/muxviz.php' target='_blank'>project page</a> or the <a href='https://github.com/manlius/muxViz' target='_blank'>Github repo</a>"),
HTML(paste(
'<h3>Credits</h3>',
'This work has been partially supported by <a href="http://www.plexmath.eu/" target="_blank">European Commission FET-Proactive project PLEXMATH (Grant No. 317614)</a>, the European project devoted to the investigation of multi-level complex systems and has been developed at the <a href="http://deim.urv.cat/~alephsys/" target="_blank">Alephsys Lab</a>.<br><br>',
'I am in debt with <a href="http://deim.urv.cat/~aarenas/" target="_blank">A. Arenas</a> for proposing this project, with <a href="http://people.maths.ox.ac.uk/porterm/" target="_blank">Mason A. Porter</a> and with the muxViz community for invaluable suggestions and feedbacks.',
'<br><br>',
'I would like to thank Inderjit S. Jutla, Lucas G. S. Jeub, and Peter J. Mucha for making their code about multislice community detection available.',
'<br><br>',
'Finally, I would like to acknowledge the precious help of S. Agnello in designing and testing this Graphical User Interface to muxViz.',
tags$hr(),
'<br>'
))
),
value=5
)
),
tabPanel("License",
mainPanel(
htmlWidgetOutput(
outputId = 'tabLicense',
HTML("<img src='img/logo_small.jpg' alt=''/>"),
HTML(paste(
'<h3>License</h3>',
'<span>muxViz</span> makes use of many packages and its license is compatible with the license of each used package. <span>muxViz</span> is Open Source and makes use of free software only: <a href="http://www.r-project.org/" target="_blank">R</a> (GNU GPLv2) and <a href="" target="_blank">muxNet</a> (Next release, GNU GPLv3 License, <a href="muxnet_license.txt" target="_blank">see the original license</a>).<br><br>',
'This code has no warranty whatsoever and any kind of support is provided. You are free to do what you like with this code as long as you leave this copyright in place. Please, explicitly cite <span>muxViz</span> if you find it useful for your visualizations and analyses.',
'<br><br>',
'(C) Copyright 2013-2017, Manlio De Domenico (manlio.dedomenico at urv.cat)',
'<br><br>',
'<span>muxViz</span> is free software: you can redistribute it and/or modify it under the terms of the <a href="http://www.gnu.org/licenses/gpl-3.0.html" target="_blank">GNU General Public License</a> as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.',
'<br><br>',
'<span>muxViz</span> is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.',
'<br><br>',
'You should have received a copy of the GNU General Public License along with the package. If not, see <a href="http://www.gnu.org/licenses/" target="_blank">www.gnu.org/licenses/</a>.',
tags$hr(),
'<br>'
))
),
value=6
)
),
tabPanel("Donate",
mainPanel(
htmlWidgetOutput(
outputId = 'tabDonate',
HTML("<img src='img/logo_small.jpg' alt=''/>"),
HTML(paste(
'<h3>Donation</h3>',
'<span>muxViz</span> is a free and open-source platform that has been used for scientific purposes in a variety of disciplines, including computational social science, computational neuroscience, computational biology, computational psycholinguistics, multi-modal transportation engineering and physics. <br><br>Since January 2016, <span>muxViz</span> is periodically updated and maintained for free by its developer and its enthusiastic community of users (the muxVizers).<br><br>',
'If <span>muxViz</span> helps you with your research and reduces your time to develop, you can give us a cup of good coffee :)',
tags$br(),
tags$br(),
'<strong>BTC</strong>: 19RGUCZjSzvbjY5xEWz3GNg7MnMiPyEgbB',
tags$br(),
tags$br(),
'<strong>ETH</strong>: 0xe5027b44782a4b832a23773ffdb57658aff62e31',
tags$br(),
tags$br(),
'<strong>XMR</strong>: 49pQ1B2m2UHaKotqF8h1E89um9rnMPvAHEfGUET1icQUaxBV1KFhuTNVpsF6Kf4bf5dZwWvmdzYn4D7rKcL4v2ee3tH4E2L',
tags$br(),
tags$br(),
'<strong>Paypal</strong>:<br>',
tags$br(),
'<a href="https://www.paypal.com/cgi-bin/webscr?cmd=_donations&business=manlio.dedomenico@gmail.com&item_name=muxViz&item_number=muxViz+development¤cy_code=USD" target="_blank"><img src="https://www.paypalobjects.com/en_US/i/btn/btn_donateCC_LG.gif" border=0></a>',
tags$hr(),
tags$br()
))
),
value=7
)
)
)
)
)
})
manlius/muxViz documentation built on March 1, 2023, 10:28 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
library(shiny)
library(ShinyDash)
library(markdown)
library(shinydashboard)
library(rCharts)
#library(shinyIncubator)
library(digest)
library(shinyjs)
library(colourpicker)
library(d3heatmap)
library(networkD3)
source("version.R")
source("language.R")
#library("shinythemes")
#RGB colors table
#http://www.javascripter.net/faq/rgbtohex.htm
paletteWeb <- "<a href='http://www.colorschemer.com/online.html' target='_blank'>Online Color Palette</a>, <a href='http://colorbrewer2.org'>Online Color Scheme</a>"
myBoxCnt <- 0
#http://getbootstrap.com/components/#glyphicons
#http://fontawesome.io/icons/
#http://rstudio.github.io/shinydashboard/appearance.html#icons
#interactive heatmaps
#http://www.statsblogs.com/2013/12/15/visualization-of-2012-crime-rates-of-different-states-in-the-us-using-rcharts/
paletteChoiceArray <- sort(row.names(brewer.pal.info[1]))
buildPath <- function(folder,objname){
folder <- gsub("\"","", folder )
objname <- gsub("\"","", objname )
if( Sys.info()["sysname"]=="Windows" ){
#return( paste(getwd(),folder,objname,sep="\\") )
return( paste0("\"",paste(getwd(),folder,objname,sep="\\"),"\"") )
}else{
#return( paste(getwd(),folder,objname,sep="/") )
return( paste(getwd(),folder,objname,sep="/") )
}
}
buildTmpPath <- function(objname){
return( buildPath("tmp",objname) )
}
concatenatePath <- function(folder,objname){
folder <- gsub("\"","", folder )
objname <- gsub("\"","", objname )
if( Sys.info()["sysname"]=="Windows" ){
return( paste0("\"",paste(folder, paste0(objname, collapse="\\"), sep="\\"),"\"") )
}else{
return( paste(folder, paste0(objname, collapse="/"), sep="/") )
}
}
getExecutablePath <- function(exec_name){
path <- ""
if( Sys.info()["sysname"]=="Windows" ){
path <- buildPath("bin",paste0(exec_name,"_windows.exe"))
}else if( Sys.info()["sysname"]=="Linux" ){
path <- buildPath("bin",paste0(exec_name,"_linux"))
}else{
path <- buildPath("bin",paste0(exec_name,"_macosx"))
}
return(path)
}
fanmodCheck <- function(){
res <- system(getExecutablePath("fanmod"), ignore.stdout = F, ignore.stderr = F, intern=F)
if(res==255){
return(paste0("<i class='fa fa-check'></i> ",getText("txtFanmodCheck"),"<br>"))
}else{
return(paste0("<i class='fa fa-warning'></i> ",getText("txtFanmodCheckWarning"),"<br>"))
}
}
multimapCheck <- function(){
res <- system(getExecutablePath("multiplex-infomap"), ignore.stdout = F, ignore.stderr = F, intern=F)
if(res==255){
return(paste0("<i class='fa fa-check'></i> ",getText("txtMultimapCheck"),"<br>"))
}else{
return(paste0("<i class='fa fa-warning'></i> ",getText("txtMultimapCheckWarning"),"<br>"))
}
}
muxbenchCheck <- function(){
res1 <- system(getExecutablePath("muxbench1"), ignore.stdout = F, ignore.stderr = F, intern=F)
res2 <- system(getExecutablePath("muxbench2"), ignore.stdout = F, ignore.stderr = F, intern=F)
res3 <- system(getExecutablePath("muxbench3"), ignore.stdout = F, ignore.stderr = F, intern=F)
if(res1==0 && res2==0 && res3==0){
return(paste0("<i class='fa fa-check'></i> ",getText("txtMuxbenchCheck"),"<br>"))
}else{
return(paste0("<i class='fa fa-warning'></i> ",getText("txtMuxbenchCheck"),"<br>"))
}
}
myBox <- function(id, Title, Type="basic", ...){
myBoxCnt <<- myBoxCnt + 1
if(Type=="basic"){
return(
div(style="background-color: #FFFFFF; border-width: 1px; border-style: solid; border-color: #3286AD; margin: 10px 5px 10px 5px; -moz-border-radius: 15px; border-radius: 15px;",
div(style="background-color: #3286AD; color: #FFFFFF; -moz-border-top-right-radius: 15px; -moz-border-top-left-radius: 15px; border-top-left-radius: 15px; border-top-right-radius: 15px; text-align: center; font-family: 'Arial';", HTML(paste0("<font size='+1'><strong>",Title,"</strong></font> <i id=\"btnRollBox",myBoxCnt,"\" class=\"fa fa-caret-square-o-up\" onclick=\"rollBox(",paste0("btnRollBox",myBoxCnt,", RollBox",myBoxCnt),")\"></i>"))),
div(style="padding: 5px 5px 5px 5px;", id=paste0("RollBox",myBoxCnt),
list(...)
)
)
)
}
if(Type=="info"){
return(
div(style="background-color: #FFFFFF; border-width: 1px; border-style: solid; border-color: #165400; margin: 10px 5px 10px 5px; -moz-border-radius: 15px; border-radius: 15px;",
div(style="background-color: #165400; color: #FFFFFF; -moz-border-top-right-radius: 15px; -moz-border-top-left-radius: 15px; border-top-left-radius: 15px; border-top-right-radius: 15px; text-align: center; font-family: 'Arial';", HTML(paste0("<font size='+1'><strong>",Title,"</strong></font>"))),
div(style="padding: 5px 5px 5px 5px;",
list(...)
)
)
)
}
}
textInputRow <- function (inputId, label, value = "", width=NULL) {
div(style="display:inline-block",
tags$label(label, `for` = inputId),
tags$input(id = inputId, type = "text", value = value,class="input-small", width=width))
}
checkboxInputRow <- function (inputId, label, value = "") {
div(style="display:inline-block",
tags$label(label, `for` = inputId),
tags$input(id = inputId, type = "checkbox", value = value, class="input-small"))
}
placeHelp <- function(){
HTML(paste("<div style=\"float: right;\">", icon("question-circle"), "Help", "</div>"))
}
placeInfo <- function(){
HTML(paste(icon("info-circle"), "Info"))
}
placeWarn <- function(){
HTML(paste("<font color=\"red\">",icon("exclamation-circle"), "Re-apply layout", "</font>"))
}
shinyUI(function(request) {
bootstrapPage(
#shinyUI(fluidPage(shinythemes::themeSelector(),
tags$head(tags$link(rel='stylesheet', type='text/css', href='styles.css')),
# Load D3.js
tags$head(tags$script(src = 'http://d3js.org/d3.v3.min.js')),
tags$head(tags$script(src = "muxviz.js")),
tags$head(tags$title("muxViz")),
#headerPanel("muxViz Graphical User Interface"),
navbarPage("",
tabPanel(icon("home"),
sidebarLayout(position = "right",
sidebarPanel(
helpText(HTML(paste(getText("muxVizVersion"),muxVizVersion))),
helpText(HTML(paste(getText("muxVizUpdate"),muxVizUpdate))),
hr(),
helpText(HTML(paste(getText("muxVizSystem"),Sys.info()["sysname"]))),
helpText(HTML(paste(Sys.info()["version"]))),
hr(),
helpText(HTML(paste(version["version.string"][[1]]))),
hr(),
HTML(multimapCheck()),
HTML(fanmodCheck())
#HTML(muxbenchCheck())
),
mainPanel(
HTML("<img src='img/home.png' height='550' style='{margin-left: auto; margin-right: auto;}'>")
)
)
),
navbarMenu(getText("navBarFile"),
tabPanel("Import",
actionLink("btnImportHelp", placeHelp() ),
tabsetPanel(
tabPanel("Import Networks",
fluidRow(
column(width = 9,
myBox("boxNetworkModel", getText("NetworkModel"), "basic",
HTML("<img src='img/network_type.png' width='100%' alt=''/>"),
radioButtons('radMultiplexModel', '',
c(Edge_Colored='MULTIPLEX_IS_EDGECOLORED',
Interconnected_Multiplex='MULTIPLEX_IS_INTERCONNECTED',
Interdependent_Multiplex='MULTIPLEX_IS_INTERDEPENDENT',
General_Multilayer='MULTIPLEX_IS_MULTILAYER'
),
selected='MULTIPLEX_IS_EDGECOLORED',
inline=T
)
)
),
column(width = 3,
conditionalPanel(condition="input.radMultiplexModel=='MULTIPLEX_IS_EDGECOLORED'",
myBox("boxMultiplexType", getText("boxMultiplexType"), "basic",
radioButtons('radMultiplexType', '',
c(Ordinal='MULTIPLEX_IS_ORDERED',
Categorical='MULTIPLEX_IS_CATEGORICAL'),
selected='MULTIPLEX_IS_CATEGORICAL'
),
actionLink("btnMultiplexTypeInfo", placeInfo() ),
tags$br(),
tags$br(),
textInputRow("txtOmega", label=HTML(getText("txtOmega")), "1"),
helpText(getText("helpParameters"))
)
),
conditionalPanel(condition="input.radMultiplexModel!='MULTIPLEX_IS_EDGECOLORED'",
helpText(getText("txtNoParameters"))
)
)
),
fluidRow(
column(width = 3,
myBox("boxProjectID", getText("ProjectID"), "basic",
textInput("txtProjectName", label=HTML(paste0("<strong>",getText("txtProjectName"),"</strong>")), paste0("muxViz_",as.character(format(Sys.time(), "%d-%m-%Y_%H%M%S")))
)
),
myBox("boxConfiguration", getText("Configuration"), "basic",
#helpText(HTML("<h4>Open Configuration File</h4>")),
#helpText(HTML(paste0("<strong><font color='#262626'>",getText("ConfigurationFileFormat"),"</font></strong>"))),
checkboxInput('chkConfigFileHeader', getText("chkConfigFileHeader"), FALSE),
textInputRow("txtConfigFileSep", label=HTML(getText("txtConfigFileSep")), ";"),
fileInput('project_file', "",
accept=c('text/csv', 'text/comma-separated-values,text/plain', '.csv')
)
#HTML(paste0("<strong>",getText("ConfigurationFile"),"</strong>"))
)
),
#todo: here conditional panel depending on project_file
column(width = 3,
myBox("boxInputFormat", getText("InputFormat"), "basic",
checkboxInput('chkEdgeListFileHeader', getText("chkEdgeListFileHeader"), FALSE),
textInput("txtEdgeListFileSep", label=getText("txtEdgeListFileSep"), " "),
helpText(getText("txtEdgeListFileSepHelp2")),
checkboxInput("chkEdgeListLabel", getText("chkEdgeListLabel"), FALSE),
conditionalPanel("input.chkEdgeListLabel",
checkboxInput("chkEdgeListLabel2", getText("chkEdgeListLabel2"), FALSE)
),
actionLink("btnEdgeListFileSepInfo", placeInfo() )
)
),
column(width = 3,
myBox("boxNetworkFormat", getText("NetworkFormat"), "basic",
selectInput("selEdgeListType", HTML(paste0("<strong>",getText("selEdgeListType"),"</strong>")),
choices = c(getText("Undirected"), getText("Directed"))),
checkboxInput("chkEdgeListWeighted", getText("chkEdgeListWeighted"), FALSE),
checkboxInput("chkEdgeListUndirectedBoth", getText("chkEdgeListUndirectedBoth"), FALSE),
checkboxInput("chkRESCALE_WEIGHT",getText("chkRESCALE_WEIGHT"),FALSE),
checkboxInput('chkOutputEdgelistTable',HTML(getText("chkOutputEdgelistTable")),FALSE)
),
HTML("<center>"),
actionButton("btnImportNetworks", getText("btnImportNetworks")),
HTML("</center>")
)
),
tags$hr(),
helpText(HTML(paste0("<h4>",getText("ConfigurationFileSummary"),"</h4>"))),
tableOutput("layersTable"),
tags$hr(),
conditionalPanel(condition="input.btnImportNetworks>0",
myBox("boxNetworkSummary", getText("NetworkSummary"),"info",
#helpText(HTML("<h4>Summary for the multilayer network</h4>")),
htmlWidgetOutput(
outputId = 'projectSummaryHTML',
HTML("Layers: <span id=\"sumLayers\"></span><br>Type of layer: <span id=\"sumLayerType\"></span><br><br>Number of nodes: <span id=\"sumNodes\"></span><br> Minimum ID: <span id=\"sumMinNodeID\"></span><br> Maximum ID: <span id=\"sumMaxNodeID\"></span><br>Number of edges: <span id=\"sumEdges\"></span><br><br>External layout: <span id=\"sumIsLayoutExternal\"></span><br>Is geographical: <span id=\"sumIsLayoutGeographic\"></span><br>")
#seems that I cant use the getText here, it does not load the HTML..
)
),
tags$hr(),
HTML("<h4>Matrix Explorer</h4>"),
checkboxInput("chkShowMatrixExplorer", HTML(getText("chkShowMatrixExplorer"))),
tabPanel("",
selectInput("selMatrixEplorerHeatmapColorPalette", HTML(getText("ColorPalette")), choices = paletteChoiceArray),
actionLink("btnMatrixExplorerPaletteInfo", placeInfo() ),
checkboxInput("chkMatrixEplorerHeatmapShowDendrogram", getText("ApplyClustering")),
tabsetPanel(id="tabsetMatrixEplorerMultilayer",
tabPanel("Multilayer",
uiOutput("matrixExplorerHeatmapMultilayerUI")
),
tabPanel("Aggregate",
uiOutput("matrixExplorerHeatmapAggregateUI")
)
)
)
)
),
tabPanel("Edges Tables",
helpText(HTML(paste0("<h4>",getText("ImportedEdgeLists"),"</h4>"))),
conditionalPanel(condition="input.btnImportNetworks>0",
checkboxInput(inputId = "edgelistTablePageable", label = getText("Pageable"), TRUE),
conditionalPanel("input.edgelistTablePageable==true",
numericInput(inputId = "edgelistTablePageSize",label = getText("EdgesPerPage"),100)
),
htmlOutput("edgelistTable")
)
)
),
tags$hr(),
value=1
),
tabPanel("Console",
actionLink("btnConsoleHelp", placeHelp() ),
tags$textarea(id="Console", rows=20, cols=145, ""),
HTML("<center>"),
actionButton("btnRunConsole" ,getText("Run")),
HTML("</center>")
),
tabPanel("Load/Save session",
actionLink("btnSessionManagerHelp", placeHelp() ),
HTML(paste("<font color=\"red\">",icon("exclamation-circle"), getText("WarningMessage1"), "</font>")),
fluidRow(
column(width = 5,
myBox("boxLoadSession", "Session Manager", "basic",
uiOutput("selOutputSavedSessionsList"),
checkboxInput('chkConfirmDeleteSavedSession', getText("chkConfirmDeleteSavedSession"), FALSE),
actionButton("btnLoadSession", HTML(paste(icon("upload"), getText("btnLoadSession")))),
actionButton("btnDeleteSavedSession", HTML(paste(icon("trash"), getText("btnDeleteSavedSession")))),
bookmarkButton(getText("btnSaveSession"))
)
)
)
)
# tabPanel("Generate report",
# HTML("<center>"),
# downloadButton("btnGenerateReport", getText("btnGenerateReport")),
# HTML("</center>")
# )
# tabPanel("Open",
# HTML("<center>"),
# fileInput('session_file', HTML(paste0("<strong>",getText("SessionFile"),"</strong>")),
# accept=c('.mux')),
# actionButton("btnOpenSession" ,getText("btnOpenSession")),
# HTML("</center>")
# ),
# tabPanel("Save",
# HTML("<center>"),
# actionButton("btnSaveSession" ,getText("btnSaveSession")),
# HTML("</center>")
# )
),
tabPanel("Query",
actionLink("btnQueryHelp", placeHelp() ),
conditionalPanel(condition="input.btnImportNetworks>0",
fluidRow(
column(width = 3,
myBox("boxQuerySetUp", getText("QuerySetUp"), "basic",
selectInput("selQueryType", HTML(getText("selQueryType")), choices = c(getText("Nodes"), getText("Edges"))),
conditionalPanel(condition="input.selQueryType=='Nodes'",
uiOutput("selQueryNodesOutputID"),
uiOutput("selQueryNodesLayersOutputID")
),
conditionalPanel(condition="input.selQueryType=='Edges'",
uiOutput("selQueryEdgesNodesFromOutputID"),
uiOutput("selQueryEdgesNodesToOutputID"),
uiOutput("selQueryEdgesLayersOutputID")
),
checkboxInput("chkQueryShowLabels", getText("chkQueryShowLabels"), F),
HTML("<center>"),
actionButton("btnQuery", getText("Query")),
HTML("</center>")
)
)
),
htmlOutput("queryNodesTable"),
downloadButton('downQueryNodesTable', getText("downQueryNodesTable"))
)
),
tabPanel("Diagnostics",
tabsetPanel(id="tabsetDiagnostics",
tabPanel("Statistics",
tabsetPanel(id="tabsetStatistics",
tabPanel("Nodes",
fluidRow(
column(width = 3,
myBox("boxNodes", getText("Nodes"), "basic",
helpText(getText("txtNumbNonIsolated")),
checkboxInput(inputId = "nodeStatisticsLogy", label = "Log y", F),
HTML("<center>"),
actionButton("btnNodeStatistics", getText("Plot")),
HTML("</center>")
)
),
column(width=6,
showOutput("nodeStatisticsPlot","nvd3")
)
)
),
tabPanel("Edges",
fluidRow(
column(width = 3,
myBox("boxEdges", getText("Edges"), "basic",
helpText(getText("txtNumbEdgesPerLayer")),
checkboxInput(inputId = "edgeStatisticsLogy", label = "Log y", F),
HTML("<center>"),
actionButton("btnEdgeStatistics", getText("Plot")),
HTML("</center>")
)
),
column(width=6,
showOutput("edgeStatisticsPlot","nvd3")
)
)
),
tabPanel("Density",
fluidRow(
column(width = 3,
myBox("boxDensity", getText("Density"), "basic",
helpText(getText("txtDensityPerLayer")),
checkboxInput(inputId = "densityStatisticsLogy", label = "Log y", F),
HTML("<center>"),
actionButton("btnDensityStatistics", getText("Plot")),
HTML("</center>")
)
),
column(width=6,
showOutput("densityStatisticsPlot","nvd3")
)
)
),
tabPanel("Components",
fluidRow(
column(width = 3,
myBox("boxComponents", getText("Components"), "basic",
helpText(getText("txtComponentsPerLayer")),
checkboxInput(inputId = "componentsStatisticsLogy", label = "Log y", F),
HTML("<center>"),
actionButton("btnComponentsStatistics", getText("Plot")),
HTML("</center>")
)
),
column(width=6,
showOutput("componentsStatisticsPlot","nvd3")
)
)
),
tabPanel("Diameter",
fluidRow(
column(width = 3,
myBox("boxDiameter", getText("Diameter"), "basic",
helpText(getText("txtDiameterPerLayer")),
checkboxInput(inputId = "diameterStatisticsLogy", label = "Log y", F),
HTML("<center>"),
actionButton("btnDiameterStatistics", getText("Plot")),
HTML("</center>")
)
),
column(width=6,
showOutput("diameterStatisticsPlot","nvd3")
)
)
),
tabPanel("Mean Path Length",
fluidRow(
column(width = 3,
myBox("boxMeanPathLength", getText("MeanPathLength"), "basic",
helpText(getText("txtMPLPerLayer")),
checkboxInput(inputId = "meanPathLengthStatisticsLogy", label = "Log y", F),
HTML("<center>"),
actionButton("btnMeanPathLengthStatistics", getText("Plot")),
HTML("</center>")
)
),
column(width=6,
showOutput("meanPathLengthStatisticsPlot","nvd3")
)
)
)
)
),
tabPanel("Correlation",
actionLink("btnGlobalDiagnosticsCorrelationHelp", placeHelp() ),
conditionalPanel(condition="input.radMultiplexModel=='MULTIPLEX_IS_INTERDEPENDENT'",
helpText(getText("txtNoParametersInterdependent"))
),
conditionalPanel(condition="input.radMultiplexModel!='MULTIPLEX_IS_INTERDEPENDENT'",
fluidRow(
column(width = 3,
myBox("boxInterLayerCorrelation", getText("txtInterLayerCorrelation"), "basic",
#HTML('<h4>General diagnostics</h4>'),
checkboxInput('chkMULTIPLEX_NODEOVERLAPPING', getText("chkMULTIPLEX_NODEOVERLAPPING"), TRUE),
checkboxInput('chkMULTIPLEX_OVERLAPPING', getText("chkMULTIPLEX_OVERLAPPING"), TRUE),
checkboxInput('chkMULTIPLEX_INTERASSORTATIVITY_PEARSON', getText("chkMULTIPLEX_INTERASSORTATIVITY_PEARSON"), TRUE),
checkboxInput('chkMULTIPLEX_INTERASSORTATIVITY_SPEARMAN', getText("chkMULTIPLEX_INTERASSORTATIVITY_SPEARMAN"), TRUE),
checkboxInput('chkMULTIPLEX_SHORTESTPATH', getText("chkMULTIPLEX_SHORTESTPATH"), TRUE),
selectInput("selAssortativityType", HTML(getText("selAssortativityType")),
choices = c("TT", "II", "OO", "IO", "OI"))
)
),
column(width = 3,
myBox("boxCorrelationGraphicalOptions", getText("txtGraphicalOptions"),"basic",
checkboxInput('chkEXPORT_MATRIX_PLOT', HTML(getText("chkEXPORT_MATRIX_PLOT")), FALSE),
selectInput("selAssortativityTypeColorPalette", HTML(getText("ColorPalette")),
choices = paletteChoiceArray),
actionLink("btnAssortativityPaletteInfo", placeInfo() )
),
HTML("<center>"),
actionButton("btnCalculateCorrelationDiagnostics", getText("btnCalculateCorrelationDiagnostics")),
HTML("</center>")
)
),
tags$hr(),
HTML(paste0('<h4>',getText("txtGlobalDiagnostics"),'</h4>')),
tabsetPanel(
tabPanel("Node Overlapping",
conditionalPanel(condition="input.btnCalculateCorrelationDiagnostics>0 && input.chkMULTIPLEX_NODEOVERLAPPING",
HTML(paste0('<h5>',getText("txtNodeOverlapping"),'</h5>')),
checkboxInput("chkOverlappingNodeHeatmapShowDendrogram", getText("ApplyClustering"), F),
uiOutput("overlappingNodeHeatmapUI"),
tags$br(),
htmlOutput("overlappingNodeSummaryTable"),
downloadButton('downOverlappingNodeSummaryTable', getText("downOverlappingNodeSummaryTable")),
tags$hr()
)
),
tabPanel("Edge Overlapping",
conditionalPanel(condition="input.btnCalculateCorrelationDiagnostics>0 && input.chkMULTIPLEX_OVERLAPPING",
htmlWidgetOutput(
outputId = 'globalDiagnosticsOverlapping',
HTML(paste(
'<h5>Edge Overlapping</h5>',
'Mean Global Overlapping: <span id="sumAvgGlobalOverlapping"></span><br>',
'<br>'
))
),
checkboxInput("chkOverlappingEdgeHeatmapShowDendrogram", getText("ApplyClustering"), F),
uiOutput("overlappingEdgeHeatmapUI"),
tags$br(),
htmlOutput("overlappingSummaryTable"),
downloadButton('downOverlappingSummaryTable', getText("downOverlappingSummaryTable")),
tags$hr()
)
),
tabPanel("Deg. Pearson",
conditionalPanel(condition="input.btnCalculateCorrelationDiagnostics>0 && input.chkMULTIPLEX_INTERASSORTATIVITY_PEARSON",
helpText(HTML(paste0("<h5>",getText("txtInterlayerAssortativityPearson"),"</h5>"))),
checkboxInput("chkInterPearsonHeatmapShowDendrogram", getText("ApplyClustering"), F),
uiOutput("interPearsonHeatmapUI"),
tags$br(),
htmlOutput("interPearsonSummaryTable"),
downloadButton('downInterPearsonSummaryTable', getText("downInterPearsonSummaryTable")),
tags$hr()
)
),
tabPanel("Deg. Spearman",
conditionalPanel(condition="input.btnCalculateCorrelationDiagnostics>0 && input.chkMULTIPLEX_INTERASSORTATIVITY_SPEARMAN",
helpText(HTML(paste0("<h5>",getText("txtInterlayerAssortativitySpearman"),"</h5>"))),
checkboxInput("chkInterSpearmanHeatmapShowDendrogram", getText("ApplyClustering"), F),
uiOutput("interSpearmanHeatmapUI"),
tags$br(),
htmlOutput("interSpearmanSummaryTable"),
downloadButton('downInterSpearmanSummaryTable', getText("downInterSpearmanSummaryTable"))
)
),
tabPanel("SP Distance",
conditionalPanel(condition="input.btnCalculateCorrelationDiagnostics>0 && input.chkMULTIPLEX_SHORTESTPATH",
helpText(HTML(paste0("<h5>",getText("ShortestPathDistanceSimilarity"),"</h5>"))),
checkboxInput("chkDistanceSimilarityHeatmapShowDendrogram", getText("ApplyClustering"), F),
uiOutput("distanceSimilarityHeatmapUI"),
tags$br(),
htmlOutput("distanceSimilaritySummaryTable"),
downloadButton('downDistanceSimilaritySummaryTable', getText("downDistanceSimilaritySummaryTable"))
)
)
)
)
),
tabPanel("Centrality",
actionLink("btnCentralityHelp", placeHelp() ),
fluidRow(
column(width = 3,
myBox("boxCentrality", "Centrality", "basic",
radioButtons('radCentralityAlgorithm', '',
c(Multilayer='CENTRALITY_MULTILAYER',
Single_Layer='CENTRALITY_SINGLELAYER'),
selected='CENTRALITY_MULTILAYER'
)
#checkboxInput("chkNODE_CENTRALITY_MULTIPLEX",getText("chkNODE_CENTRALITY_MULTIPLEX"),TRUE)
),
HTML("<center>"),
actionButton("btnCalculateCentralityDiagnostics", getText("btnCalculateCentralityDiagnostics")),
HTML("</center>")
),
column(width = 3,
myBox("boxDescriptors", "Descriptors", "basic",
#HTML('<h4>Centrality</h4>'),
checkboxInput("chkNODE_CENTRALITY_DEGREE","Degree (in-, out- & tot)",TRUE),
checkboxInput("chkNODE_CENTRALITY_STRENGTH","Strength (in-, out- & tot)",F),
checkboxInput("chkNODE_CENTRALITY_PAGERANK","PageRank",F),
checkboxInput("chkNODE_CENTRALITY_EIGENVECTOR","Eigenvector",F),
checkboxInput("chkNODE_CENTRALITY_HUB","Hub",F),
checkboxInput("chkNODE_CENTRALITY_AUTHORITY","Authority",F),
checkboxInput("chkNODE_CENTRALITY_KATZ","Katz",F),
checkboxInput("chkNODE_CENTRALITY_KCORE","K-core",F),
checkboxInput("chkNODE_CENTRALITY_MULTIPLEXITY","Multiplexity",F)
)
)
),
tags$hr(),
HTML(paste0('<h4>',getText("txtCentralityDiagnostics"),'</h4>')),
conditionalPanel(condition="input.btnCalculateCentralityDiagnostics>0",
checkboxInput(inputId = "centralityTablePageable", label = getText("Pageable"), TRUE),
conditionalPanel("input.centralityTablePageable==true",
uiOutput("numOutputCentralityTableNodesPerPage")
),
tabsetPanel(
tabPanel("Multilayer",
htmlOutput("centralityTable"),
downloadButton('downCentralityTable', getText("downCentralityTable"))
),
tabPanel("Single layer",
htmlOutput("centralityTableSingleLayer"),
downloadButton('downCentralityTableSingleLayer', getText("downCentralityTableSingleLayer"))
)
),
tags$hr(),
fluidRow(
column(width = 3,
myBox("boxDiagnosticsAnalysis", getText("txtDiagnosticsAnalysis"), "basic",
uiOutput("selDiagnosticsCentralityVizOutputID"),
radioButtons('radDiagnosticsCentralityType', getText("Analysis"),
c(TopRanked='DIAGNOSTICS_ANALYSIS_TOPRANKED',
Distribution='DIAGNOSTICS_ANALYSIS_DISTRIBUTION',
Scatter='DIAGNOSTICS_ANALYSIS_SCATTER'),
selected='DIAGNOSTICS_ANALYSIS_TOPRANKED'
),
HTML(paste0("<strong>",getText("txtNetworksToInclude"),"</strong>:")),
checkboxInput(inputId = "chkCentralityAnalysisStructureMultiplex", label = "Multilayer", T),
checkboxInput(inputId = "chkCentralityAnalysisStructureLayer", label = "Layer(s)", F),
conditionalPanel(condition="input.chkCentralityAnalysisStructureLayer",
textInput("txtDiagnosticsCentralityStructureLayer", label=HTML(paste0("<strong>",getText("txtDiagnosticsCentralityStructureLayer"),"</strong>")), "1")
),
checkboxInput(inputId = "chkCentralityAnalysisStructureAggregate", label = "Aggregate", T),
conditionalPanel(condition="input.radDiagnosticsCentralityType == 'DIAGNOSTICS_ANALYSIS_DISTRIBUTION'",
textInput("txtDiagnosticsCentralityDistributionBins", label=HTML(paste0("<strong>",getText("txtDiagnosticsCentralityDistributionBins"),"</strong>")), "30"),
checkboxInput(inputId = "centralityAnalysisDistributionLogx", label = "Log x", F),
checkboxInput(inputId = "centralityAnalysisDistributionLogy", label = "Log y", F)
),
conditionalPanel(condition="input.radDiagnosticsCentralityType == 'DIAGNOSTICS_ANALYSIS_TOPRANKED'",
textInput("txtDiagnosticsCentralityTopRankedBins", label=HTML(paste0("<strong>",getText("txtDiagnosticsCentralityTopRankedBins"),"</strong>")), "20"),
checkboxInput(inputId = "centralityAnalysisTopRankedLog", label = "Log", F)
),
conditionalPanel(condition="input.radDiagnosticsCentralityType == 'DIAGNOSTICS_ANALYSIS_SCATTER'",
uiOutput("selDiagnosticsCentralityVizScatterOutputID"),
textInput('txtDiagnosticsCentralityVizScatterColorTransparency', label=getText("txtDiagnosticsCentralityVizScatterColorTransparency"), "0.7"),
uiOutput("selDiagnosticsCentralityVizScatterSizeOutputID"),
checkboxInput(inputId = "centralityAnalysisScatterLogx", label = "Log x", F),
checkboxInput(inputId = "centralityAnalysisScatterLogy", label = "Log y", F),
checkboxInput(inputId = "centralityAnalysisScatterLogRadius", label = "Log Radius", F)
),
HTML("<center>"),
actionButton("btnCentralityDiagnosticsAnalysis", getText("Plot")),
HTML("</center>")
)
),
column(width=6,
showOutput("centralityAnalysisPlot","nvd3")
)
),
tags$hr()
)
),
tabPanel("Triads",
actionLink("btnTriadsHelp", placeHelp() ),
fluidRow(
column(width = 3,
myBox("boxTriads", "Triadic closure", "basic",
#helpText("Note that directed networks will be transformed to undirected before calculation."),
radioButtons('radTriadicClosureAlgorithm', '',
c(Multilayer='TRIADIC_CLOSURE_MULTILAYER',
Single_Layer='TRIADIC_CLOSURE_SINGLELAYER'),
selected='TRIADIC_CLOSURE_MULTILAYER'
),
conditionalPanel(condition="input.radTriadicClosureAlgorithm=='TRIADIC_CLOSURE_MULTILAYER'"
)
),
HTML("<center>"),
actionButton("btnCalculateTriadsDiagnostics", "Calculate Triadic Closure"),
conditionalPanel(condition="input.btnCalculateTriadsDiagnostics>0",
actionButton("btnRefreshTriadsDiagnostics", HTML(paste(icon("refresh"), getText("RefreshResults"))))
),
HTML("</center>")
)
),
tags$hr(),
HTML('<h4>Triadic Closure</h4>'),
conditionalPanel(condition="input.btnCalculateTriadsDiagnostics>0",
selectInput("selTriadsHeatmapColorPalette", HTML(getText("ColorPalette")), choices = paletteChoiceArray),
actionLink("btnTriadsPaletteInfo", placeInfo() ),
checkboxInput("chkTriadsHeatmapShowDendrogram", getText("ApplyClustering")),
checkboxInput(inputId = "triadsTablePageable", label = getText("Pageable"), TRUE),
checkboxInput(inputId = "triadsHeatmapShowLabels", label = getText("ShowNodeLabels"), TRUE),
conditionalPanel("input.triadsTablePageable==true",
uiOutput("numOutputTriadsTableNodesPerPage")
),
tabsetPanel(
tabPanel("Multilayer",
uiOutput("triadsHeatmapUI"),
tags$br(),
HTML(paste0('<h5>',getText("triadsHeatmapUI"),'</h5>')),
showOutput("triadsDistributionPlot","nvd3"),
HTML('<h5>Tables</h5>'),
htmlOutput("triadsSummaryTable"),
downloadButton('downTriadsSummaryTable', getText("downTriadsSummaryTable")),
tags$hr(),
htmlOutput("triadsTable"),
downloadButton('downTriadsTable', getText("downTriadsTable"))
),
tabPanel("Single layer",
uiOutput("triadsHeatmapSingleLayerUI"),
tags$br(),
HTML(paste0('<h5>',getText("triadsHeatmapSingleLayerUI"),'</h5>')),
showOutput("triadsDistributionPlotSingleLayer","nvd3"),
HTML('<h5>Tables</h5>'),
htmlOutput("triadsSummaryTableSingleLayer"),
downloadButton('downTriadsSummaryTableSingleLayer', getText("downTriadsSummaryTableSingleLayer")),
tags$hr(),
htmlOutput("triadsTableSingleLayer"),
downloadButton('downTriadsTableSingleLayer', getText("downTriadsTableSingleLayer"))
)
)
)
),
tabPanel("Motifs",
actionLink("btnMotifsHelp", placeHelp() ),
fluidRow(
column(width = 3,
myBox("boxMotifs", "Algorithm options","basic",
selectInput("selMotifSize", HTML(paste0("<strong>",getText("selMotifSize"),"</strong>")), choices = as.character(3:4)),
textInput("txtMotifSamples", HTML(paste0("<strong>",getText("txtMotifSamples"),"</strong>")), "100000"),
selectInput("selMotifNullModel", HTML(paste0("<strong>",getText("selMotifNullModel"),"</strong>")),
choices = c("Local const", "Global const", "No regard")),
textInput("txtMotifRandomNetworks", HTML(paste0("<strong>",getText("txtMotifRandomNetworks"),"</strong>")), "1000"),
textInputRow("txtMotifRandomExchangePerEdges", HTML("<strong>Exchanges per edge:</strong>"), "3"),
textInputRow("txtMotifRandomExchangeAttempts", HTML("<strong>Exchange attempts:</strong>"), "3", width="10px")
)
),
column(width = 3,
myBox("boxMotifs2", "Statistical cuts","basic",
checkboxInputRow('chkMotifAbsZscore', HTML("<strong>|Z-score| ></strong>"), FALSE),
textInputRow("txtMotifAbsZscore", "", "3"),
checkboxInputRow('chkMotifPvalue', HTML("<strong>p-value <</strong>"), FALSE),
textInputRow("txtMotifPvalue", "", "0.05"),
checkboxInputRow('chkMotifFrequency', HTML("<strong>Frequency ></strong>"), FALSE),
textInputRow("txtMotifFrequency", "", "0.01")
),
myBox("boxMotifs3", "Graphical options", "basic",
selectInput("selMotifResultsSortBy", HTML(paste0("<strong>",getText("SortBy"),"</strong>")),
choices = c("Frequency", "Z-score", "p-value")),
selectInput("selMotifColorPalette", HTML(getText("ColorPalette")),
choices = append(as.vector(paletteChoiceArray),"random")),
actionLink("btnMotifsPaletteInfo", placeInfo() ),
helpText(getText("selMotifColorPalette"))
),
HTML("<center>"),
actionButton("btnCalculateMotifs", getText("btnCalculateMotifs")),
HTML("</center>")
)
),
tags$hr(),
HTML('<h4>Multilayer motifs</h4>'),
conditionalPanel(condition="input.btnCalculateMotifs>0",
#imageOutput("jsdMatrixSummaryImage",width = "100%", height = "700px"),
#imageOutput("reducibilityDendrogramSummaryImage",width = "100%", height = "700px"),
#HTML('<center><h5>Quality function</h5></center>'),
#showOutput("reducibilityQualityFunction","nvd3"),
#dataTableOutput('motifsTable'),
plotOutput("motifsColorLegend"),
htmlOutput('motifsGvisTable'),
downloadButton('downMotifsTable', getText("downMotifsTable")),
tags$hr()
)
),
tabPanel("Conn. Components",
actionLink("btnComponentsHelp", placeHelp() ),
fluidRow(
column(width = 3,
myBox("boxConnectedComponents", "Connected Components", "basic",
helpText(getText("helpBoxConnectedComponents")),
radioButtons('radConnectedComponentsAlgorithm', '',
c(Multilayer='CONNECTED_COMPONENTS_MULTILAYER',
Single_Layer='CONNECTED_COMPONENTS_SINGLELAYER'),
selected='CONNECTED_COMPONENTS_MULTILAYER'
),
conditionalPanel(condition="input.radConnectedComponentsAlgorithm=='CONNECTED_COMPONENTS_MULTILAYER'"
#selectInput("selConnectedComponentsMuxType", "Method:",
# choices = c("Simple", "Extended")),
# conditionalPanel(condition="input.radMultiplexModel=='MULTIPLEX_IS_EDGECOLORED'",
# helpText("Hint: for Multilayer, the inter-layer strength must be set > 0 from the 'Mux Set Up' tab")
# )
)
#conditionalPanel(condition="input.radConnectedComponentsAlgorithm==''CONNECTED_COMPONENTS_SINGLELAYER",
# selectInput("selConnectedComponentsSingleLayerType", HTML("Components type:"),
# choices = c("Weak", "Strong"))
# ),
),
HTML("<center>"),
actionButton("btnCalculateComponentsDiagnostics", getText("btnCalculateComponentsDiagnostics")),
conditionalPanel(condition="input.btnCalculateComponentsDiagnostics>0",
actionButton("btnRefreshComponentsDiagnostics", HTML(paste(icon("refresh"), getText("RefreshResults"))))
),
HTML("</center>")
)
),
tags$hr(),
HTML('<h4>Connected Components</h4>'),
conditionalPanel(condition="input.btnCalculateComponentsDiagnostics>0",
selectInput("selComponentsHeatmapColorPalette", HTML(getText("ColorPalette")), choices = paletteChoiceArray),
actionLink("btnComponentsPaletteInfo", placeInfo() ),
checkboxInput("chkComponentsHeatmapShowDendrogram", getText("ApplyClustering")),
checkboxInput(inputId = "componentsTablePageable", label = getText("Pageable"), TRUE),
checkboxInput(inputId = "componentsHeatmapShowLabels", label = getText("ShowNodeLabels"), TRUE),
conditionalPanel("input.componentsTablePageable==true",
uiOutput("numOutputComponentsTableNodesPerPage")
),
tabsetPanel(
tabPanel("Multilayer",
uiOutput("componentsHeatmapUI"),
tags$br(),
HTML(paste0('<h5>',getText("componentsHeatmapUI"),'</h5>')),
showOutput("componentsDistributionPlot","nvd3"),
HTML('<h5>Tables</h5>'),
htmlOutput("componentsSummaryTable"),
downloadButton('downComponentsSummaryTable', getText("downComponentsSummaryTable")),
tags$hr(),
htmlOutput("componentsTable"),
downloadButton('downComponentsTable', getText("downComponentsTable"))
),
tabPanel("Single layer",
uiOutput("componentsHeatmapSingleLayerUI"),
tags$br(),
HTML(paste0('<h5>',getText("componentsHeatmapSingleLayerUI"),'</h5>')),
showOutput("componentsDistributionPlotSingleLayer","nvd3"),
HTML('<h5>Tables</h5>'),
htmlOutput("componentsSummaryTableSingleLayer"),
downloadButton('downComponentsSummaryTableSingleLayer', getText("downComponentsSummaryTableSingleLayer")),
tags$hr(),
htmlOutput("componentsTableSingleLayer"),
downloadButton('downComponentsTableSingleLayer', getText("downComponentsTableSingleLayer"))
)
)
)
),
tabPanel("Community",
actionLink("btnCommunityHelp", placeHelp() ),
fluidRow(
column(width = 3,
myBox("boxCommunity", "Algorithm", "basic",
uiOutput("communityChoices"),
uiOutput("communityParameters")
),
HTML("<center>"),
actionButton("btnCalculateCommunityDiagnostics", getText("btnCalculateCommunityDiagnostics")),
conditionalPanel(condition="input.btnCalculateCommunityDiagnostics>0",
actionButton("btnRefreshCommunityDiagnostics", HTML(paste(icon("refresh"), getText("RefreshResults"))))
),
HTML("</center>")
)
),
tags$hr(),
HTML('<h4>Communities</h4>'),
conditionalPanel(condition="input.btnCalculateCommunityDiagnostics>0",
selectInput("selCommunityHeatmapColorPalette", HTML(getText("ColorPalette")), choices = paletteChoiceArray),
actionLink("btnCommunityPaletteInfo", placeInfo() ),
checkboxInput("chkCommunityHeatmapShowDendrogram", getText("ApplyClustering")),
checkboxInput(inputId = "communityTablePageable", label = getText("Pageable"), TRUE),
checkboxInput(inputId = "communityHeatmapShowLabels", label = getText("ShowNodeLabels"), TRUE),
conditionalPanel("input.communityTablePageable==true",
uiOutput("numOutputCommunityTableNodesPerPage")
),
tabsetPanel(
tabPanel("Multilayer",
uiOutput("communityHeatmapUI"),
tags$br(),
tags$br(),
HTML(paste0('<h5>',getText("communityMultiplexAlternativeViz"),'</h5>')),
fluidRow(
column(3,
HTML("<img src='img/chord.png' height='64' width='64' style='{margin-left: auto; margin-right: auto;}'>"),
actionButton("btnPrintCommunityMultiplexChord",
getText("btnPrintCommunityMultiplexChord"))
)
),
tags$br(),
tags$br(),
conditionalPanel("input.chkMultimapBatchExploration",
HTML(paste0('<h5>',getText("communityMultiplexBatchViz"),'</h5>')),
fluidRow(
column(3,
HTML("<img src='img/sankey.png' height='64' width='64' style='{margin-left: auto; margin-right: auto;}'>"),
actionButton("btnPrintCommunityMultiplexSankey",
getText("btnPrintCommunityMultiplexSankey"))
)
),
tags$br(),
fluidRow(
column(4,
showOutput("batchMultiplexCommunityData1","nvd3")
),
column(4,
showOutput("batchMultiplexCommunityData2","nvd3")
)
)
),
tags$br(),
tags$br(),
HTML(paste0('<h5>',getText("communityHeatmapUI"),'</h5>')),
showOutput("communityDistributionPlot","nvd3"),
HTML('<h5>Tables</h5>'),
htmlOutput("communitySummaryTable"),
downloadButton('downCommunitySummaryTable', getText("downCommunitySummaryTable")),
tags$hr(),
htmlOutput("communityTable"),
downloadButton('downCommunityTable', getText("downCommunityTable")),
tags$hr(),
conditionalPanel("input.chkMultimapBatchExploration",
htmlOutput("communityBatchTable"),
downloadButton('downCommunityBatchTable', getText("downCommunityBatchTable"))
)
),
tabPanel("Single layer",
uiOutput("communityHeatmapSingleLayerUI"),
tags$br(),
HTML(paste0('<h5>',getText("communityHeatmapSingleLayerUI"),'</h5>')),
showOutput("communityDistributionPlotSingleLayer","nvd3"),
HTML('<h5>Tables</h5>'),
htmlOutput("communitySummaryTableSingleLayer"),
downloadButton('downCommunitySummaryTableSingleLayer', getText("downCommunitySummaryTableSingleLayer")),
tags$hr(),
htmlOutput("communityTableSingleLayer"),
downloadButton('downCommunityTableSingleLayer', getText("downCommunityTableSingleLayer"))
)
)
)
),
tabPanel("Network of layers",
actionLink("btnGlobalDiagnosticsNetworkLayersHelp", placeHelp() ),
conditionalPanel(condition="input.radMultiplexModel!='MULTIPLEX_IS_EDGECOLORED'",
HTML("<center>"),
tags$br(),
actionButton("btnRenderNetworkOfLayers", getText("btnRenderNetworkOfLayers")),
HTML("</center>"),
HTML("<center>"),
htmlOutput('networkOfLayersPlot'),
HTML("</center>")
)
),
tabPanel("Annular Viz",
actionLink("btnGlobalDiagnosticsAnnularVizHelp", placeHelp() ),
conditionalPanel(condition="input.radMultiplexModel=='MULTIPLEX_IS_INTERDEPENDENT'",
helpText(getText("panelGlobalDiagnosticsAnnularVizHelp"))
),
conditionalPanel(condition="input.radMultiplexModel!='MULTIPLEX_IS_INTERDEPENDENT'",
fluidRow(
column(width = 3,
myBox("boxAnnular", "Metric", "basic",
radioButtons('radAnularVizCorrelationMethod', getText("radAnularVizCorrelationMethod"),
c(Spearman='ANULAR_VIZ_CORRELATION_SPEARMAN',
Pearson='ANULAR_VIZ_CORRELATION_PEARSON',
Jensen_Shannon_Divergence='ANULAR_VIZ_CORRELATION_JSD'),
selected='ANULAR_VIZ_CORRELATION_SPEARMAN'
),
textInput("txtANULAR_VIZ_BINS",label=getText("txtANULAR_VIZ_BINS"),"50"),
checkboxInput("chkANULAR_VIZ_LOG",getText("chkANULAR_VIZ_LOG"),FALSE)
),
HTML("<center>"),
actionButton("btnAnularViz", getText("btnAnularViz")),
HTML("</center>")
),
column(width = 3,
myBox("boxAnnular2", "Graphical Options","basic",
uiOutput("selAnularVizOutputFeatureID"),
uiOutput("selAnularVizOutputLayerID"),
textInputRow("txtANULAR_VIZ_RCORE",label=getText("txtANULAR_VIZ_RCORE"),"0.3"),
textInputRow("txtANULAR_VIZ_RING_DISPLACEMENT", label=getText("txtANULAR_VIZ_RING_DISPLACEMENT"),"0.01"),
checkboxInput("chkANULAR_VIZ_CELL_BORDER", getText("chkANULAR_VIZ_CELL_BORDER"),FALSE),
checkboxInput("chkANULAR_VIZ_SHOW_NODE_LABEL", getText("chkANULAR_VIZ_SHOW_NODE_LABEL"),FALSE),
textInputRow("txtANULAR_VIZ_FONT_SIZE", label=getText("txtANULAR_VIZ_FONT_SIZE"),"1.5"),
selectInput("selAnularColorPalette", HTML(getText("ColorPalette")),
choices = paletteChoiceArray),
actionLink("btnAnnularPaletteInfo", placeInfo() )
)
)
),
tags$hr(),
conditionalPanel(condition="input.btnAnularViz>0 && input.btnCalculateCentralityDiagnostics>0",
helpText(HTML("<h5>Multiplex</h5>")),
helpText(getText("helpAnularVizSummaryMuxImage")),
imageOutput("anularVizSummaryMuxImage",width = "100%", height = "600px"),
tags$hr(),
helpText(HTML(paste0("<h5>",getText("outputAnularVizImages"),"</h5>"))),
helpText(getText("helpOutputAnularVizImages")),
uiOutput("outputAnularVizImages"),
tags$hr()
),
tags$hr()
)
)
)
),
tabPanel("Visualization",
actionLink("btnVisualizationHelp", placeHelp() ),
HTML(paste("<div style=\"float: right; margin: 10px;\">",
actionButton("btnRenderNetworks", getText("btnRenderNetworks")),
"</div>")),
HTML(paste("<div style=\"float: right; margin: 10px;\">",
actionButton("btnApplyLayout", getText("btnApplyLayout")),
"</div>")),
tabsetPanel(
tabPanel("Layout",
fluidRow(
column(width = 9,
myBox("boxVisualization", "Layout Algorithm (Network of Layers)", "basic",
HTML("<img src='img/layout_type.png' width='100%' alt=''/>"),
radioButtons('radNetworkOfLayersLayoutType', '',
c(One_line='NETWORK_LAYERS_LAYOUT_ONELINE',
Multi_line='NETWORK_LAYERS_LAYOUT_MULTILINE',
Force_directed='NETWORK_LAYERS_LAYOUT_FORCEDIRECTED',
Matrix='NETWORK_LAYERS_LAYOUT_MATRIX'
),
selected='NETWORK_LAYERS_LAYOUT_ONELINE',
inline=T
),
conditionalPanel(condition="input.radNetworkOfLayersLayoutType == 'NETWORK_LAYERS_LAYOUT_MULTILINE'",
textInputRow("txtNetworkLayersMultilineRows", label=getText("txtNetworkLayersMultilineRows"), 2),
textInputRow("txtNetworkLayersMultilineCols", label=getText("txtNetworkLayersMultilineCols"), 2),
helpText(getText("helptxtNetworkLayersMultilineCols"))
),
conditionalPanel(condition="input.radNetworkOfLayersLayoutType == 'NETWORK_LAYERS_LAYOUT_MATRIX'",
textInputRow("txtNetworkLayersMatrixRows", label=getText("txtNetworkLayersMatrixRows"), 2),
textInputRow("txtNetworkLayersMatrixCols", label=getText("txtNetworkLayersMatrixCols"), 2),
helpText(getText("helptxtNetworkLayersMatrixCols"))
),
conditionalPanel(condition="input.radNetworkOfLayersLayoutType == 'NETWORK_LAYERS_LAYOUT_FORCEDIRECTED'",
HTML(paste("<font color=\"red\">",icon("exclamation-circle"), getText("boxVisualization1"), "</font>")),
helpText(getText("boxVisualization1b"))
)
)
)
),
fluidRow(
column(width = 4,
myBox("boxVisualization2", "Layout Algorithm (Layer)", "basic",
#HTML('<h4>Algorithm to be used to visualize nodes in the multiplex network</h4>'),
radioButtons('radLayoutAlgorithm', '',
c(Fruchterman_Reingold='LAYOUT_FRUCHTERMAN_REINGOLD',
LGL='LAYOUT_LGL',
DRL='LAYOUT_DRL',
Spring='LAYOUT_SPRING',
Kamada_Kawai='LAYOUT_KAMADA_KAWAI',
Reingold_Tilford='LAYOUT_REINGOLD_TILFORD',
Combined='LAYOUT_COMBINED'),
selected='LAYOUT_COMBINED'
),
conditionalPanel(condition="input.radNetworkOfLayersLayoutType == 'NETWORK_LAYERS_LAYOUT_ONELINE'",
radioButtons('radLayoutDimension', '',
c(Two_Dimensional='LAYOUT_DIMENSION_2D',
Three_Dimensional='LAYOUT_DIMENSION_3D'),
selected='LAYOUT_DIMENSION_2D', inline=TRUE
),
checkboxInput("chkPLOT_AS_EDGE_COLORED", HTML(getText("chkPLOT_AS_EDGE_COLORED")),FALSE),
checkboxInput("chkPLOT_WITH_RGL",HTML("openGL"),TRUE),
helpText(getText("helpchkPLOT_WITH_RGL"))
),
actionLink("btnWarn1", placeWarn())
)
),
column(width = 4,
myBox("boxVisualization3", "Graphical Options","basic",
#HTML('<h4>Type of visualization</h4>'),
radioButtons('radLayoutType', getText("radLayoutType"),
c(Multiplex='LAYOUT_MULTIPLEX',
By_LayerID='LAYOUT_BY_LAYER_ID',
Independent='LAYOUT_INDEPENDENT'),
selected='LAYOUT_MULTIPLEX', inline=TRUE
),
conditionalPanel(condition="input.radLayoutType=='LAYOUT_MULTIPLEX'",
radioButtons('radLayoutTypeMultiplex', getText("radLayoutTypeMultiplex"),
c(Aggregate='LAYOUT_MULTIPLEX_AGGREGATE',
Union='LAYOUT_MULTIPLEX_UNION',
Intersection='LAYOUT_MULTIPLEX_INTERSECTION'),
selected='LAYOUT_MULTIPLEX_AGGREGATE', inline=FALSE
)
),
conditionalPanel(condition="input.radLayoutType=='LAYOUT_BY_LAYER_ID'",
#this is a dynamic object changing because of input
uiOutput("selOutputLayerID")
),
textInputRow("txtLAYOUT_MAXITER",
label=HTML(getText("txtLAYOUT_MAXITER")),
value="1000", width="20px"
),
tags$br(),
actionLink("btnWarn2", placeWarn())
)
)
)
),
tabPanel("Graphics",
fluidRow(
column(width = 4,
myBox("boxVisualization4", "Plot Options","basic",
#HTML('<h4>Options for the rendering of the multiplex</h4>'),
textInputRow('txtPLOT_TITLE', label=getText("txtPLOT_TITLE"), "", width="70px"),
textInputRow('txtPLOT_SUBTITLE', label=getText("txtPLOT_SUBTITLE"), "", width="50px"),
colourpicker::colourInput("colBACKGROUND_COLOR", getText("colBACKGROUND_COLOR"), "white")
),
conditionalPanel(condition="input.chkPLOT_WITH_RGL",
myBox("boxVisualization5", "Light Options (RGL)","basic",
checkboxInput("chkPLOT_LIGHT", getText("chkPLOT_LIGHT"),FALSE),
textInputRow('txtPLOT_LIGHT_PHI', label=getText("txtPLOT_LIGHT_PHI"), "20", width="30px"),
textInputRow('txtPLOT_LIGHT_THETA', label=getText("txtPLOT_LIGHT_THETA"), "30", width="30px"),
HTML("<center>"),
actionButton("btnResetLights", getText("btnResetLights")),
HTML("</center>"),
helpText(getText("helpbtnResetLights"))
)
),
conditionalPanel(condition="!input.chkPLOT_WITH_RGL",
myBox("boxVisualization6", "Window relative margins","basic",
helpText(getText("helpboxVisualization6")),
textInputRow('txtMARGIN_LEFT', label=getText("txtMARGIN_LEFT"), "1"),
textInputRow('txtMARGIN_RIGHT', label=getText("txtMARGIN_RIGHT"), "1"),
textInputRow('txtMARGIN_TOP', label=getText("txtMARGIN_TOP"), "1"),
textInputRow('txtMARGIN_BOTTOM', label=getText("txtMARGIN_BOTTOM"), "1"),
actionLink("btnWarn3", placeWarn())
)
)
),
column(width = 4,
myBox("boxVisualization7", "3D Options", "basic",
conditionalPanel(condition="input.chkPLOT_WITH_RGL",
checkboxInput('chkPLOT_AXES3D', label=getText("chkPLOT_AXES3D"), F),
checkboxInput("chkPLOT_REMEMBER_ORIENTATION", getText("chkPLOT_REMEMBER_ORIENTATION"),TRUE),
textInputRow('txtPLOT_FOV', label=HTML(getText("txtPLOT_FOV")), "20", width=15)
),
conditionalPanel(condition="!input.chkPLOT_WITH_RGL",
HTML(getText("boxVisualization7a")),
tags$br(),
textInputRow('txtPLOT_ROTX', label=HTML('X-axis:'), "0", width="30"),
textInputRow('txtPLOT_ROTY', label=HTML('Y-axis:'), "60", width="30"),
textInputRow('txtPLOT_ROTZ', label=HTML('Z-axis:'), "0", width="30"),
helpText(getText("boxVisualization7b")),
actionLink("btnWarn4", placeWarn()),
# radioButtons('radPlotNonRGLQuickLayout', 'Quick layout:',
# c(Horizontal='PLOT_NONRGL_QUICK_LAYOUT_HORIZONTAL',
# Vertical='PLOT_NONRGL_QUICK_LAYOUT_VERTICAL',
# Custom='PLOT_NONRGL_QUICK_LAYOUT_NONE'),
# selected='PLOT_NONRGL_QUICK_LAYOUT_HORIZONTAL', inline=TRUE
# ),
helpText("Horizontal layout: x=0°, y=60°, z=0°, shift>0."),
helpText("Vertical layout: x=60°, y=45°, z=-45°, shift=0")
),
tags$hr(),
HTML(getText("boxVisualization7c")),
textInputRow('txtLAYER_SHIFT_X', label=HTML('X-axis:'), "0.8", width="30"),
textInputRow('txtLAYER_SHIFT_Y', label=HTML('Y-axis:'), "0", width="30"),
textInputRow('txtLAYER_SCALE', label=HTML(getText("txtLAYER_SCALE")), "4"),
textInputRow('txtLAYER_SPACE', label=HTML(getText("txtLAYER_SPACE")), "3", width="30"),
tags$br(),
actionLink("btnWarn5", placeWarn())
)
)
)
),
tabPanel("Multiplex",
conditionalPanel(condition="input.radMultiplexModel!='MULTIPLEX_IS_EDGECOLORED'",
fluidRow(
column(width = 4,
myBox("boxVisualization8", "Inter-link Options","basic",
checkboxInput("chkINTERLINK_SHOW",HTML(getText("chkINTERLINK_SHOW")),TRUE),
HTML(paste("<font color=\"red\">",icon("exclamation-circle"), getText("boxVisualization8"), "</font>")),
colourpicker::colourInput("colINTERLINK_COLOR", getText("colINTERLINK_COLOR"), "#D8D8D8"),
selectInput('selINTERLINK_TYPE', getText("selINTERLINK_TYPE"), choices= c("dotted", "solid", "dashed", "dotdash", "longdash", "twodash")),
textInputRow('txtINTERLINK_WIDTH', label=getText("txtINTERLINK_WIDTH"), "0.4"),
textInputRow('txtINTERLINK_TRANSP', label=getText("txtINTERLINK_TRANSP"), "0.2"),
helpText(getText("boxVisualization8b"))
)
)
)
),
conditionalPanel(condition="input.radMultiplexModel=='MULTIPLEX_IS_EDGECOLORED'",
helpText(getText("boxVisualization8c"))
)
),
tabPanel("Layers",
fluidRow(
column(width = 4,
conditionalPanel(condition="input.chkPLOT_WITH_RGL",
myBox("boxVisualization9", "Layer Options", "basic",
checkboxInput("chkLAYER_SHOW","Show layers",TRUE),
textInputRow('txtLAYER_LABEL_PREFIX', label=getText("txtLAYER_LABEL_PREFIX"), "L"),
helpText(getText("helptxtLAYER_LABEL_PREFIX")),
colourpicker::colourInput("colLAYER_COLOR", getText("colLAYER_COLOR"), "grey"),
helpText(getText("helpcolLAYER_COLOR")),
textInputRow('txtLAYER_TRANSP', label=getText("txtLAYER_TRANSP"), "0.08"),
helpText(getText("txtLAYER_TRANSPb")),
helpText(getText("txtLAYER_TRANSPc")),
HTML(paste0("<strong>",getText("boxVisualization9b"),"</strong>")),
checkboxInput("chkLAYER_ID_SHOW_TOPLEFT","top-left",FALSE),
checkboxInput("chkLAYER_ID_SHOW_TOPRIGHT","top-right",FALSE),
checkboxInput("chkLAYER_ID_SHOW_BOTTOMLEFT","bottom-left",TRUE),
checkboxInput("chkLAYER_ID_SHOW_BOTTOMRIGHT","bottom-right",FALSE),
textInputRow('txtLAYER_ID_FONTSIZE', label=getText("txtLAYER_ID_FONTSIZE"), "1.5")
)
)
),
column(width = 4,
conditionalPanel(condition="input.chkPLOT_WITH_RGL",
myBox("boxVisualization10", "Aggregate Options", "basic",
checkboxInput("chkAGGREGATE_SHOW",HTML(getText("chkAGGREGATE_SHOW")),FALSE),
actionLink("btnWarn6", placeWarn()),
tags$hr(),
textInputRow('txtLAYER_AGGREGATE_LABEL_PREFIX', label=getText("txtLAYER_AGGREGATE_LABEL_PREFIX"), "Aggregate"),
colourpicker::colourInput("colLAYER_AGGREGATE_COLOR", getText("colLAYER_AGGREGATE_COLOR"), "blue"),
textInputRow('txtLAYER_AGGREGATE_TRANSP', label=getText("txtLAYER_AGGREGATE_TRANSP"), "0.08"),
helpText(getText("txtLAYER_AGGREGATE_TRANSPb"))
)
),
myBox("boxVisualization11", "Inactive Layers","basic",
textInput("txtLAYERS_ACTIVE", label=getText("txtLAYERS_ACTIVE")),
helpText(getText("txtLAYERS_ACTIVEb"))
)
),
# ),
# fluidRow(
column(width = 4,
conditionalPanel(condition="input.chkPLOT_WITH_RGL",
myBox("boxVisualization12", "Geographical Options", "basic",
helpText(getText("boxVisualization12b")),
checkboxInput("chkGEOGRAPHIC_BOUNDARIES_SHOW", HTML(paste0("<strong>Layer</strong> ",getText("chkGEOGRAPHIC_BOUNDARIES_SHOW"))),TRUE),
checkboxInput("chkGEOGRAPHIC_BOUNDARIES_AGGREGATE_SHOW", HTML(paste0("<strong>Aggregate</strong> ",getText("chkGEOGRAPHIC_BOUNDARIES_AGGREGATE_SHOW"))),TRUE),
selectInput("selOSMType", HTML(getText("selOSMType")),
choices = c("bing","mapbox","mapquest-aerial","osm","osm-bbike-german","osm-transport","stamen-toner","stamen-watercolor")),
actionLink("btnGeographicMap", placeInfo() ),
tags$hr(),
helpText(paste0(HTML("<h5>",getText("boxVisualization12d"),"</h5>"))),
textInputRow('txtGEOGRAPHIC_LAT_MIN', label='Min lat:', ""),
textInputRow('txtGEOGRAPHIC_LAT_MAX', label='Max lat:', ""),
textInputRow('txtGEOGRAPHIC_LONG_MIN', label='Min lon:', ""),
textInputRow('txtGEOGRAPHIC_LONG_MAX', label='Max lon:', ""),
helpText(getText("boxVisualization12c")),
actionLink("btnWarn7", placeWarn())
)
)
)
)
),
tabPanel("Nodes",
fluidRow(
column(width = 3,
myBox("boxVisualization13", "Node Size", "basic",
conditionalPanel(condition="input.btnCalculateCentralityDiagnostics==0",
radioButtons('radNodeSizeType', getText("radNodeSizeType"),
c(Uniform='NODE_SIZE_PROPORTIONAL_TO_UNIFORM',
External='NODE_SIZE_PROPORTIONAL_TO_EXTERNAL'
),
selected='NODE_SIZE_PROPORTIONAL_TO_UNIFORM'
)
),
conditionalPanel(condition="input.btnCalculateCentralityDiagnostics>0",
uiOutput("selVizNodeSizeOutputID")
),
radioButtons('radNodeSizeType2', getText("radNodeSizeType2"),
c(Constant='NODE_SIZE_PROPORTIONAL_TYPE_NORMAL',
Log='NODE_SIZE_PROPORTIONAL_TYPE_LOG',
LogLog='NODE_SIZE_PROPORTIONAL_TYPE_LOGLOG'),
selected='NODE_SIZE_PROPORTIONAL_TYPE_LOGLOG', inline=F
),
textInputRow('txtNODE_DEFAULT_SIZE', label=getText("txtNODE_DEFAULT_SIZE"), "10")
)
),
column(width = 3,
myBox("boxVisualization14", "Node Color", "basic",
radioButtons('radNodeColor', getText("radNodeColor"),
c(Random='NODE_COLOR_RANDOM',
Community='NODE_COLOR_COMMUNITY',
Component='NODE_COLOR_COMPONENT',
Centrality='NODE_COLOR_CENTRALITY',
TopRank='NODE_COLOR_TOPRANK',
Uniform='NODE_COLOR_UNIFORM',
Query='NODE_COLOR_QUERY',
External='NODE_COLOR_EXTERNAL'),
selected='NODE_COLOR_UNIFORM'
),
hr(),
conditionalPanel(condition="input.radNodeColor=='NODE_COLOR_EXTERNAL'",
colourpicker::colourInput("colNodeColorFileDefaultNodesColor", getText("colNodeColorFileDefaultNodesColor"), "#959595")
),
conditionalPanel(condition="input.radNodeColor=='NODE_COLOR_CENTRALITY' && input.btnCalculateCentralityDiagnostics>0",
uiOutput("selVizNodeColorOutputID"),
radioButtons('radNodeColorType2', getText("radNodeColorType2"),
c(Constant='NODE_COLOR_PROPORTIONAL_TYPE_NORMAL',
Log='NODE_COLOR_PROPORTIONAL_TYPE_LOG',
LogLog='NODE_COLOR_PROPORTIONAL_TYPE_LOGLOG'),
selected='NODE_COLOR_PROPORTIONAL_TYPE_NORMAL'
),
selectInput("selCentralityColorPalette", HTML(getText("ColorPalette")),
choices = as.vector(paletteChoiceArray)),
actionLink("btnCentralityColorPaletteInfo", placeInfo() ),
textInputRow("txtNODE_COLOR_CENTRALITY_BINS", label="Bins:", "30")
),
conditionalPanel(condition="input.radNodeColor=='NODE_COLOR_CENTRALITY' && input.btnCalculateCentralityDiagnostics==0",
helpText(getText("helpText1"))
),
conditionalPanel(condition="input.radNodeColor=='NODE_COLOR_RANDOM'",
selectInput("selMultiplexColorPalette", HTML(getText("ColorPalette")),
choices = append(as.vector(paletteChoiceArray),"random")),
actionLink("btnMultiplexColorPaletteInfo", placeInfo() )
),
conditionalPanel(condition="input.radNodeColor=='NODE_COLOR_UNIFORM'",
colourpicker::colourInput("colNODE_COLOR_UNIFORM_COLOR", getText("colNODE_COLOR_UNIFORM_COLOR"), "#F2F2F2")
),
conditionalPanel(condition="input.radNodeColor=='NODE_COLOR_TOPRANK' && input.btnCalculateCentralityDiagnostics>0",
uiOutput("selVizNodeColorTopOutputID"),
textInput('txtNODE_COLOR_TOP', label=getText("txtNODE_COLOR_TOP"), "5"),
colourpicker::colourInput("colNODE_COLOR_TOP_COLOR_TOP", getText("colNODE_COLOR_TOP_COLOR_TOP"), "#FF0000"),
colourpicker::colourInput('colNODE_COLOR_TOP_COLOR_OTHERS', getText("colNODE_COLOR_TOP_COLOR_OTHERS"), "#F2F2F2"),
checkboxInput("chkNODE_LABELS_SHOW_ONLY_TOP", getText("chkNODE_LABELS_SHOW_ONLY_TOP"),TRUE),
colourpicker::colourInput('colNODE_COLOR_TOP_LABELS_FONT_COLOR', getText("colNODE_COLOR_TOP_LABELS_FONT_COLOR"), "#000000")
),
conditionalPanel(condition="input.radNodeColor=='NODE_COLOR_TOPRANK' && input.btnCalculateCentralityDiagnostics==0",
helpText(getText("helpText2"))
),
conditionalPanel(condition="input.radNodeColor=='NODE_COLOR_COMMUNITY' && input.btnCalculateCommunityDiagnostics>0",
#textInput("txtCOMMUNITY_MIN_SIZE",label="Color-code with the same RGB all nodes in communities smaller than (useful for evidencing larger communities, not valid for the multiplex):","1"),
uiOutput("selVizNodeColorCommunityTypeOutputID"),
selectInput("selCommunityColorPalette", HTML(getText("ColorPalette")),
choices = append(as.vector(paletteChoiceArray),"random")),
actionLink("btnCommunityColorPaletteInfo", placeInfo() )
),
conditionalPanel(condition="input.radNodeColor=='NODE_COLOR_QUERY' && input.btnQuery>0",
colourpicker::colourInput('colQUERY_NODES_NODE_COLOR', getText("colQUERY_NODES_NODE_COLOR"), "#FF6246"),
colourpicker::colourInput('colQUERY_NODES_NODE_NEIGH_COLOR', getText("colQUERY_NODES_NODE_NEIGH_COLOR"), "#669DC1"),
colourpicker::colourInput('colQUERY_NODES_NODE_OTHER_COLOR', getText("colQUERY_NODES_NODE_OTHER_COLOR"), "#959595"),
checkboxInput("chkNODE_LABELS_SHOW_ONLY_QUERY", getText("chkNODE_LABELS_SHOW_ONLY_QUERY"),TRUE),
colourpicker::colourInput('colNODE_COLOR_QUERY_LABELS_FONT_COLOR', getText("colNODE_COLOR_QUERY_LABELS_FONT_COLOR"), "#000000")
),
conditionalPanel(condition="input.radNodeColor=='NODE_COLOR_COMMUNITY' && input.btnCalculateCommunityDiagnostics==0",
helpText(getText("helpText3"))
),
conditionalPanel(condition="input.radNodeColor=='NODE_COLOR_COMPONENT' && input.btnCalculateComponentsDiagnostics>0",
uiOutput("selVizNodeColorComponentTypeOutputID"),
selectInput("selComponentColorPalette", HTML(getText("ColorPalette")),
choices = append(as.vector(paletteChoiceArray),"random")),
actionLink("btnComponentColorPaletteInfo", placeInfo() )
),
conditionalPanel(condition="input.radNodeColor=='NODE_COLOR_COMPONENT' && input.btnCalculateComponentsDiagnostics==0",
helpText(getText("helpText4"))
),
conditionalPanel(condition="input.radNodeColor=='NODE_COLOR_QUERY' && input.btnQuery==0",
helpText(getText("helpText5"))
)
)
),
# ),
# fluidRow(
column(width = 4,
myBox("boxVisualization15", "Other Options", "basic",
checkboxInput("chkNODE_ISOLATED_HIDE", getText("chkNODE_ISOLATED_HIDE"),TRUE),
conditionalPanel(condition="input.chkNODE_ISOLATED_HIDE && input.radMultiplexModel!='MULTIPLEX_IS_EDGECOLORED'",
checkboxInput("chkNODE_ISOLATED_HIDE_INTERLINKS", getText("chkNODE_ISOLATED_HIDE_INTERLINKS"),TRUE)
),
textInputRow('txtNODE_TRANSP', label=getText("txtNODE_TRANSP"), "0.8"),
helpText(getText("helpText6")),
textInput("txtNODE_FRAME_COLOR", getText("txtNODE_FRAME_COLOR"),""),
helpText(getText("helpText7")),
checkboxInput("chkNODE_LABELS_SHOW", getText("chkNODE_LABELS_SHOW"),FALSE),
helpText(getText("helpText8")),
conditionalPanel("input.chkNODE_LABELS_SHOW",
checkboxInput("chkNODE_LABELS_SHOW_WRAP", getText("chkNODE_LABELS_SHOW_WRAP"),FALSE),
conditionalPanel(condition="input.chkNODE_LABELS_SHOW_WRAP",
textInputRow('txtNODE_LABELS_WRAP', label=getText("txtNODE_LABELS_WRAP"), "10"),
helpText(getText("helpText9")),
textInputRow('txtNODE_LABELS_WRAP_OFFSET', label=getText("txtNODE_LABELS_WRAP_OFFSET"), "0"),
helpText(getText("helpText10"))
),
textInputRow('txtNODE_LABELS_DISTANCE', label=getText("txtNODE_LABELS_DISTANCE"), "1."),
textInputRow('txtNODE_LABELS_FONT_SIZE', label=getText("txtNODE_LABELS_FONT_SIZE"), "0.5"),
colourpicker::colourInput('colNODE_LABELS_FONT_COLOR', getText("colNODE_LABELS_FONT_COLOR"), "#2F2F2F")
)
)
),
column(width = 3,
conditionalPanel(condition="input.radNodeColor=='NODE_COLOR_EXTERNAL' || input.selVizNodeSizeID=='External' || input.radNodeSizeType=='NODE_SIZE_PROPORTIONAL_TO_EXTERNAL'",
myBox("boxVisualization16", "External color/size", "basic",
helpText(getText("helpText11")),
#checkboxInput('chkNodeColorFileHeader', 'Header', TRUE),
textInput("txtNodeColorFileSep", label=getText("txtNodeColorFileSep"), " "),
fileInput('nodecolor_file', HTML(paste0("<strong>* ",getText("nodecolor_file"),"</strong>")),
accept=c('text/csv', 'text/comma-separated-values,text/plain', '.csv')),
HTML("<center>"),
actionButton("btnImportNodeColor", getText("Import")),
HTML("</center>")
)
)
)
)
),
tabPanel("Edges",
fluidRow(
column(width = 3,
myBox("boxVisualization17", "Edge Size","basic",
radioButtons('radEdgeSizeType', getText("radEdgeSizeType"),
c(Uniform='EDGE_SIZE_PROPORTIONAL_TO_UNIFORM',
External='EDGE_SIZE_PROPORTIONAL_TO_EXTERNAL',
Weight='EDGE_SIZE_PROPORTIONAL_TO_WEIGHT'),
selected='EDGE_SIZE_PROPORTIONAL_TO_WEIGHT', inline=F
),
radioButtons('radEdgeSizeType2', getText("radEdgeSizeType2"),
c(Constant='EDGE_SIZE_PROPORTIONAL_TYPE_NORMAL',
Log='EDGE_SIZE_PROPORTIONAL_TYPE_LOG',
LogLog='EDGE_SIZE_PROPORTIONAL_TYPE_LOGLOG'),
selected='EDGE_SIZE_PROPORTIONAL_TYPE_LOGLOG', inline=F
),
textInputRow('txtEDGE_DEFAULT_SIZE', label=getText("txtEDGE_DEFAULT_SIZE"), "2")
)
),
column(width = 3,
myBox("boxVisualization18", "Edge Color", "basic",
radioButtons('radEdgeColor', getText("radEdgeColor"),
c(Random='EDGE_COLOR_RANDOM',
Uniform='EDGE_COLOR_UNIFORM',
External='EDGE_COLOR_EXTERNAL'),
selected='EDGE_COLOR_UNIFORM'
),
hr(),
conditionalPanel(condition="input.radEdgeColor=='EDGE_COLOR_EXTERNAL'",
colourpicker::colourInput("colEdgeColorFileDefaultEdgesColor", getText("colEdgeColorFileDefaultEdgesColor"), "#F2F2F2")
),
conditionalPanel(condition="input.radEdgeColor=='EDGE_COLOR_RANDOM'",
selectInput("selMultiplexEdgeColorPalette", HTML(getText("ColorPalette")),
choices = append(as.vector(paletteChoiceArray),"random")),
actionLink("btnMultiplexEdgeColorPaletteInfo", placeInfo() )
),
conditionalPanel(condition="input.radEdgeColor=='EDGE_COLOR_UNIFORM'",
colourpicker::colourInput('colEDGE_COLOR', getText("colEDGE_COLOR"), "#F2F2F2")
#helpText(getText("helpText12"))
)
)
),
# ),
# fluidRow(
column(width = 4,
myBox("boxVisualization19", "Other Options", "basic",
textInputRow('txtEDGE_BENDING', label=getText("txtEDGE_BENDING"), "0"),
helpText("0 means straight; max 1"),
textInputRow('txtEDGE_TRANSP', label=getText("txtEDGE_TRANSP"), "0.2"),
helpText(getText("helpText13")),
textInputRow('txtLAYER_ARROW_SIZE', label=getText("txtLAYER_ARROW_SIZE"), "0.2"),
textInputRow('txtLAYER_ARROW_WIDTH', label=getText("txtLAYER_ARROW_WIDTH"), "0.2")
)
),
column(width = 3,
conditionalPanel(condition="input.radEdgeColor=='EDGE_COLOR_EXTERNAL' || input.radEdgeSizeType=='EDGE_SIZE_PROPORTIONAL_TO_EXTERNAL'",
myBox("boxVisualization21", "External color/size", "basic",
helpText(getText("helpText20")),
#checkboxInput('chkEdgeColorFileHeader', 'Header', TRUE),
textInput("txtEdgeColorFileSep", label=getText("txtEdgeColorFileSep"), " "),
fileInput('edgecolor_file', HTML(paste0("<strong>* ",getText("edgecolor_file"),"</strong>")),
accept=c('text/csv', 'text/comma-separated-values,text/plain', '.csv')),
HTML("<center>"),
actionButton("btnImportEdgeColor", getText("Import")),
HTML("</center>")
)
)
)
)
),
tabPanel("Export",
br(),
fluidRow(
column(width = 4,
myBox("boxVisualization20", "Options", "basic",
conditionalPanel(condition="input.chkPLOT_WITH_RGL",
radioButtons('radRGLExport', getText("radRGLExport"),
c(PNG='RGL_EXPORT_PNG',
PDF='RGL_EXPORT_PDF',
SVG='RGL_EXPORT_SVG',
webGL='RGL_EXPORT_WEBGL'),
selected='RGL_EXPORT_PNG', inline=TRUE
),
HTML("<center>"),
conditionalPanel(condition="input.radRGLExport=='RGL_EXPORT_PNG'",
actionButton("btnExportRendering","Export PNG")
),
conditionalPanel(condition="input.radRGLExport=='RGL_EXPORT_PDF'",
actionButton("btnExportRenderingPDF","Export PDF")
),
conditionalPanel(condition="input.radRGLExport=='RGL_EXPORT_SVG'",
actionButton("btnExportRenderingSVG","Export SVG")
),
conditionalPanel(condition="input.radRGLExport=='RGL_EXPORT_WEBGL'",
actionButton("btnExportRenderingWeb","Export webGL")
),
HTML("</center>")
),
conditionalPanel(condition="!input.chkPLOT_WITH_RGL",
radioButtons('radNORGLExport', getText("radNORGLExport"),
c(PNG='NORGL_EXPORT_PNG',
PDF='NORGL_EXPORT_PDF'),
selected='NORGL_EXPORT_PNG', inline=TRUE
),
conditionalPanel(condition="input.radNORGLExport=='NORGL_EXPORT_PNG'",
textInputRow("txtExportRenderingClassicPNGWidth", "Width (px):", "1024"),
textInputRow("txtExportRenderingClassicPNGHeight", "Height (px):", "768"),
textInputRow("txtExportRenderingClassicPNGResolution", "Resolution (dpi):", "300"),
tags$br(),
HTML("<center>"),
actionButton("btnExportRenderingClassicPNG","Export PNG"),
HTML("</center>")
),
conditionalPanel(condition="input.radNORGLExport=='NORGL_EXPORT_PDF'",
textInputRow("txtExportRenderingClassicPDFWidth", "Width (px):", "1024"),
textInputRow("txtExportRenderingClassicPDFHeight", "Height (px):", "768"),
tags$br(),
HTML("<center>"),
actionButton("btnExportRenderingClassicPDF","Export PDF"),
HTML("</center>")
)
)
)
)
)
)
),
value=0
),
tabPanel("Reducibility",
actionLink("btnReducibilityHelp", placeHelp() ),
conditionalPanel(condition="input.radMultiplexModel=='MULTIPLEX_IS_INTERDEPENDENT'",
helpText(getText("helpText14"))
),
conditionalPanel(condition="input.radMultiplexModel!='MULTIPLEX_IS_INTERDEPENDENT'",
fluidRow(
column(width = 3,
myBox("boxReducibility", "Algorithms","basic",
#HTML('<h4>Algorithms to be used to calculate the correlation between layers and clustering</h4>'),
radioButtons('radReducibilityCorrelationMethod', getText("radReducibilityCorrelationMethod"),
c(Jensen_Shannon_Divergence='REDUCIBILITY_METHOD_CORRELATION_JENSEN_SHANNON'),
selected='REDUCIBILITY_METHOD_CORRELATION_JENSEN_SHANNON'),
tags$hr(),
selectInput("selReducibilityClusterMethod", getText("selReducibilityClusterMethod"),
choices = c("ward.D2","single","complete","average","mcquitty","median","centroid"))
)
),
column(width = 3,
myBox("boxReducibility2", "Graphical Options", "basic",
selectInput("selReducibilityColorPalette", HTML(getText("ColorPalette")),
choices = paletteChoiceArray),
actionLink("btnReducibilityPaletteInfo", placeInfo() ),
textInputRow("txtREDUCIBILITY_HEATMAP_FONT_SIZE",label=getText("txtREDUCIBILITY_HEATMAP_FONT_SIZE"),"1.5")
),
HTML("<center>"),
actionButton("btnCalculateReducibility", getText("btnCalculateReducibility")),
HTML("</center>")
#actionButton("btnExportReducibilityRendering","Export PNG"),
)
),
tags$hr(),
HTML('<h4>Structural reducibility</h4>'),
conditionalPanel(condition="input.btnCalculateReducibility>0",
uiOutput("reducibilityHeatmapUI"),
#imageOutput("jsdMatrixSummaryImage",width = "100%", height = "700px"),
#imageOutput("reducibilityDendrogramSummaryImage",width = "100%", height = "700px"),
tags$br(),
HTML('<h5>Reduction Quality</h5>'),
showOutput("reducibilityQualityFunction","nvd3"),
tags$hr()
)
)
),
tabPanel("Dynamics",
actionLink("btnDynamicsHelp", placeHelp() ),
fluidRow(
column(width = 3,
myBox("boxDynamics", "Timeline file","basic",
#helpText(HTML("<h4>Open Timeline File</h4>")),
helpText(HTML(paste0("<strong><font color='#262626'>* ", getText("helpText16"),"</font></strong>"))),
#checkboxInput('chkTimelineFileHeader', 'Header', TRUE),
textInput("txtTimelineFileSep", label=getText("txtTimelineFileSep"), " "),
fileInput('timeline_file', HTML(paste0("<strong>* ", getText("timeline_file"),"</strong>")),
accept=c('text/csv', 'text/comma-separated-values,text/plain', '.csv')
),
HTML("<center>"),
actionButton("btnImportTimeline", getText("btnImportTimeline")),
HTML("</center>")
),
HTML("<center>"),
checkboxInput("chkTIMELINE_RENDER_TO_FILE", getText("chkTIMELINE_RENDER_TO_FILE"),FALSE),
actionButton("btnRenderDynamicsSnapshots", getText("btnRenderDynamicsSnapshots")),
hr(),
actionButton("btnFFMPEGDynamicsSnapshots", getText("btnFFMPEGDynamicsSnapshots")),
HTML("</center>")
),
column(width = 4,
myBox("boxDynamics2", "Graphical Options", "basic",
textInput("txtTimelineDefaultNodesSize", label=getText("txtTimelineDefaultNodesSize"), "10"),
helpText(getText("helpText17")),
colourpicker::colourInput("colTimelineDefaultNodesColor", getText("colTimelineDefaultNodesColor"), "#959595"),
textInput("txtTimelineDefaultEdgesSize", label=getText("txtTimelineDefaultEdgesSize"), "1"),
helpText(getText("helpText18")),
colourpicker::colourInput("colTimelineDefaultEdgesColor", getText("colTimelineDefaultEdgesColor"), "#959595"),
helpText(getText("helpText18"))
#tags$hr(),
#textInput("txtFFMPEG_PATH",label="Full path of your ffmpeg binary to make the video (if not valid, video will not be made):",""),
#textInput("txtFFMPEG_FLAGS",label="Parameters to be passed to ffmpeg (if not valid, video will not be made):",""),
)
)
),
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'I am in debt with <a href="http://deim.urv.cat/~aarenas/" target="_blank">A. Arenas</a> for proposing this project, with <a href="http://people.maths.ox.ac.uk/porterm/" target="_blank">Mason A. Porter</a> and with the muxViz community for invaluable suggestions and feedbacks.',
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tags$br(),
tags$br(),
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tags$br(),
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tags$hr(),
tags$br()
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