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ui.R
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1328 lines (1001 loc) · 151 KB
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# Guane: a shiny app for phylogenetic comparative methods
# Author: Viviana Romero Alarcon
# Creation date: July 7 2023
# UI File
#------------------ Libraries ---------------
library(shiny)
library(bslib)
library(shinyWidgets)
library(dplyr)
library(shinyjs)
library(esquisse)
library(shinyAce)
#-----------
library(ape)
library(phytools)
library(geiger)
library(rhandsontable)
#------------------ Sources ---------------
source("Functions/GenFunctions.R")
source("Theme/Guane_theme.R")
#------------------ UI ---------------
shinyUI(navbarPage(title = div( "", img(src = "Picture1.png",
id = "simulation",
height = "75px",
width = "70px",
style = "position: relative; margin:0px 0px; display:center-align;")),
id = "GnavbarPage",
selected = "Intro",
position = "static-top",
inverse = FALSE,
collapsible = TRUE,
fluid = TRUE,
windowTitle = "Guane",
theme = theme,
# Module to modify adminlte
header= tags$style(HTML(".nav>li>a:active, .nav>li>a:focus, .nav>li>a:hover { background: #0d4d6100;}")),
#---------------- Collapsible Menu ---------------
#---------------- Intro Panel ---------------
tabPanel(id = "Gintro",title = "Intro"),
#---------------- Method Panels ---------------
# Collapsible panels
navbarMenu( title = "Methods",menuName = "GnavbarMenu",
#---------------- Phylo Signal ---------------
tabPanel(id = "PhySignal", title = "Phylogenetic Signal",
tabsetPanel(id="TabsPhySignal",type="tabs",
#-------------------------------------------Phylo Signal DATA ----------------------------------------------------
tabPanel(id="PhySignalDT",title = "DATA",
# Use Div to reset panels
useShinyjs(),
div(id = "PhySignalDTReset",
fluidRow(
column(10,
fluidRow(
column(3,sidebarPanel(width = "100%",
p("Setting up", style = "align:center;text-align:center; font-weight: bold"),
hr(),
)),
column(9,fluidRow(column(8,card(height = "680px",full_screen = TRUE, card_header( strong("Main Plot")),
card_body( plotOutput("plotPhySignalDT", inline = T)),
)),
column(4, card(full_screen = TRUE, card_header( strong("Data Structure")),
verbatimTextOutput("srtPhySignalDT")),
card(full_screen = TRUE,
card_header( strong("Messages/Errors")),
verbatimTextOutput("infoPhySignalDT"))
))))),
column(2, sidebarPanel(width = "100%",p("Graphic Controls", style = "align:center;text-align:center; font-weight: bold"),hr(),
awesomeCheckbox(inputId = "ViewPlotPhySignalDT",label = strong("Display Plot"),
value = T,status = "info"), hr(),
sliderInput(inputId = "HeightPhySignalDT" ,
label = " Height",min =0 ,max = 10000,value = 400),
sliderInput(inputId = "WidthPhySignalDT" ,
label = " Width",min =0 ,max = 10000,value = 600 ),
hr(),
accordion_panel( title = h5(" \ Tree and edge design"),
value = "SetTreePhySignalDT",
open = FALSE,icon = icon("greater-than")),
hr(),
accordion_panel( title = h5(" \ Lables"),
value = "labels PhySignalDT",
open = FALSE,icon = icon("greater-than")),
hr(),
accordion_panel( title = h5(" \ Margins"),
value = "marginsPhySignalDT",
open = FALSE,icon = icon("greater-than")),
hr(),
accordion_panel( title = h5(" \ Nodes"),
value = "NodesPhySignalDT",
open = FALSE,icon = icon("greater-than")),
),fluidRow(sidebarPanel(width = "100%",p("Download", style = "align:center;text-align:center; font-weight: bold")))
))
# Finish Div: PhySignalDTReset
),
actionButton("ResetPhySignalDT",width = "100%",label = "Restart initial values")
# Finish tabPanel: PhySignalDT
),
#-------------------------------------------Phylo Signal ANALYSIS ----------------------------------------------------
tabPanel(id="PhySignalANA",title = "ANALYSIS",
tabsetPanel(id="PillsDiverModANA",type="pills",
#-------------------------------------------Phylo Signal ANALYSIS: Maxumum Likelihood ----------------------------------------------------
tabPanel(id="MLPhySignalANA",title = "Maxumum Likelihood",
# Use Div to reset panels
useShinyjs(),
div(id = "MLPhySignalANAReset",
fluidRow(
column(10,
fluidRow(
column(3,sidebarPanel(width = "100%",
p("Setting up", style = "align:center;text-align:center; font-weight: bold"),
hr(),
)),
column(9,fluidRow(column(8,card(height = "680px",full_screen = TRUE, card_header( strong("Main Plot")),
card_body( plotOutput("plotMLPhySignalANA", inline = T)),
)),
column(4, card(full_screen = TRUE, card_header( strong("Data Structure")),
verbatimTextOutput("srtMLPhySignalANA")),
card(full_screen = TRUE,
card_header( strong("Messages/Errors")),
verbatimTextOutput("infoMLPhySignalANA"))
))))),
column(2, sidebarPanel(width = "100%",p("Graphic Controls", style = "align:center;text-align:center; font-weight: bold"),hr(),
awesomeCheckbox(inputId = "ViewPlotMLPhySignalANA",label = strong("Display Plot"),
value = T,status = "info"), hr(),
sliderInput(inputId = "HeightMLPhySignalANA" ,
label = " Height",min =0 ,max = 10000,value = 400),
sliderInput(inputId = "WidthMLPhySignalANA" ,
label = " Width",min =0 ,max = 10000,value = 600 ),
hr(),
accordion_panel( title = h5(" \ Tree and edge design"),
value = "SetTreeMLPhySignalANA",
open = FALSE,icon = icon("greater-than")),
hr(),
accordion_panel( title = h5(" \ Lables"),
value = "labels MLPhySignalANA",
open = FALSE,icon = icon("greater-than")),
hr(),
accordion_panel( title = h5(" \ Margins"),
value = "marginsMLPhySignalANA",
open = FALSE,icon = icon("greater-than")),
hr(),
accordion_panel( title = h5(" \ Nodes"),
value = "NodesMLPhySignalANA",
open = FALSE,icon = icon("greater-than")),
),fluidRow(sidebarPanel(width = "100%",p("Download", style = "align:center;text-align:center; font-weight: bold")))
))
# Finish Div: MLPhySignalANAReset
),
actionButton("ResetMLPhySignalANA",width = "100%",label = "Restart initial values")
#Finish TabPanel: MLPhySignalANA
),
#-------------------------------------------Phylo Signal ANALYSIS: MCMC ----------------------------------------------------
tabPanel(id="BIPhySignalANA",title = "Stochastic mapping",
# Use Div to reset panels
useShinyjs(),
div(id = "BIPhySignalANAReset",
fluidRow(
column(10,
fluidRow(
column(3,sidebarPanel(width = "100%",
p("Setting up", style = "align:center;text-align:center; font-weight: bold"),
hr(),
)),
column(9,fluidRow(column(8,card(height = "680px",full_screen = TRUE, card_header( strong("Main Plot")),
card_body( plotOutput("plotBIPhySignalANA", inline = T)),
)),
column(4, card(full_screen = TRUE, card_header( strong("Data Structure")),
verbatimTextOutput("srtBIPhySignalANA")),
card(full_screen = TRUE,
card_header( strong("Messages/Errors")),
verbatimTextOutput("infoBIPhySignalANA"))
))))),
column(2, sidebarPanel(width = "100%",p("Graphic Controls", style = "align:center;text-align:center; font-weight: bold"),hr(),
awesomeCheckbox(inputId = "ViewPlotBIPhySignalANA",label = strong("Display Plot"),
value = T,status = "info"), hr(),
sliderInput(inputId = "HeightBIPhySignalANA" ,
label = " Height",min =0 ,max = 10000,value = 400),
sliderInput(inputId = "WidthBIPhySignalANA" ,
label = " Width",min =0 ,max = 10000,value = 600 ),
hr(),
accordion_panel( title = h5(" \ Tree and edge design"),
value = "SetTreeBIPhySignalANA",
open = FALSE,icon = icon("greater-than")),
hr(),
accordion_panel( title = h5(" \ Lables"),
value = "labels BIPhySignalANA",
open = FALSE,icon = icon("greater-than")),
hr(),
accordion_panel( title = h5(" \ Margins"),
value = "marginsBIPhySignalANA",
open = FALSE,icon = icon("greater-than")),
hr(),
accordion_panel( title = h5(" \ Nodes"),
value = "NodesBIPhySignalANA",
open = FALSE,icon = icon("greater-than")),
),fluidRow(sidebarPanel(width = "100%",p("Download", style = "align:center;text-align:center; font-weight: bold")))
))
# Finish Div: BIPhySignalANAReset
),
actionButton("ResetBIPhySignalANA",width = "100%",label = "Restart initial values")
#Finish TabPanel: BIPhySignalANA
),
#Finish TabsetPanel: PillsPhySignalANA
)
# Finish tabPanel: PhySignalANA
)
# Finish tabsetPanel: TabsPhySignal
)
# Finish tabPanel: PhySignal
),
"----",
"Ancestral State Estimation",
#-------------------------------------------ANS Discrete Characters----------------------------------------------------
tabPanel(id = "DisChar", title = "Discrete Characters",
tabsetPanel(id="TabsDisChar",type="tabs",
#-------------------------------------------ANS Discrete Characters DATA ----------------------------------------------------
tabPanel(id="DisCharDT",title = "DATA",
# Use Div to reset panels
useShinyjs(),
div(id = "DisCharDTReset",
fluidRow(
column(10,
fluidRow(
column(3,sidebarPanel(width = "100%",
p("Setting up", style = "align:center;text-align:center; font-weight: bold"),
hr(),
fileInput(inputId = "treeDisDT",
label = strong("Load tree"),
width = "100%",
accept = c(".tree",".tre",".nexus",".phy",".nex")),
fluidRow(column(6,aling="center",
materialSwitch(inputId = "EgTreeDisDT",label = "Use example",
value = FALSE,status = "info",right = TRUE)),
column(6,align= "right",actionButton(inputId = "loadTreeDisDT",
label = NULL,icon =icon(name = "upload"),
width = "25%"))),
hr(),
fileInput(inputId = "csvDisDT",
label = strong('Load Character(s)'),
width = "100%",
accept = c(".csv",".txt",".text")),
fluidRow(column(6,aling="center",
materialSwitch(inputId = "EgCSVDisDT",label = "Use example",
value = FALSE,status = "info",right = TRUE)),
column(6,align= "right",actionButton(inputId = "loadCSVDisDT",
label = NULL,icon =icon(name = "upload"),
width = "25%"))),
hr(),
awesomeCheckbox(inputId = "chckNamesDisDT",label = strong("Check tree & data names"),
value = F,status = "info"),
uiOutput(outputId = "RslvNamesDisDT"),
hr(),
selectInput(inputId = "chooseVarDisDT",label = strong("Select your discrete character"), choices = "Select"),
selectInput(inputId = "chooseTupeDisDT",label = strong("Select characther type"), choices = c("Select","monomorphic", "polymorphic"),selected = NULL,multiple = F),
),),
column(9,fluidRow(column(8,card(height = "680px",full_screen = TRUE, card_header( strong("Main Plot")),
card_body( plotOutput("plotDisDT", inline = T)),
)),
column(4, card(full_screen = TRUE, card_header( strong("Data Structure")),
verbatimTextOutput("srtDisDT")),
card(full_screen = TRUE,
card_header( strong("Messages/Errors")),
verbatimTextOutput("infoDisDT")
)
))))),
column(2, sidebarPanel(width = "100%",p("Graphic Controls", style = "align:center;text-align:center; font-weight: bold"),hr(),
awesomeCheckbox(inputId = "ViewPlotDisDT",label = strong("Display Plot"),
value = T,status = "info"), hr(),
sliderInput(inputId = "HeightDisDT" ,
label = " Height",min =0 ,max = 10000,value = 400),
sliderInput(inputId = "WidthDisDT" ,
label = " Width",min =0 ,max = 10000,value = 600 ),
hr(),
accordion_panel( title = h5(" \ Tree and edge design"),
value = "SetTreeDisDT",
pickerInput(selected = "regular",
inputId = "ladderizeDisDT",
label = strong('Type'),
choices = c("regular",
"ascending", "descending")
),
pickerInput(selected = "phylogram",
inputId = "typeDisDT",
label = strong('Sort Tree'),
choices = c("phylogram" ,
"cladogram", "fan","unrooted","radial","tidy"),
),
pickerInput(selected = "rightwards",
inputId = "directionDisDT",
label = strong('Direction'),
choices = c("rightwards" ,
"leftwards", "upwards",
"downwards"),
),
conditionalPanel(condition= "input.typeDisDT == 'fan' || input.typeDisDT == 'radial' ",
numericInput(inputId = "rotateTreeDisDT",
label = "Rotate tree",value = 0 ,min =-360,
max =360 ,step =0.1 ,width = "40%"),
numericInput(inputId = "openAngleDisDT",
label = "Open angle",
value = 0.1 ,min =0.1,
max =360 ,step =0.1 ,width = "40%"),
),
awesomeCheckbox(inputId = "edgeLenghtDisDT",
label = strong("Use edge lengths"),
value = T,status = "info"),
numericInput(inputId = "edgeWidthDisDT",
label = "set edge width",value = 1 ,
min =0.1 ,max =10 ,step =0.01 ,width = "40%"),
selectInput(selected = "plain",
inputId = "edgetlyDisDT",
label = strong('Line Type'),
choices = c( "plain" = "1" , "dashed" = "2",
"dotted" = "3", "dotdash" = "4",
"longdash" = "5" , "twodash" = "6")
),
open = FALSE,icon = icon("greater-than")),
hr(),
accordion_panel( title = h5(" \ Lables"),
value = "lablesDisDT",
awesomeCheckbox(inputId = "tipLabelsDisDT",label = strong("Show tip lables"),
value = T,status = "info"),
awesomeCheckbox(inputId = "aligntiplabelDisDT",
label = strong("Align tip label"),
value = F,status = "info"),
awesomeCheckbox(inputId = "underscoreDisDT",
label = strong("Underscore"),
value = F,status = "info"),
selectInput(selected = "plain text",
inputId = "fontDisDT",
label = strong('Font'),
choices = c( "plain text" = "1" , "bold" = "2",
"italic" = "3", "bold-italic" = "4")),
numericInput(inputId = "cexDisDT",
label = "size labels",value = 1 ,
min =0.1 ,max =10 ,step =0.001 ,width = "40%"),
selectInput(selected = NULL,
inputId = "adjDisDT",
label = strong('Justification'),
choices = c( "left-justification" = "0" , "centering" = "0.5",
"right-justification" = "1", NULL)),
numericInput(inputId = "srtDisDT",
label = "Label rotation",
value = 0.1 ,min =0.1,
max =360 ,step =0.1 ,width = "40%"),
numericInput(inputId = "labeloffsetDisDT",
label = "Label offset",value = 0.01 ,
min =0.1 ,max =10 ,step =0.001 ,width = "40%"),
selectInput(selected = "horizontal",
inputId = "lab4utDisDT",
label = strong('Labels for unroot'),
choices = c( "horizontal" , "axial")),
open = FALSE,icon = icon("greater-than")),
hr(),
accordion_panel( title = h5(" \ Margins"),
value = "marginsDisDT",
awesomeCheckbox(inputId = "nomarginDisDT",
label = strong("No margin"),
value = T,status = "info"),
# numericInput(inputId = "xlimDisDT",
# label = "x lim",value = 0.1,
# min =0.1 ,max =10 ,step =0.001 ,width = "40%"),
# numericInput(inputId = "ylimDisDT",
# label = "y lim",value = 0.1,
# min =0.1 ,max =10 ,step =0.001 ,width = "40%"),
open = FALSE,icon = icon("greater-than")),
hr(),
accordion_panel( title = h5(" \ Nodes"),
value = "NodesDisDT",
awesomeCheckbox(inputId = "nodelabelDisDT",
label = strong("Show node label"),
value = F,status = "info"),
numericInput(inputId = "nodeWidthDisDT",
label = "Node width",value = 1 ,
min =0.1 ,max =10 ,step =0.01 ,width = "40%"),
selectInput(selected = "plain",
inputId = "nodeltyDisDT",
label = strong('Line Type'),
choices = c( "plain" = "1" , "dashed" = "2",
"dotted" = "3", "dotdash" = "4",
"longdash" = "5" , "twodash" = "6")),
open = FALSE,icon = icon("greater-than")),
),fluidRow(sidebarPanel(width = "100%",p("Download", style = "align:center;text-align:center; font-weight: bold")))
))
# Finish Div: DisCharDTReset
),
actionButton("ResetDisCharDT",width = "100%",label = "Restart initial values")
# Finish tabPanel: DisCharDT
),
#-------------------------------------------ANS Discrete Characters ANALYSIS ----------------------------------------------------
tabPanel(id="DisCharAN",title = "ANALYSIS",
# Use Div to reset panels
useShinyjs(),
div(id = "DisMLReset",
fluidRow(
column(10,
fluidRow(
column(3,sidebarPanel(width = "100%",
p("Setting up", style = "align:center;text-align:center; font-weight: bold"),
hr(),
actionButton(inputId = "loadDisML",label = "Load/Refresh data" ,width = "100%"),hr(),
selectInput("select", label = "Estimation",
choices = list("Marginal" = "marginal", "Joint" = "joint"),
selected = "marginal"),
selectInput("ModDisML", "Set models",choices = NULL,multiple = TRUE),
uiOutput("addModel3States"),
conditionalPanel("input.addModDisML > 0",
br(), rHandsontableOutput("w1"), br(),
actionButton('SubmAddModel','Submit')),
actionButton('RunDisML','Run'), hr(),
#---------------- mono and
)),
column(9,fluidRow(column(8,card(height = "680px",full_screen = TRUE, card_header( strong("Main Plot")),
card_body( plotOutput("plotDisML", inline = T)),
)),
column(4, card(full_screen = TRUE, card_header( strong("Data Structure")),
verbatimTextOutput("srtDisML")),
card(full_screen = TRUE,
card_header( strong("Messages/Errors")),
verbatimTextOutput("infoDisML"))
))))),
column(2, sidebarPanel(width = "100%",p("Graphic Controls", style = "align:center;text-align:center; font-weight: bold"),hr(),
awesomeCheckbox(inputId = "ViewPlotDisML",label = strong("Display Plot"),
value = T,status = "info"), hr(),
sliderInput(inputId = "HeightDisML" ,
label = " Height",min =0 ,max = 10000,value = 400),
sliderInput(inputId = "WidthDisML" ,
label = " Width",min =0 ,max = 10000,value = 600 ),
hr(),
accordion_panel( title = h5(" \ Tree and edge design"),
value = "SetTreeDisML",
pickerInput(selected = "regular",
inputId = "ladderizeDisML",
label = strong('Type'),
choices = c("regular",
"ascending", "descending")
),
pickerInput(selected = "phylogram",
inputId = "typeDisML",
label = strong('Sort Tree'),
choices = c("phylogram" ,
"cladogram", "fan","unrooted","radial","tidy"),
),
pickerInput(selected = "rightwards",
inputId = "directionDisML",
label = strong('Direction'),
choices = c("rightwards" ,
"leftwards", "upwards",
"downwards"),
),
conditionalPanel(condition= "input.typeDisML == 'fan' || input.typeDisML == 'radial' ",
numericInput(inputId = "rotateTreeDisML",
label = "Rotate tree",value = 0 ,min =-360,
max =360 ,step =0.1 ,width = "40%"),
numericInput(inputId = "openAngleDisML",
label = "Open angle",
value = 0.1 ,min =0.1,
max =360 ,step =0.1 ,width = "40%"),
),
awesomeCheckbox(inputId = "edgeLenghtDisML",
label = strong("Use edge lengths"),
value = T,status = "info"),
numericInput(inputId = "edgeWidthDisML",
label = "set edge width",value = 1 ,
min =0.1 ,max =10 ,step =0.01 ,width = "40%"),
selectInput(selected = "plain",
inputId = "edgetlyDisML",
label = strong('Line Type'),
choices = c( "plain" = "1" , "dashed" = "2",
"dotted" = "3", "dotdash" = "4",
"longdash" = "5" , "twodash" = "6")
),
open = FALSE,icon = icon("greater-than")),
hr(),
accordion_panel( title = h5(" \ Lables"),
value = "lablesDisML",
awesomeCheckbox(inputId = "tipLabelsDisML",label = strong("Show tip lables"),
value = T,status = "info"),
awesomeCheckbox(inputId = "aligntiplabelDisML",
label = strong("Align tip label"),
value = F,status = "info"),
awesomeCheckbox(inputId = "underscoreDisML",
label = strong("Underscore"),
value = F,status = "info"),
selectInput(selected = "plain text",
inputId = "fontDisML",
label = strong('Font'),
choices = c( "plain text" = "1" , "bold" = "2",
"italic" = "3", "bold-italic" = "4")),
numericInput(inputId = "cexDisML",
label = "size labels",value = 1 ,
min =0.1 ,max =10 ,step =0.001 ,width = "40%"),
selectInput(selected = NULL,
inputId = "adjDisML",
label = strong('Justification'),
choices = c( "left-justification" = "0" , "centering" = "0.5",
"right-justification" = "1", NULL)),
numericInput(inputId = "srtDisML",
label = "Label rotation",
value = 0.1 ,min =0.1,
max =360 ,step =0.1 ,width = "40%"),
numericInput(inputId = "labeloffsetDisML",
label = "Label offset",value = 0.01 ,
min =0.1 ,max =10 ,step =0.001 ,width = "40%"),
selectInput(selected = "horizontal",
inputId = "lab4utDisML",
label = strong('Labels for unroot'),
choices = c( "horizontal" , "axial")),
open = FALSE,icon = icon("greater-than")),
hr(),
accordion_panel( title = h5(" \ Margins"),
value = "marginsDisML",
awesomeCheckbox(inputId = "nomarginDisML",
label = strong("No margin"),
value = T,status = "info"),
# numericInput(inputId = "xlimDisDT",
# label = "x lim",value = 0.1,
# min =0.1 ,max =10 ,step =0.001 ,width = "40%"),
# numericInput(inputId = "ylimDisDT",
# label = "y lim",value = 0.1,
# min =0.1 ,max =10 ,step =0.001 ,width = "40%"),
open = FALSE,icon = icon("greater-than")),
hr(),
accordion_panel( title = h5(" \ Nodes"),
value = "NodesDisML",
awesomeCheckbox(inputId = "nodelabelDisML",
label = strong("Show node label"),
value = F,status = "info"),
numericInput(inputId = "nodeWidthDisML",
label = "Node width",value = 1 ,
min =0.1 ,max =10 ,step =0.01 ,width = "40%"),
selectInput(selected = "plain",
inputId = "nodeltyDisML",
label = strong('Line Type'),
choices = c( "plain" = "1" , "dashed" = "2",
"dotted" = "3", "dotdash" = "4",
"longdash" = "5" , "twodash" = "6")),
open = FALSE,icon = icon("greater-than")),
),fluidRow(sidebarPanel(width = "100%",p("Download", style = "align:center;text-align:center; font-weight: bold")))
))
# Finish Div: DisML
),
actionButton("DisMLReset",width = "100%",label = "Restart initial values")
# Finish tabPanel: DisCharANA
),
# Finish tabsetPanel: TabsDisChar
)
# Finish tabPanel: DisChar
),
#-------------------------------------------ANS Continuous Characters ----------------------------------------------------
tabPanel(id = "ConChar", title = "Continuous Characters",
tabsetPanel(id="TabsConChar",type="tabs",
#-------------------------------------------ANS Continuous Characters DATA----------------------------------------------------
tabPanel(id="ConCharDT",title = "DATA",
# Use Div to reset panels
useShinyjs(),
div(id = "ConCharDTReset",
fluidRow(
column(10,
fluidRow(
column(3,sidebarPanel(width = "100%",
p("Setting up", style = "align:center;text-align:center; font-weight: bold"),
hr(),
)),
column(9,fluidRow(column(8,card(height = "680px",full_screen = TRUE, card_header( strong("Main Plot")),
card_body( plotOutput("plotConCharDT", inline = T)),
)),
column(4, card(full_screen = TRUE, card_header( strong("Data Structure")),
verbatimTextOutput("srtConCharDT")),
card(full_screen = TRUE,
card_header( strong("Messages/Errors")),
verbatimTextOutput("infoConCharDT"))
))))),
column(2, sidebarPanel(width = "100%",p("Graphic Controls", style = "align:center;text-align:center; font-weight: bold"),hr(),
awesomeCheckbox(inputId = "ViewPlotConCharDT",label = strong("Display Plot"),
value = T,status = "info"), hr(),
sliderInput(inputId = "HeightConCharDT" ,
label = " Height",min =0 ,max = 10000,value = 400),
sliderInput(inputId = "WidthConCharDT" ,
label = " Width",min =0 ,max = 10000,value = 600 ),
hr(),
accordion_panel( title = h5(" \ Tree and edge design"),
value = "SetTreeConCharDT",
open = FALSE,icon = icon("greater-than")),
hr(),
accordion_panel( title = h5(" \ Lables"),
value = "labels ConCharDT",
open = FALSE,icon = icon("greater-than")),
hr(),
accordion_panel( title = h5(" \ Margins"),
value = "marginsConCharDT",
open = FALSE,icon = icon("greater-than")),
hr(),
accordion_panel( title = h5(" \ Nodes"),
value = "NodesConCharDT",
open = FALSE,icon = icon("greater-than")),
),fluidRow(sidebarPanel(width = "100%",p("Download", style = "align:center;text-align:center; font-weight: bold")))
))
# Finish Div: ConCharDTReset
),
actionButton("ResetConCharDT",width = "100%",label = "Restart initial values")
# Finish tabPanel: ConCharDT
),
#-------------------------------------------ANS Continuous Characters ANALYSIS ----------------------------------------------------
tabPanel(id="ConCharANA",title = "ANALYSIS",
tabsetPanel(id="PillsDiverModANA",type="pills",
#-------------------------------------------ANS Characters ANALYSIS: Maxumum Likelihood ----------------------------------------------------
tabPanel(id="MLConCharANA",title = "Maxumum Likelihood",
# Use Div to reset panels
useShinyjs(),
div(id = "MLConCharANAReset",
fluidRow(
column(10,
fluidRow(
column(3,sidebarPanel(width = "100%",
p("Setting up", style = "align:center;text-align:center; font-weight: bold"),
hr(),
)),
column(9,fluidRow(column(8,card(height = "680px",full_screen = TRUE, card_header( strong("Main Plot")),
card_body( plotOutput("plotMLConCharANA", inline = T)),
)),
column(4, card(full_screen = TRUE, card_header( strong("Data Structure")),
verbatimTextOutput("srtMLConCharANA")),
card(full_screen = TRUE,
card_header( strong("Messages/Errors")),
verbatimTextOutput("infoMLConCharANA"))
))))),
column(2, sidebarPanel(width = "100%",p("Graphic Controls", style = "align:center;text-align:center; font-weight: bold"),hr(),
awesomeCheckbox(inputId = "ViewPlotMLConCharANA",label = strong("Display Plot"),
value = T,status = "info"), hr(),
sliderInput(inputId = "HeightMLConCharANA" ,
label = " Height",min =0 ,max = 10000,value = 400),
sliderInput(inputId = "WidthMLConCharANA" ,
label = " Width",min =0 ,max = 10000,value = 600 ),
hr(),
accordion_panel( title = h5(" \ Tree and edge design"),
value = "SetTreeMLConCharANA",
open = FALSE,icon = icon("greater-than")),
hr(),
accordion_panel( title = h5(" \ Lables"),
value = "labels MLConCharANA",
open = FALSE,icon = icon("greater-than")),
hr(),
accordion_panel( title = h5(" \ Margins"),
value = "marginsMLConCharANA",
open = FALSE,icon = icon("greater-than")),
hr(),
accordion_panel( title = h5(" \ Nodes"),
value = "NodesMLConCharANA",
open = FALSE,icon = icon("greater-than")),
),fluidRow(sidebarPanel(width = "100%",p("Download", style = "align:center;text-align:center; font-weight: bold")))
))
# Finish Div: MLConCharANAReset
),
actionButton("ResetMLConCharANA",width = "100%",label = "Restart initial values")
#Finish TabPanel: MLConCharANA
),
#-------------------------------------------ANS ANALYSIS: MCMC ----------------------------------------------------
tabPanel(id="BIConCharANA",title = "Stochastic mapping",
# Use Div to reset panels
useShinyjs(),
div(id = "BIConCharANAReset",
fluidRow(
column(10,
fluidRow(
column(3,sidebarPanel(width = "100%",
p("Setting up", style = "align:center;text-align:center; font-weight: bold"),
hr(),
)),
column(9,fluidRow(column(8,card(height = "680px",full_screen = TRUE, card_header( strong("Main Plot")),
card_body( plotOutput("plotBIConCharANA", inline = T)),
)),
column(4, card(full_screen = TRUE, card_header( strong("Data Structure")),
verbatimTextOutput("srtBIConCharANA")),
card(full_screen = TRUE,
card_header( strong("Messages/Errors")),
verbatimTextOutput("infoBIConCharANA"))
))))),
column(2, sidebarPanel(width = "100%",p("Graphic Controls", style = "align:center;text-align:center; font-weight: bold"),hr(),
awesomeCheckbox(inputId = "ViewPlotBIConCharANA",label = strong("Display Plot"),
value = T,status = "info"), hr(),
sliderInput(inputId = "HeightBIConCharANA" ,
label = " Height",min =0 ,max = 10000,value = 400),
sliderInput(inputId = "WidthBIConCharANA" ,
label = " Width",min =0 ,max = 10000,value = 600 ),
hr(),
accordion_panel( title = h5(" \ Tree and edge design"),
value = "SetTreeBIConCharANA",
open = FALSE,icon = icon("greater-than")),
hr(),
accordion_panel( title = h5(" \ Lables"),
value = "labels BIConCharANA",
open = FALSE,icon = icon("greater-than")),
hr(),
accordion_panel( title = h5(" \ Margins"),
value = "marginsBIConCharANA",
open = FALSE,icon = icon("greater-than")),
hr(),
accordion_panel( title = h5(" \ Nodes"),
value = "NodesBIConCharANA",
open = FALSE,icon = icon("greater-than")),
),fluidRow(sidebarPanel(width = "100%",p("Download", style = "align:center;text-align:center; font-weight: bold")))
))
# Finish Div: BIConCharANAReset
),
actionButton("ResetBIConCharANA",width = "100%",label = "Restart initial values")
#Finish TabPanel: BIConCharANA
),
#Finish TabsetPanel: PillsConCharANA
)
# Finish tabPanel: ConCharANA
)
# Finish tabsetPanel: TabsConChar
)
# Finish tabPanel: ConChar
),
"----",
"Basic Diversification Analyses",
#-------------------------------------------LTT ----------------------------------------------------
tabPanel(id = "Ltt", title = "Phylogenetic Signal",
tabsetPanel(id="TabsLtt",type="tabs",
#-------------------------------------------LTT DATA ----------------------------------------------------
tabPanel(id="LttDT",title = "DATA",
# Use Div to reset panels
useShinyjs(),
div(id = "LttDTReset",
fluidRow(
column(10,
fluidRow(
column(3,sidebarPanel(width = "100%",
p("Setting up", style = "align:center;text-align:center; font-weight: bold"),
hr(),
)),
column(9,fluidRow(column(8,card(height = "680px",full_screen = TRUE, card_header( strong("Main Plot")),
card_body( plotOutput("plotLttDT", inline = T)),
)),
column(4, card(full_screen = TRUE, card_header( strong("Data Structure")),
verbatimTextOutput("srtLttDT")),
card(full_screen = TRUE,
card_header( strong("Messages/Errors")),
verbatimTextOutput("infoLttDT"))
))))),
column(2, sidebarPanel(width = "100%",p("Graphic Controls", style = "align:center;text-align:center; font-weight: bold"),hr(),
awesomeCheckbox(inputId = "ViewPlotLttDT",label = strong("Display Plot"),
value = T,status = "info"), hr(),
sliderInput(inputId = "HeightLttDT" ,
label = " Height",min =0 ,max = 10000,value = 400),
sliderInput(inputId = "WidthLttDT" ,
label = " Width",min =0 ,max = 10000,value = 600 ),
hr(),
accordion_panel( title = h5(" \ Tree and edge design"),
value = "SetTreeLttDT",
open = FALSE,icon = icon("greater-than")),
hr(),
accordion_panel( title = h5(" \ Lables"),
value = "labels LttDT",
open = FALSE,icon = icon("greater-than")),
hr(),
accordion_panel( title = h5(" \ Margins"),
value = "marginsLttDT",
open = FALSE,icon = icon("greater-than")),
hr(),
accordion_panel( title = h5(" \ Nodes"),
value = "NodesLttDT",
open = FALSE,icon = icon("greater-than")),
),fluidRow(sidebarPanel(width = "100%",p("Download", style = "align:center;text-align:center; font-weight: bold")))