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UI.R
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690 lines (649 loc) · 35.9 KB
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library(networkD3)
library(dplyr)
library(igraph)
library(visNetwork)
library(stringr)
library(png)
library(shinyjs)
library(DT)
library(rintrojs)
library(ggplot2)
library(qdapTools)
library(RColorBrewer)
library(shinyWidgets)
shinyWidgets::shinyWidgetsGallery()
source("helper_function.R")
ui <- shinyUI(navbarPage(
##########################
### Design Layout ###
##########################
title = div(
img(src = "UOL_blue.png", height = "50px", style = "margin-right: 20px;"),
img(src = "metarep.jpg", height = "50px")
),
id = "navBar",
theme = "bootstrap.css",
collapsible = TRUE,
inverse = TRUE,
windowTitle = "METEOR - forking paths in fMRI preprocessing",
position = "fixed-top",
header = tags$style(
HTML("
.navbar {
min-height: 70px; /* Adjust this value to increase the height */
background-color: #f8f9fa; /* Light grey color */
}
.navbar-brand {
height: 70px; /* Adjust this value to match the navbar height */
padding: 10px 15px; /* Adjust padding to center the images vertically */
}
.navbar-nav > li > a {
padding-top: 25px; /* Adjust this value to center the text vertically */
padding-bottom: 25px; /* Adjust this value to center the text vertically */
color: #007bff; /* Blue color for the text */
font-size: 14px; /* Increase font size */
font-weight: bold; /* Make text bold */
}
.navbar-nav > li > a:hover {
color: grey !important; /* Darker blue color for the text on hover */
}
body {
padding-top: 100px;
}
")
),
tags$head(
tags$style(HTML('
.navbar-nav { float: right !important; }
.hidden-tab { display: none !important; }
.custom-home-icon {
cursor: pointer;
padding: 25px;
display: flex;
align-items: center;
}
.custom-home-icon i {
margin-right: 5px;
}
.custom-home-icon span {
font-weight: bold;
color: dark blue; /* Blue color for the text */
font-size: 14px; /* Increase font size */
}
.navbar-nav > li > a:hover {
color: grey !important; /* Darker blue color for the text on hover */
}
body {
padding-top: 100px;
}
')),
tags$script(HTML('
$(document).ready(function() {
$(".navbar-nav > li").addClass("hidden-tab");
$(".navbar-nav > li:last-child").removeClass("hidden-tab");
// Add custom home icon with text
$(".navbar-nav").prepend(\'<li class="custom-home-icon"><i class="fa fa-home"></i><span>HOME</span></li>\');
// Click event for custom home icon
$(".custom-home-icon").click(function() {
var homeTab = $(".navbar-nav > li > a[data-value=\'home\']");
homeTab.click();
});
});
'))
),
##########################
### Home ###
##########################
tabPanel("Home", value = "home", icon = icon("home"),
shinyjs::useShinyjs(),
tags$head(tags$script(HTML('
function fakeClick(tabName) {
var dropdownList = document.getElementsByTagName("a");
for (var i = 0; i < dropdownList.length; i++) {
var link = dropdownList[i];
if(link.getAttribute("data-value") == tabName) {
link.click();
}
}
}
var sendToShiny = function(label) {
Shiny.onInputChange("node_clicked", label);
};
'))),
fluidRow(
align = "left",
column(
width = 12,
wellPanel(
style = "background-color: #f0f0f0; color: #000; padding: 10px; border: 1px solid #ddd;",
shiny::tags$h4("METEOR", style = "color: #000;"),
shiny::tags$h4("Mastering The Oppressive number of forking paths unfolded by noisy and complex neural data",
style = "color: #000; font-weight: normal;"),
shiny::tags$h5("This interactive shiny app allows you to investigate the multiverse of functional Magnetic
Resonance Imaging (fMRI) data preprocessing and analysis based on graph theory. ",
style = "color: #000; font-weight: normal;"),
shiny::tags$h5("Click on the node below to explore the features of this app:", style = "color: #000;"),
shiny::HTML("<br>")
)
)
),
fluidRow(
column(8,
visNetworkOutput("network_home", width = "100%", height = "600px")
),
column(4,
align = "left",
uiOutput("node_description") # Move this line here
)
)
),
##########################
### Database ###
##########################
tabPanel("Database", value = "MA",
mainPanel(
tabsetPanel(type = "tabs",
tabPanel(
"PRISMA Diagram", value = "PRISMA",
shiny::HTML("<h1>PRISMA diagram</h1>"),
fluidRow(
column(4,
shiny::HTML("<h5><b>Literature review of articles related to graph fMRI studies.</b></h5>
<b>Literature search:</b>Three databases were searched: Scopus, Web of Science,
and PubMed for publications containing the terms related to fMRI, graph theory, and cognitive abilities <br><br>
<b>Study inclusion:</b> We only included empirical studies which report
the preprocessing steps and deal with healthy subjects. Details can be found in the Preferred Reporting
Items for Systematic Reviews and Meta-Analyses (PRISMA) flowchart on the right. <br><br>
<b>Data extraction:</b> All data was coded by one coder. Other two coders coded the data
independently for 25 articles each. The codes were then compared and the discrepancies were discussed.
Information on the preprocessing steps and
their respective parameters were extracted. <br><br></h5>"),
),
column(8,
shiny::HTML("<h3>Defining the space from general fMRI articles</h3>"),
img(src='prismadia1.jpg', align = "center", width = "600px", height = "700px"),
shiny::HTML("<h3>Defining the forking paths of graph fMRI studies</h3>"),
img(src='prismadia2.jpg', align = "center", width = "600px", height = "850px")
),
# column(4, # Display the second image and caption in a 4-column layout
# shiny::HTML("<h3>Defining the forking paths of graph fMRI studies</h3>"),
# img(src='prisma2.jpg', align = "center", width = "600px", height = "900px")
# )
)
),
tabPanel(
"List of Included Articles (Review 1)", value = "list_paper1",
shiny::HTML("<h5><b>List of included articles for fMRI preprocessing steps (review 1)</b></h5>"),
DT::dataTableOutput("list_paper1")
),
tabPanel(
"List of Included Articles (Review 2)", value = "list_paper2",
shiny::HTML("<h5><b>List of included articles for graph fMRI and behavior studies (review 2)</b></h5>"),
DT::dataTableOutput("list_paper")
),
tabPanel(
"List of Steps", value = "list_steps",
shiny::HTML("<h5><b>List of identified steps</b></h5>"),
DT::dataTableOutput("list_steps")
),
tabPanel(
"List of Parameters", value = "list_parameters",
shiny::HTML("<h5><b>List of identified parameters</b></h5>"),
DT::dataTableOutput("list_decisions")
)
)
) # Closes the mainPanel
),
##########################
### Steps ###
##########################
tabPanel("Steps", value = "WH",
tabsetPanel(type = "tabs",
tabPanel(width = 12,
"Aggregated Pipelines",
sidebarLayout(
sidebarPanel( width = 3,
shiny::HTML("<h5><b>Explore the aggregated preprocessing
pipelines of all articles in a network fashion.</b><br><br>
Each node (circle) represents a preprocessing step. The
color of a node indicates the processing group the step
belongs to. <br><br>
Steps performed in succession are connected by arrows,
these are edges. The wider the arrow, the higher the number
of articles using this edge. The arrow points in the direction
of the step that is performed afterward. <br><br>
By hovering over a node you can get its name. If you click
on it you get its definition and by how many articles it was
used. By hovering over an edge you can get how many
articles used it. <br><br>
To identify edges of a specific preprocessing step, please
select it in the dropdown below. If you choose all, you will
see edges of all preprocessing steps.<br><br>"
),
selectInput("Node_WP",
label = "Explore edges of step:",
choices = list('All' = list('All'),
'Software',
'Structural Preprocessing' = (c(nodes$Names_vis[nodes$Groups=='Structural_preprocessing'])),
'Functional Preprocessing' = (c(nodes$Names_vis[nodes$Groups=='Functional_preprocessing'])),
'Noise Removal' = (c(nodes$Names_vis[nodes$Groups=='Noise_removal'])),
'FC Definition' = (c(nodes$Names_vis[nodes$Groups=='FC_def'])),
'Graph Analysis' = (c(nodes$Names_vis[nodes$Groups=='Graph_analysis']))),
selected = "All"
),
sliderInput("Thr", "Threshold article",
min = 0, max = 99,
value = 33
),
shiny::HTML("<h5>Move the threshold to only see edges used by more artciles than the threshold.</h5>"),
), # Closes sidebarPanel
mainPanel( width = 9,
forceNetworkOutput(outputId = "WP", width = "100%", height = "700px")
) # Closes the mainPanel
) # Closes the sidebarLayout
),
tabPanel(width = 12,
"Individual Step",
sidebarLayout(
sidebarPanel( width = 3,
shiny::HTML("<h5><b>Explore the individual step.</b><br><br>
Please select a specific step from drop-down menu. The list
of articles used the selected steps will be available
on the table in the main panel. <br><br>"
),
selectInput("select_IS",
label = "Select the step:",
choices = list('Software',
'Structural Preprocessing' = (c(nodes$Names_vis[nodes$Groups=='Structural_preprocessing'])),
'Functional Preprocessing' = (c(nodes$Names_vis[nodes$Groups=='Functional_preprocessing'])),
'Noise Removal' = (c(nodes$Names_vis[nodes$Groups=='Noise_removal'])),
'FC Definition' = (c(nodes$Names_vis[nodes$Groups=='FC_def'])),
'Graph Analysis' = (c(nodes$Names_vis[nodes$Groups=='Graph_analysis']))),
selected = "All"
),
), # Closes sidebarPanel
mainPanel(
fluidRow(
column(12, plotOutput("plot_IS_crowd", width = "100%",
height = "700px")),
column(12, textOutput("selected_IS")),
column(12, DT::dataTableOutput("table_IS"))
),
) # Closes the mainPanel
) # Closes the sidebarLayout
),
tabPanel(
"Combination",
sidebarPanel( width = 3,
shiny::HTML("<h5><b>Explore pairs of preprocessing steps used in
combination. </b><br><br>
Select a step from the dropdown below to see which steps were are
used in conjunction with this step. <br><br></h5>"),
selectInput("selectDecisionYN",
label = "Explore combinations of step:",
choices = list('Software',
'Structural Preprocessing' = (c(nodes$Names_vis[nodes$Groups=='Structural_preprocessing'])),
'Functional Preprocessing' = (c(nodes$Names_vis[nodes$Groups=='Functional_preprocessing'])),
'Noise Removal' = (c(nodes$Names_vis[nodes$Groups=='Noise_removal'])),
'FC Definition' = (c(nodes$Names_vis[nodes$Groups=='FC_def'])),
'Graph Analysis' = (c(nodes$Names_vis[nodes$Groups=='Graph_analysis']))),
selected = "Software"
),
shiny::HTML("<h5>Lollipop plot of the number of preprocessing steps use together with
the step selected above. Selected step in red font. Color
indicates the preprocessing group.</h5>"),
),
mainPanel(
fluidRow(
column(3),
column(6, plotOutput("plot_YN", height = 600, width = "100%")),
column(3)
)
)
),
tabPanel(
"Order",
sidebarPanel( width = 3,
shiny::HTML("<h5><b>Investigate the order of preprocessing steps.</b><br><br>
Select a preprocessing step from the dropdown below to see which
preprocessing steps were performed AFTER the selected one.<br><br></h5>"),
selectInput("selectDecisionOR",
label = "Explore steps performed after step:",
choices = list('Software',
'Structural Preprocessing' = (c(nodes$Names_vis[nodes$Groups=='Structural_preprocessing'])),
'Functional Preprocessing' = (c(nodes$Names_vis[nodes$Groups=='Functional_preprocessing'])),
'Noise Removal' = (c(nodes$Names_vis[nodes$Groups=='Noise_removal'])),
'FC Definition' = (c(nodes$Names_vis[nodes$Groups=='FC_def'])),
'Graph Analysis' = (c(nodes$Names_vis[nodes$Groups=='Graph_analysis']))),
selected = "Software"
),
shiny::HTML("<h5>Lollipop plot of the number of processing steps
used after the selected step. Selected step in red font.
Color indicates the preprocessing group.</h5>"),
),
mainPanel(
fluidRow(
column(3),
column(6, plotOutput("plot_OR", height = 600, width = "100%")),
column(3)
)
)
)
)
),
##########################
### Steps: Parameters ###
##########################
tabPanel("Steps: Parameters", value = "fa",
sidebarPanel( width = 3,
shiny::HTML("<h5><b>Explore the distribution of parameters chosen by
different articles.</b><br></h5>"),
selectInput("selectGroup",
label = "Explore the chosen parameters of step:",
choices = c(unique(nodes_op$Groups_vis)),
selected = "Software"
),
shiny::HTML("<h5>Lollipop plot of the number of articles using
various parameters of the selected step.</h5>"),
uiOutput("selectDecision"),
),
mainPanel(
fluidRow(
column(5, plotOutput("plot_group_decision", height = 600, width = "100%")),
column(7, textOutput("selected_decision")),
column(7, DT::dataTableOutput("table"))
),
),
),
##########################
### Individual Article ###
##########################
tabPanel("Individual Article", value = "IP",
tabsetPanel(type = "tabs",
tabPanel(
"Step Visualization",sidebarLayout(
sidebarPanel( width = 3,
shiny::HTML("<h5><b>Visualize the preprocessing steps taken by a
specific article.</b><br><br>
Select the key of the article in the dropdown below to get
a visualization of the preprocessing steps and to generate a
table of the preprocessing steps. You can
find the key of each study in the Database tab.<br></h5>"),
selectInput("selectPapers",
label = "Select article:",
choices = c(dat$Key),
selected = "1"
),
), # Closes sidebarPanel
mainPanel( width = 8,
textOutput("selected_paper"),
DT::dataTableOutput("table_step"),
plotOutput("plot", width = "100%")
) # Closes the mainPanel
)
),
tabPanel(
"Parameter Visualization",
sidebarLayout(
sidebarPanel( width = 3,
shiny::HTML("<h5><b>Visualize the parameters of preprocessing steps taken by a
specific article.</b><br><br>
Select the code of the article in the dropdown below to get
a visualization of the parameters of the preprocessing steps and to generate a
table of the parameters. You can
find the code of each study in the Database tab.<br></h5>"),
selectInput("selectPapers_cv",
label = "Select article:",
choices = c(dat_op$Key),
selected = "1"
),
), # Closes sidebarPanel
mainPanel( width = 8,
textOutput("selected_paper_cv"),
DT::dataTableOutput("table_option"),
plotOutput("plot_cv", width = "100%")
) # Closes the mainPanel
) # Closes the sidebarLayout
)
)
),
##########################
### Your Own Pipeline ###
##########################
tabPanel("Your Own Pipeline", value = "DIY",
sidebarLayout(
sidebarPanel( width = 3,
shiny::HTML("<h5><b>Construct your preferred pipeline for fMRI data
preprocessing</b><br><br>
Select the step you want to include with the dropdown below. You may also
select a specific parameter or any of the available ones. You can add and
delete steps with the respective buttons. <br><br>
You can count the number of studies that have used the same pipeline and
obtain a table by clicking count. You may specify whether the order of
their pipeline should be considered. If this parameter is disabled, the a
lgorithm will identify all articles that have employed the selected steps
regardless of the order.<br><br>
A plot of the distribution of the pipeline usage is also shown. The grey
bars are the number of total articles for each yeat while the blue line
represents the number of articles used the pipelines for each year. <br></h5>"),
selectInput("selectStep_DIY",
label = "Select the step you want to include",
choices = list('Software',
'Structural Preprocessing' = (c(nodes$Names_vis[nodes$Groups=='Structural_preprocessing'])),
'Functional Preprocessing' = (c(nodes$Names_vis[nodes$Groups=='Functional_preprocessing'])),
'Noise Removal' = (c(nodes$Names_vis[nodes$Groups=='Noise_removal'])),
'FC Definition' = (c(nodes$Names_vis[nodes$Groups=='FC_def'])),
'Graph Analysis' = (c(nodes$Names_vis[nodes$Groups=='Graph_analysis']))),
selected = "Software"
),
uiOutput("selectDecision_DIY"),
actionButton("add",
label = "Add",
icon = icon("arrow-circle-right", class = "fa-2x"),
width= "100px", height= "40px"
),
actionButton("delete",
label = "Delete",
icon = icon("arrow-circle-left", class = "fa-2x"),
width= "100px", height= "40px"
),
shiny::HTML("<h6>Click this Order button if you want to take the order
of the steps into consideration.</h6>"),
materialSwitch(inputId = "order",
label = "order",
status = "success",
right = T,
value = T
),
actionButton("count",
label = "Count",
icon = icon("arrow-circle-right", class = "fa-2x"),
width= "100px", height= "40px"
),
downloadButton('download',"Download the table",
width= "100px", height= "40px"
),
shiny::HTML("<h5>Information here</h5>"),
), # Closes sidebarPanel
mainPanel(
DT::DTOutput("table_DIY"),
fluidRow(style = "height:100px;"),
fluidRow(
column(12, textOutput("counted_paper")),
column(12, plotOutput("plot_time", width = "100%")),
fluidRow(style = "height:50px;"), # Add this line
column(12, DT::DTOutput("table_DIY2")),
),
) # Closes the mainPanel
) # Closes the sidebarLayout
),
##########################
### About ###
##########################
tabPanel("About", value = "about", icon = icon("info-circle"),
column(1),
column(10,
shiny::HTML("<h3>The METEOR project is based at the University of Oldenburg funded
by priority program <a href='https://www.meta-rep.uni-muenchen.de'> META-REP</a>
(SPP 2317). Meta-REP involves 15 individual projects with 50+ scholars analyzing
and optimizing replicability in the Behavioral, Social, and Cognitive Sciences.</h3><br>
<h2><center>Our team</center></h2><br>")
),
# TEAM BIO
fluidRow(
style = "height:50px;"),
fluidRow(
column(2),
# Andrea
column(2,
div(class="panel panel-default",
div(class="panel-body", width = "600px",
align = "center",
div(
tags$img(src = "andrea2.jpg",
width = "45px", height = "57px")
),
div(
tags$h5("Hildebrandt, Andrea, Prof. Dr. rer. nat."),
tags$h6( tags$i("Project Investigator"))
),
div(
"Professor for Psychological Methods and Statistics, Carl von Ossietzky Universitat Oldenburg."
)
)
)
),
# Stefan
column(2,
div(class="panel panel-default",
div(class="panel-body", width = "600px",
align = "center",
div(
tags$img(src = "stefan.jpg",
width = "50px", height = "70px")
),
div(
tags$h5("Debener, Stefan, Prof. Dr. rer. nat."),
tags$h6( tags$i("Project Investigator"))
),
div(
"Professor for Neuropsychology, Carl von Ossietzky Universitat Oldenburg."
)
)
)
),
# Carsten
column(2,
div(class="panel panel-default",
div(class="panel-body", width = "600px",
align = "center",
div(
tags$img(src = "carsten.jpg",
width = "50px", height = "50px")),
div(
tags$h5("Giessing, Carsten, Dr. rer. nat."),
tags$h6( tags$i("Project Investigator"))
),
div(
"Senior Scientist in Biological Psychology, Carl von Ossietzky Universitat Oldenburg."
)
)
)
),
# Christiane
column(2,
div(class="panel panel-default",
div(class="panel-body", width = "600px",
align = "center",
div(
tags$img(src = "christiane2.jpg",
width = "58px", height = "60px")),
div(
tags$h5("Thiel, Christiane, Prof. Dr. rer. nat."),
tags$h6( tags$i("Project Investigator"))
),
div(
"Professor for Biological Psychology, Carl von Ossietzky Universitat Oldenburg."
)
)
)
),
column(2)
),
fluidRow(
column(2),
# Nadine
column(2,
div(class="panel panel-default",
div(class="panel-body", width = "600px",
align = "center",
div(
tags$img(src = "nadine.jpg",
width = "40px", height = "55px")),
div(
tags$h5("Jacobsen, Nadine, Dr. rer. nat."),
tags$h6( tags$i("Postdoctoral Fellow"))
),
div(
"Carl von Ossietzky Universitat Oldenburg."
)
)
)
),
# Daniel
column(2,
div(class="panel panel-default",
div(class="panel-body", width = "600px",
align = "center",
div(
tags$img(src = "Daniel.jpg",
width = "40px", height = "50px")),
div(
tags$h5("Kristanto, Daniel, PhD."),
tags$h6( tags$i("Postdoctoral Fellow"))
),
div(
"Carl von Ossietzky Universitat Oldenburg."
)
)
)
),
column(2,
div(class="panel panel-default",
div(class="panel-body", width = "600px",
align = "center",
div(
tags$img(src = "cassie.jpg",
width = "50px", height = "68px")),
div(
tags$h5("Short, Cassie, PhD."),
tags$h6( tags$i("Postdoctoral Fellow"))
),
div(
"Carl von Ossietzky Universitat Oldenburg."
)
)
)
),
column(2,
div(class="panel panel-default",
div(class="panel-body", width = "600px",
align = "center",
div(
tags$img(src = "micha.jpg",
width = "50px", height = "68px")),
div(
tags$h5("Burkhardt, Micha Msc."),
tags$h6( tags$i("Doctoral student"))
),
div(
"Carl von Ossietzky Universitat Oldenburg."
)
)
)
),
),
fluidRow(style = "height:150px;")
)
)
)