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ui.R
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ui.R
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library("Metrics")
library("ggplot2")
library("rogme")
library("tibble")
library("stringi")
library("rjson")
library("viridis")
library("irr")
library("DescTools")
library("sjPlot")
library("plotly")
library("shiny")
library("shinydashboard")
source("allStats.R")
### ui header
header <- dashboardHeader(
title = "T1 mapping challenge statistics",
titleWidth = 450
)
sidebar <- dashboardSidebar(
sidebarMenu(
menuItem("Home", tabName = "menuHome", icon = icon("home")),
menuItem("NIST phantom", tabName = "menuNISTphantom", icon = icon("dashboard"),
menuSubItem(text = "Magnitude/Complex signal", tabName = "subMagComp", icon = icon("chart-bar")),
menuSubItem(text = "Measurements/Reference T1", tabName = "subMeasRef", icon = icon("chart-bar"))),
menuItem("Human brain", tabName = "menuHuman", icon = icon("brain"))
)
)
### ui body
body <- dashboardBody(
tabItems(
# First tab content
tabItem(tabName = "menuHome",
h2("Welcome to the ISMRM2020 Reproducible Challenge!"),
br(),
fluidRow(
box(width=6, status="primary",
htmlOutput("overviewTxt1"),
mainPanel(img(src='challengePitch.png', height="400%", width="150%", align = "center"))),
box(width=6, status="warning",
htmlOutput("overviewTxt2"),
mainPanel(img(src='rrsg2020Repo.png', height="300%", width="150%", align = "center")))
),
fluidRow(
box(width=6, status="primary",
htmlOutput("overviewTxt3"),
mainPanel(img(src='dataChallenge.png', height="100%", width="150%", align = "center"))),
box(width=6, status="warning",
htmlOutput("overviewTxt4"),
mainPanel(img(src='generalDashboard.png', height="300%", width="150%", align = "center")))
)
),
# Second tab content
tabItem(tabName = "subMagComp",
fluidRow(
box(width=2, solidHeader=TRUE, status="primary",
selectizeInput(
inputId = "DiffSitesID",
label = "Select site",
choices = unique(magVScomp$dataMagComp$sid),
selected = unique(magVScomp$dataMagComp$sid),
multiple = TRUE),
radioButtons(inputId = "typeComparison",
label = "Choose the type of plot to display",
choices = c("Difference", "Difference (%)"),
selected = "Difference (%)"
)),
box(title="Comparison Magnitude/Complex", width=5, status="warning", solidHeader=TRUE,
plotlyOutput(outputId = "MagComp")),
box(title="Bland-Altman plot", width=5, status="warning", solidHeader=TRUE,
plotlyOutput(outputId = "BAMagComp"))
),
fluidRow(
box(width=2, solidHeader=TRUE, status="primary",
selectizeInput(
inputId = "CorrSitesID",
label = "Select site",
choices = unique(magVScomp$dataCorr$sid),
multiple = FALSE
)),
box(title="Correlation Magnitude/Complex (mean values)", width=5, solidHeader=TRUE,
collapsible=TRUE, collapsed=TRUE, status="warning", plotlyOutput(outputId = "CorrMagComp")),
box(title="Correlation coefficients Magnitude/Complex (mean values)", width=2, solidHeader=TRUE,
status="warning", collapsible=TRUE, collapsed=TRUE, tableOutput(outputId = "PearsonCorr"))
),
fluidRow(
box(width=2, solidHeader=TRUE, status="primary",
selectizeInput(
inputId = "CorrSitesIDallDP",
label = "Select site",
choices = unique(magVScomp$PearsonCorrSphere$sid_long),
multiple = FALSE
)),
box(title="Correlation Magnitude/Complex (one site - all datapoints)", width=5, solidHeader=TRUE, status="warning",
plotlyOutput(outputId = "DispAllPointsMagComp_oneSite")),
box(title="Correlation coefficients Magnitude/Complex (one site - all datapoints)", width=3, solidHeader=TRUE, status="warning",
tableOutput(outputId = "PearsonAllPointsMagComp_oneSite"))
),
fluidRow(
column(2),
box(title="Correlation Magnitude/Complex (all sites - all datapoints)", width=5,
solidHeader=TRUE, status="warning", plotlyOutput(outputId = "DispAllPointsMagComp_allSites")),
box(title="Correlation coefficients Magnitude/Complex (all sites - all datapoints)", width=3,
solidHeader=TRUE, status="warning", tableOutput(outputId = "PearsonAllPointsMagComp_allSites"))
)
),
tabItem(tabName = "subMeasRef",
tabBox(width = 12,
tabPanel(title="General",
fluidRow(
box(width=2, solidHeader=TRUE, status="primary",
selectizeInput(
inputId = "FiltSitesID",
label = "Select group",
choices = unique(MeasSites$dataSite$sid),
selected = unique(MeasSites$dataSite$sid),
multiple = TRUE)),
box(title="Mean Measured/Reference T1 values (all sites)", width=5, solidHeader=TRUE, status="warning",
plotlyOutput(outputId = "CompFiltSites")),
box(title="Standard deviation Measured/Reference T1 (all sites)", width=5, solidHeader=TRUE, status="warning",
plotlyOutput(outputId = "sdFilteredSites"))
),
fluidRow(
box(width=2, solidHeader=TRUE, status="primary",
selectInput(inputId = "DispAllSite",
label = "Choose site:",
choices = c("Montreal","Germany","US","London","Australia"),
selected = "Montreal")),
box(title="Measured/Reference T1 values (all sites - all datapoints)", width=5, solidHeader=TRUE, status="warning",
plotlyOutput(outputId = "DispAllPoints"))
),
fluidRow(
box(width=2, solidHeader=TRUE, status="primary",
selectInput(inputId = "selectCompSite",
label = "Choose site:",
choices = c("Montreal","Germany","US","London","Australia"),
selected = "Montreal")),
box(title="Correlation Measured/Reference T1 values (by Site)", width=5, solidHeader=TRUE, status="warning",
plotlyOutput(outputId = "Disp4Site")),
box(title="Bland-Altman plot Measured/Reference T1 (by Site)", width=5, solidHeader=TRUE, status="warning",
plotlyOutput(outputId = "BA4Site"))
),
fluidRow(
box(width=2, solidHeader=TRUE, status="primary",
selectInput(inputId = "selectCompVendor",
label = "Choose MRI Vendor:",
choices = c("Siemens","GE","Philips"),
selected = "Siemens")),
box(title="Correlation Measured/Reference T1 values (by MRI Vendor)", width=5, solidHeader=TRUE, status="warning",
plotlyOutput(outputId = "Disp4Vendor")),
box(title="Bland-Altman plot Measured/Reference T1 (by MRI Vendor)", width=5, solidHeader=TRUE, status="warning",
plotlyOutput(outputId = "BA4Vendor"))
),
fluidRow(
box(width=2, solidHeader=TRUE, status="primary",
selectInput(inputId = "AcErrorAllSite",
label = "Choose site:",
choices = c("Montreal","Germany","US","London","Australia"),
selected = "Montreal"),
sliderInput(inputId = "errorThr",
label = "Accuracy error range",
min = 0, max = 50,
value = c(0,50), step = 1)),
box(title="Accuracy Error", width=5, solidHeader=TRUE, status="warning",
plotlyOutput(outputId = "AcErrorAllPoints"))
)
),
tabPanel(title="Hierarchical Shift Function (HSF)",
h2("HSF with bootstrapped confidence intervals"),
fluidRow(
box(width=6, plotlyOutput(outputId = "HSF1")),
box(width=6, plotlyOutput(outputId = "HSF2"))
),
fluidRow(
box(width=6, plotlyOutput(outputId = "HSF3")),
box(width=6, plotlyOutput(outputId = "HSF4"))
),
fluidRow(
box(width=6, plotlyOutput(outputId = "HSF5")),
box(width=6, plotlyOutput(outputId = "HSF6"))
),
fluidRow(
box(width=6, plotlyOutput(outputId = "HSF7")),
box(width=6, plotlyOutput(outputId = "HSF8"))
),
fluidRow(
box(width=6, plotlyOutput(outputId = "HSF9")),
box(width=6, plotlyOutput(outputId = "HSF10"))
),
fluidRow(
box(width=6, plotlyOutput(outputId = "HSF11")),
box(width=6, plotlyOutput(outputId = "HSF12"))
),
fluidRow(
box(width=6, plotlyOutput(outputId = "HSF13")),
box(width=6, plotlyOutput(outputId = "HSF14"))
)
)
)
),
# Third tab content
tabItem(tabName = "menuHuman",
h2("T1 value measured in different regions of the human brain"),
fluidRow(
box(title="All Sites", width=4, solidHeader=TRUE, status="warning",
plotlyOutput(outputId = "boxPlotHuman")),
box(title="Mexico", width=4, solidHeader=TRUE, status="warning",
plotlyOutput(outputId = "humanMEX_all")),
box(title="Canada", width=4, solidHeader=TRUE, status="warning",
plotlyOutput(outputId = "humanCAN_all"))
),
fluidRow(
box(title="United States", width=4, solidHeader=TRUE, status="warning",
plotlyOutput(outputId = "humanUS_all")),
box(title="Italy", width=4, solidHeader=TRUE, status="warning",
plotlyOutput(outputId = "humanITA_all")),
box(title="Germany", width=4, solidHeader=TRUE, status="warning",
plotlyOutput(outputId = "humanGER_all"))
),
fluidRow(
box(title="Australia", width=4, solidHeader=TRUE, status="warning",
plotlyOutput(outputId = "humanAUS_all"))
),
h2("T1 values by two vendors (MEXICO)"),
fluidRow(
box(width=2, solidHeader=TRUE, status="primary",
selectInput(inputId = "selectMEXVendor",
label = "Choose MRI Vendor:",
choices = c("Philips","GE"),
selected = "Philips")),
box(title="Measured T1 values (by MRI Vendor)", width=5, solidHeader=TRUE, status="warning",
plotlyOutput(outputId = "humanMEX_vendor"))
),
fluidRow(
box(width=2, solidHeader=TRUE, status="primary",
selectizeInput(
inputId = "FiltHumanSitesID",
label = "Select site",
choices = unique(dfmeanHuman$Site),
selected = unique(dfmeanHuman$Site),
multiple = TRUE)),
box(title="Percentage difference (%) with MEX as reference", width=5, solidHeader=TRUE, status="warning",
plotlyOutput(outputId = "CompHumanSites"))
),
fluidRow(
column(2),
box(title="Measured T1 value VS Age (all sites)", width=5, solidHeader=TRUE, status="warning",
plotlyOutput(outputId = "humanAge_all"))
),
h2("Comparison of NIST phantom and Human data"),
fluidRow(
box(width=2, solidHeader=TRUE, status="primary",
radioButtons(inputId = "cov_std",
label = "Select:",
choices = c("Coefficient of variation", "Standard deviation"),
selected = "Coefficient of variation")),
box(title="NIST Phantom dataset", width=10, solidHeader=TRUE, status="warning",
plotlyOutput(outputId = "NISTHumanCOV_STD_np"))
),
fluidRow(
column(2),
box(title="Human dataset", width=10, solidHeader=TRUE, status="warning",
plotlyOutput(outputId = "NISTHumanCOV_STD_h"))
)
)
)
)
dashboardPage(skin = "blue",
header,
sidebar,
body
)