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ui.R
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ui.R
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ui <-
navbarPage("CiliaMiner", collapsible = TRUE, inverse = TRUE, theme = shinytheme("simplex"),
#Home page
{tabPanel("Homepage",
tags$head(includeHTML(("google-analytics/google-analytics.html"))),
tags$head(
tags$link(rel = "icon", type = "image/png", sizes = "32x32", href = "/favicon-32x32.png"),
tags$link(rel = "shortcut icon", href = "favicon.png"),
tags$link(rel = "icon", type = "image/png", sizes = "16x16", href = "/favicon-16x16.png"),
tags$style(HTML(".navbar {font-size:large;")),
tags$style(HTML(".navbar .navbar-nav {float:left; margin: 0; display:flex; width: 90%; justify-content: space-between; } ")),
tags$style(HTML(".navbar-brand {font-size: large;"))),
fixedRow(
column(6,
p(strong("CiliaMiner"), style = "font-size:50px; color: #FF4500"),
headerPanel(h1("",align = "center")),
tags$head(tags$style("#search_table table {background-color: #74b3ce; }", media="screen", type="text/css")),
tags$head(tags$style("#search_cilia_table table {background-color: #74b3ce ; }", media="screen", type="text/css")),
tabsetPanel(type= "pills",
#Gene Search Input
tabPanel("Gene Search",column(11,align="left",
#Search Box
searchInput(inputId = "search",label = "",
placeholder = "Search by Human Gene Name and Gene ID",
btnSearch = icon("search"),
btnReset = icon("remove",verify_fa = FALSE),
width = "90%",),
tags$style(type="text/css", "#search_text {font-size: 160%;height:50px}"),
tags$style(type="text/css", "#search_search {font-size: x-large;height:50px}"),
tags$style(type="text/css", "#search_reset {font-size: x-large;height:50px}"),
tags$style(type="text/css", ".nav-pills {font-size: x-large;}"),
HTML(rep("<br/><br/>", 1)),
#Gene Search Result Table
fixedRow(box(width = 12,background = "orange",status = 'primary',align = "left",
dataTableOutput('search_table'),br(),style = "font-size:100%; width:100%")),)),
#Ciliopathy Search Input
tabPanel("Ciliopathy Search",column(12, align = "left",
#Search Box
autocomplete_input(id = "disease_search", label = "", unique(homosapiens_ciliopathy$Ciliopathy),placeholder = "Search by Disease Name",
create = TRUE,max_options = 3,hide_values = FALSE,width = "80%"),
tags$style(type="text/css", "#disease_search {font-size: x-large;height:50px}"),
#Popover for Search Box
bsPopover(id = "disease_search", content = "Select a ciliopathy type", title = "", placement = "right",trigger = "hover",
options = list(container = "body")),
HTML(rep("<br/><br/>", 1)),
#Ciliopathy Search Result Table
fixedRow(column(width = 12,align = "left",dataTableOutput('search_cilia_table'),br(),style = "font-size:100%; width:100%")),),
)
),
),
#Homepage graphs are bubble, piechart, and barplot respectively.
column(6,align = "center",verticalLayout(HTML(rep("<br/><br/><br/><br/>", 1)),shinycssloaders::withSpinner(plotlyOutput("bubble",height = "100%",width = "100%"),type = 5,color = "#C81E1E") ,br(),
plotlyOutput("piechart",height = "50%"),br(),
plotlyOutput("barplot",height = "50%")),
),
))},
#Ciliopathy Names Page
{tabPanel("Ciliopathy Names",
fluidPage(
tabsetPanel(
#Pure Ciliopathies Panel
{tabPanel("Primary Ciliopathies",
#Tags for tooltip
tags$head(tags$style(HTML("#Digestive .tooltip {width: 300px;}"))),
tags$head(tags$style(HTML( ".dropdown-toggle .css {background-color: red; }" ))),
br(),
p("This website contains a list of human genes for primary ciliopathies. The localization of protein products of disease-associated genes, articles, and disease/gene-related extensions are give"),
br(),
#sidebar
sidebarLayout(
sidebarPanel(
#Pure Ciliopathy input
pickerInput(inputId = "namepures",label = "Choose a pure ciliopathy",
choices = c("All Pure Ciliopathy",unique(purelist$Ciliopathy)),options = list('live-search' = TRUE,size = 7,'style' = "btn-link")),
#Heatmap input
multiInput(
inputId = "heatmaps", label = "Choose a Pure Ciliopathy for Heatmap:",
choices = unique(purelist$Ciliopathy),
selected = "Standart"),
actionButton("all", "All"),
actionButton("none", "Clear"),
div(style = "margin-top: 30px"),
p(strong(" Disease Symptom Summary"),style = "font-size: 200%;text-align:center;color:#bd552e;"),
br(),
#Disease Symptom Summary Figures.
splitLayout(htmlOutput("Aural",align = "center"),htmlOutput("neural",align = "center"),htmlOutput("ophthalmic",align = "center"),htmlOutput("skeletal",align = "center")),
splitLayout(htmlOutput("respiratory",align = "center"),htmlOutput("hormonal", align = "center"),htmlOutput("Reproductive",align = "center"),htmlOutput("Facial",align = 'center')),
splitLayout(htmlOutput("cerebral",style = "text-align:center;width:initial"),htmlOutput("Renal",style = "text-align:center;width:initial"),htmlOutput("Coronary",style = "text-align:center;width:initial"),htmlOutput("Nasal",style = "text-align:center;width:initial")),
splitLayout(htmlOutput("liver",style = "text-align:center;width:initial"),htmlOutput("Cognitive",style = "text-align:center;width:initial"),htmlOutput("Digestive",style = "text-align:center;width:initial"),htmlOutput("Organ",style = "text-align:center;width:initial")),
#Disease Symptom Summary Figures' Popovers
bsPopover(id = "cerebral", content = "Cerabral Anomalies", title = "", placement = "top",trigger = "hover"),
bsPopover(id = "Renal", content = "Renal Anomalies", title = "", placement = "top",trigger = "hover"),
bsPopover(id = "Coronary", content = "Coronary and Vascular Anomalies", title = "", placement = "top",trigger = "hover"),
bsPopover(id = "Nasal", content = "Nasal Anomalies", title = "", placement = "left",trigger = "hover"),
bsPopover(id = "liver", content = "Liver Anomalies", title = "", placement = "top",trigger = "hover"),
bsPopover(id = "Cognitive", content = "Cognitive Anomalies", title ="", placement = "top", trigger = "hover"),
bsPopover(id = "Digestive", content = "Digestive Anomalies", title ="", placement = "top", trigger = "hover"),
bsPopover(id = "Organ", content = "Organ Anomalies", title ="", placement = "left", trigger = "hover"),
width =3),
mainPanel(
#Result Table output
fluidRow(column(6,dataTableOutput('namepuresout'),h5("*: Uncertain localisation data from related paper"),style = "font-size:100%; width:100%")),
br(),
p("The Disease/Gene Reference column in the table offers a PubMed ID relating to associated diseases and genes, whilst the ciliary localization column displays data from mammalian and worm studies."),
#Heatmap Output
shinycssloaders::withSpinner(plotlyOutput('namepuresout2'),type = 5,color = "#C81E1E"),
br(),
br(),
br(),
#Explanation of the represented diseases
textOutput("outputtext"),
),
position = c("left"),
fluid = TRUE
))},
#Secondary Ciliopathies Panel
{tabPanel("Secondary Diseases",
br(),
p("This website contains a list of human genes for secondary diseases. The localization of protein products of disease-associated genes, articles, and disease/gene-related extensions are give"),
br(),
sidebarLayout(
sidebarPanel(
#Secondary Ciliopathy input
pickerInput(inputId = "namesecondary",label = "Choose a secondary ciliopathy",
choices = c("All Secondary Ciliopathy",unique(secondarylist$Ciliopathy)),options = list('live-search' = TRUE,size = 7,'style' = "btn-link"),
choicesOpt = list( content = stringr::str_trunc(c("All Secondary Ciliopathy",unique(secondarylist$Ciliopathy)), width = 70)
)),
#Disease heatmap input
multiInput(
inputId = "heatmaps2", label = "Choose Secondary Ciliopathy for Heatmap:",
choices = unique(secondarylist$Ciliopathy),
selected = "Standart"),
actionButton("all2", "All"),
actionButton("none2", "Clear"),
div(style = "margin-top: 30px"),
p(strong(" Disease Symptom Summary"),style = "font-size: 200%;text-align:center;color:#bd552e;"),
br(),
#Disease Symptom Summary Figures.
splitLayout(htmlOutput("Aural1",align = "center"),htmlOutput("neural1",align = "center"),htmlOutput("ophthalmic1",align = "center"),htmlOutput("skeletal1",align = "center")),
splitLayout(htmlOutput("respiratory1",align = "center"),htmlOutput("hormonal1", align = "center"),htmlOutput("Reproductive1",align = "center"),htmlOutput("Facial1",align = 'center')),
splitLayout(htmlOutput("cerebral1",style = "text-align:center;width:initial"),htmlOutput("Renal1",style = "text-align:center;width:initial"),htmlOutput("Coronary1",style = "text-align:center;width:initial"),htmlOutput("Nasal1",style = "text-align:center;width:initial")),
splitLayout(htmlOutput("liver1",style = "text-align:center;width:initial"),htmlOutput("Other",style = "text-align:center;width:initial"),htmlOutput("Digestive1",style = "text-align:center;width:initial"),htmlOutput("Organ1",style = "text-align:center;width:initial")),
#Disease Symptom Summary Figures' Popovers
bsPopover(id = "cerebral1", content = "Cerabral Anomalies", title = "", placement = "top",trigger = "hover"),
bsPopover(id = "Renal1", content = "Renal Anomalies", title = "", placement = "top",trigger = "hover"),
bsPopover(id = "Coronary1", content = "Coronary and Vascular Anomalies", title = "", placement = "top",trigger = "hover"),
bsPopover(id = "Nasal1", content = "Nasal Anomalies", title = "", placement = "left",trigger = "hover"),
bsPopover(id = "liver1", content = "Liver Anomalies", title = "", placement = "top",trigger = "hover"),
bsPopover(id = "Digestive1", content = "Digestive Anomalies", title ="", placement = "top", trigger = "hover"),
bsPopover(id = "Organ1", content = "Organ Anomalies", title ="", placement = "left", trigger = "hover"),
width =3),
#Secondary Ciliopathies Table Output
mainPanel(
fluidRow(column(7,dataTableOutput('namesecondsout'),style = "font-size:100%; width:100%")),
br(),
p("The Disease/Gene Reference column in the table offers a PubMed ID relating to associated diseases and genes, whilst the ciliary localization column displays data from mammalian and worm studies."),
shinycssloaders::withSpinner(plotlyOutput('namesecondsout2'),type = 5,color = "#C81E1E"),
br(),
br(),
br(),
#Explanation of the represented diseases
textOutput("outputtext2"),
),
position = c("left"),
fluid = TRUE
))},
#Motile Ciliopathies Panel
{tabPanel("Motile Ciliopathies",
br(),
p("This website lists human genes of motile ciliopathies. The localization of protein products of disease-associated genes, articles, and disease/gene-related extensions are given."),
br(),
sidebarLayout(
sidebarPanel(
#Motile Ciliopathy input
pickerInput(inputId = "name_motile",label = "Choose a secondary ciliopathy",
choices = c("All Motile Ciliopathy",unique(motile$Ciliopathy)),options = list('live-search' = TRUE,size = 7,'style' = "btn-link"),
choicesOpt = list( content = stringr::str_trunc(c("All Motile Ciliopathy",unique(motile$Ciliopathy)), width = 70))),
br(),
p(strong(" Disease Symptom Summary"),style = "font-size: 200%;text-align:center;color:#bd552e;"),
#Disease Symptom Summary Figures.
splitLayout(htmlOutput("Aural2",align = "center"),htmlOutput("neural2",align = "center"),htmlOutput("ophthalmic2",align = "center"),htmlOutput("skeletal2",align = "center")),
splitLayout(htmlOutput("respiratory2",align = "center"),htmlOutput("hormonal2", align = "center"),htmlOutput("Reproductive2",align = "center"),htmlOutput("Facial2",align = 'center')),
splitLayout(htmlOutput("cerebral2",style = "text-align:center;width:initial"),htmlOutput("Renal2",style = "text-align:center;width:initial"),htmlOutput("Coronary2",style = "text-align:center;width:initial"),htmlOutput("Nasal2",style = "text-align:center;width:initial")),
splitLayout(htmlOutput("liver2",style = "text-align:center;width:initial"),htmlOutput("Other2",style = "text-align:center;width:initial"),htmlOutput("Digestive2",style = "text-align:center;width:initial"),htmlOutput("Organ2",style = "text-align:center;width:initial")),
#Disease Symptom Summary Figures' Popovers
bsPopover(id = "cerebral2", content = "Cerabral Anomalies", title = "", placement = "top",trigger = "hover"),
bsPopover(id = "Renal2", content = "Renal Anomalies", title = "", placement = "top",trigger = "hover"),
bsPopover(id = "Coronary2", content = "Coronary and Vascular Anomalies", title = "", placement = "top",trigger = "hover"),
bsPopover(id = "Nasal2", content = "Nasal Anomalies", title = "", placement = "left",trigger = "hover"),
bsPopover(id = "liver2", content = "Liver Anomalies", title = "", placement = "top",trigger = "hover"),
bsPopover(id = "Digestive2", content = "Digestive Anomalies", title ="", placement = "top", trigger = "hover"),
bsPopover(id = "Organ2", content = "Organ Anomalies", title ="", placement = "left", trigger = "hover"),
width = 3),
mainPanel(
fluidRow(column(7,shinycssloaders::withSpinner(dataTableOutput('motile_table'),type = 5,color = "#C81E1E"),
style = "font-size:100%; width:100%")),
shinycssloaders::withSpinner(plotlyOutput('heatmap_motile'),type = 5,color = "#C81E1E"),
),position = c("left"),
fluid = TRUE ))},
#Atypical Ciliopathies Panel
{tabPanel("Atypical Ciliopathies",
br(),
p("Unclassified ciliopathy disease-related genes have been collected on this page using the search term 'ciliopathy'."),
br(),
#Atypical Ciliopathies Table Output
mainPanel(fluidRow(column(6,dataTableOutput('atypical_ciliopathy'),style = "font-size:100%; width:150%"))))},
#Potential Ciliopathies Panel
tabPanel("Potential Ciliopathy Genes",
br(),
p("The list of candidate ciliopathy genes in this subtab includes genes that are primarily found in the cilia as well as genes that are associated with the formation and maintenance of cilia."),
br(),
#Potential Ciliopathies Table and Heatmap output
mainPanel(splitLayout(dataTableOutput('potential_ciliopathy_genes'),p(),
plotlyOutput("potential_ciliopathy_genes_heatmap",height = '600%'),cellWidths = c("75%","5%","73%"),
cellArgs = list(style = "padding:10px")
),h5("*: Uncertain ciliary process from related paper")
)
))))},
#Gene Search Page
{
tabPanel("Gene Search",fixedRow(column(12,
p(strong("Search for a gene to list associated ciliopathy disorder(s)"),align = "middle", style = "font-size:30px; color: #ff7f0e"),
tabPanel("Gene Search",column(12,align="middle",
#Search Box
searchInput(inputId = "search_gene",label = "",
placeholder = "Search by Gene Name, Ensembl Gene ID or Gene ID",
btnSearch = icon("search"),
btnReset = icon("remove",verify_fa = FALSE),
width = "50%",),
tags$style(type="text/css", "#search_text {font-size: 160%;height:50px}"),
tags$style(type="text/css", "#search_search {font-size: x-large;height:50px;color: #ff7f0e}"),
tags$style(type="text/css", "#search_reset {font-size: x-large;height:50px;color: #ff7f0e}"),
tags$style(type="text/css", ".nav-pills {font-size: x-large;}"),
HTML(rep("<br/><br/>", 1)),
#Gene Search Result Table
fluidRow(column(11,align = "left",dataTableOutput('search_gene_table') ,style = "font-size:100%; width:100%")),))
)))
},
#Ciliopathy Gene Orthologs Page
{
tabPanel("Ciliopathy Genes and Orthologs",
br(),
tabPanel("Organisms"),
fluidPage(
tabsetPanel(
#Homo sapiens Genes and Orthologs
tabPanel(em("Homo sapiens"),
br(),
p("This page lists all human genes based on both pure and secondary ciliopaties with localisation referances.
The Disease/Gene Reference column in the table offers a PubMed ID relating to associated diseases and genes, whilst the ciliary localization column displays data from mammalian and worm studies."),
br(),
fluidPage(
column(6,
#Homo sapiens Table Output
div(DT::dataTableOutput("homosapiens_ciliopathy")),h5("*: Uncertain localisation data from related paper"),
style = "font-size:100%; width:100%"))),
#Mus musculus Genes and Orthologs
tabPanel(em("Mus musculus"),
br(),
p("This page lists small house mouse ciliopathy genes which are orthologs with human genes.
The Disease/Gene Reference column in the table offers a PubMed ID relating to associated diseases and genes, whilst the ciliary localization column displays data from mammalian and worm studies."),
br(),
fluidPage(
column(6,
#Mus musculus Table Output
div(DT::dataTableOutput("ortholog_human_mmusculus")),h5("*: Uncertain localisation data from related paper"),
style = "font-size:100%; width:100%"))),
#Danio rerio Genes and Orthologs
tabPanel(em("Danio rerio"),
br(),
p("This page lists zebrafish ciliopathy genes which are orthologs with human genes.
The Disease/Gene Reference column in the table offers a PubMed ID relating to associated diseases and genes, whilst the ciliary localization column displays data from mammalian and worm studies."),
br(),
fluidPage(
column(6,
#Danio rerio Table Output
div(DT::dataTableOutput("ortholog_human_drerio")),h5("*: Uncertain localisation data from related paper"),
style = "font-size:100%; width:100%"))),
#Xenopus laevis Genes and Orthologs
tabPanel(em("Xenopus laevis"),
br(),
p("This page lists clawed frog ciliopathy genes which are orthologs with human genes.
The Disease/Gene Reference column in the table offers a PubMed ID relating to associated diseases and genes, whilst the ciliary localization column displays data from mammalian and worm studies."),
br(),
fluidPage(
column(6,
#Xenopus laevis Table Output
div(DT::dataTableOutput('ortholog_human_xlaevis')),h5("*: Uncertain localisation data from related paper"),
style = "font-size:100%; width:100%")
)),
#Drosophila melanogaster Genes and Orthologs
tabPanel(em("Drosophila melanogaster"),
br(),
p("This page lists fruit fly ciliopathy genes which are orthologs with human genes.
The Disease/Gene Reference column in the table offers a PubMed ID relating to associated diseases and genes, whilst the ciliary localization column displays data from mammalian and worm studies."),
br(),
fluidPage(
column(6,
#Drosophila melanogaster Table Output
div(DT::dataTableOutput("ortholog_human_drosophila")),h5("*: Uncertain localisation data from related paper"),
style = "font-size:100%; width:100%"))),
#Caenorhabditis elegans Genes and Orthologs
tabPanel(em("Caenorhabditis elegans"),
br(),
p("This page lists nematode worm ciliopathy genes which are orthologs with human genes.
The Disease/Gene Reference column in the table offers a PubMed ID relating to associated diseases and genes, whilst the ciliary localization column displays data from mammalian and worm studies."),
br(),
fluidPage(
column(6,
#Caenorhabditis elegans Table Output
div(DT::dataTableOutput("ortholog_human_celegans")),
style = "font-size:100%; width:100%"))),
#Chlamydomonas reinhardtii Genes and Orthologs
tabPanel(em("Chlamydomonas reinhardtii"),
br(),
p("This page lists unicellular green algea ciliopathy genes which are orthologs with human genes.
The Disease/Gene Reference column in the table offers a PubMed ID relating to associated diseases and genes, whilst the ciliary localization column displays data from mammalian and worm studies."),
br(),
fluidPage(
column(6,
#Chlamydomonas reinhardtiis Table Output
div(DT::dataTableOutput("ortholog_human_creinhardtii")),
style = "font-size:100%; width:100%")))
)))},
#Symptomes and Diseases Page
{
tabPanel("Symptoms and Diseases",
fluidPage(
shinyjs::useShinyjs(),
br(),
br(),
#Syptoms Select Box
sidebarLayout(
sidebarPanel(
radioButtons("search_option","Choose Search Option: ",
c("Disease Based" = "disease_bsd",
"Symptoms Based" = "symptom_bsd")),
selectInput("disease_bsd_search","Choose a Disease",
choices = unique(list_Df$Ciliopathy)),
autocomplete_input(id = 'symptome', label = 'Search a symptom', placeholder = "Search by Symptom Name",
unique(c(clinical_feature_pure$Clinical_features,clinical_feature_secondary$Clinical_features)),
create = TRUE,max_options = 8,hide_values = FALSE,width = "100%"),
selectInput("symptome2",'Choose a ciliopathy',choices = NULL),
radioButtons("disp", "Display Type:",
c("Normal" = "norm",
"Just Name" = "name")),
width =3),
mainPanel(
fluidRow(column(6,div(DT::dataTableOutput("primary_symp")),style = "font-size:100%; width:100%"))
),
position = c("left"),
fluid = TRUE
)))},
#Submit Your Gene Page
{
tabPanel("Submit Your Gene",fluidPage(
#Submit Gene Form
tags$iframe(src = 'https://forms.gle/knog1LnXVnDW57fL6',
width = '50%',
style="height: 100vh;",
id = "google_form",
frameborder = 0,
marginheight = 0)),align = "center")
},
#About Page
{
tabPanel("About",
fluidPage(
h2(strong("CiliaMiner")),
div(style = "margin-left: 5%; margin-right: 5%;",
h4("The 'CiliaMiner' database fills the requirement for an
all-encompassing database to gather data on ciliopathies and their associated genes.
The number of ciliopathy diseases and associated genes has rapidly increased over the past
20 years, making it difficult for researchers to get reliable and current information from
many sources. The authors create the CiliaMiner database as a solution to this problem and
as a useful tool for ciliopathies researchers, physicians, and fundamental scientists."),
h4(strong("Comprehensive Gene and Disease Information: "),"CiliaMiner offers a comprehensive list of
ciliopathy diseases both known and unknown, along with associated symptoms and gene names.
The database is divided into primary, secondary, and motile ciliopathies, with each
category having details on certain genes and diseases."),
h4(strong("Data on Subcellular Localization:"), "The database contains details on the
subcellular localization of proteins that are produced by genes that cause disease.
The study, for instance, shows that specific proteins are found in cilia, basal bodies,
transition zones, and other cellular compartments."),
h4(strong("Tools for Visualization:"), "CiliaMiner provides a number of visualization tools
for side-by-side examination. Users can compare clinical signs and traits across various
ciliopathies using heatmaps. These resources help researchers spot similarities and
distinctions between ciliopathy illnesses."),
h4(strong("Ortholog Information:"), "For researchers working with model organisms,
CiliaMiner provides information about orthologs of human ciliopathy-associated genes in
model species like mice, zebrafish, frogs, fruit flies, and worms. This feature facilitates
the study of ciliopathies in these organisms."),
h4(strong("Continuously Updated:"),"The database will be continually updated to reflect the
most recent data when new discoveries are made and new data becomes available. "),
h4(strong("Potential Candidate Genes:"),"The database not only includes a list of known
ciliopathy genes, but also prospective ciliopathy gene candidates. For researchers
looking for novel genetic connections to ciliopathies, this feature is helpful.
User-Friendly Interface: The CiliaMiner website has a simple user interface with search
options for disease, gene, and symptom names. Users can easily search the database for the
data they require.")),
br(),
h2(strong("Teams behind CiliaMiner")),
div(style = "margin-left: 5%; margin-right: 5%",
h4(a("Sebiha Çevik Kaplan", href = "https://scholar.google.de/citations?user=_o6sKOUAAAAJ",target="_blank")),
h4(a("Oktay İsmail Kaplan",href = "https://scholar.google.com/citations?user=YFzvQQUAAAAJ",target="_blank")),
h4(a("Merve Gül Turan",href = "https://scholar.google.com/citations?user=c7fjHRcAAAAJ",target="_blank")),
h4(a("Mehmet Emin Orhan",href = "https://scholar.google.com.tr/citations?user=74bs5g8AAAAJ",target="_blank"))),
h2(strong("Cite")),
h4("Merve Gül Turan, Mehmet Emin Orhan and others, CiliaMiner: an integrated database for ciliopathy genes
and ciliopathies, Database, Volume 2023, 2023, baad047,",a("https://doi.org/10.1093/database/baad047",
href = "https://doi.org/10.1093/database/baad047",
target = "_blank"))
))}
)