inst/shinyApp/ui.R
In isglobal-brge/ShinyDataSHIELD: Shiny app for DataSHIELD
library(DSI)
library(DSOpal)
library(dsBaseClient)
library(dsOmicsClient)
library(dsSurvivalClient)
library(shinydashboard)
library(shiny)
library(shinyalert)
library(DT)
library(data.table)
library(shinyjs)
library(shinyBS)
library(ggplot2)
library(shinycssloaders)
library(shinyWidgets)
library(stringr)
#library(thematic)
library(fresh)
library(ggthemr)
source("ggeditLiteModule.R", local = TRUE)
# thematic::thematic_shiny()
jscode <- '
$(document).keyup(function(event) {
if ($("#password1").is(":focus") && (event.keyCode == 13)) {
$("#connect_server1").click();
};
if ($("#pat1").is(":focus") && (event.keyCode == 13)) {
$("#connect_server1").click();
}
});
'
jscode_tab <- "
shinyjs.disableTab = function(name) {
var tab = $('.nav li a[data-value=' + name + ']');
tab.bind('click.tab', function(e) {
e.preventDefault();
return false;
});
tab.addClass('disabled');
}
shinyjs.enableTab = function(name) {
var tab = $('.nav li a[data-value=' + name + ']');
tab.unbind('click.tab');
tab.removeClass('disabled');
}
"
css_tab <- "
.nav li a.disabled {
background-color: #aaa !important;
color: #333 !important;
cursor: not-allowed !important;
border-color: #aaa !important;
}"
# Insert Favicon
tags$head(tags$link(rel="shortcut icon", type = "image/x-icon", href="www/favicon.ico"))
options(sass.cache = FALSE)
sass::sass(
sass::sass_file("www/theme.scss"),
output = "www/theme.css"
)
p_color <- fread("www/theme.scss", skip = "$top_bar_colour: ", nrows = 1)
p_color <- substr(colnames(p_color), 18,24)[1]
# Set p_color for withSpinner CSS
options(spinner.color = p_color)
## ui.R ##
sidebar <- dashboardSidebar(
sidebarMenu(
id = "tabs",
uiOutput("userpanel"),
menuItem("Connect to server", tabName = "server_connect"),
hidden(menuItem("Table columns types", tabName = "table_columns_a")),
hidden(menuItem("Descriptive statistics", tabName = "d_statistics")),
hidden(menuItem("Statistic models", tabName = "statistic_models")),
# hidden(menuItem("Mixed statistic models", tabName = "statistic_models_mixed")),
hidden(menuItem("Genomics", tabName = "genomics",
menuSubItem("Analysis with BioConductor", tabName = "vcf_files"),
menuSubItem("Analysis with PLINK", tabName = "plink")
)),
hidden(menuItem("Omics", tabName = "omics",
menuSubItem("LIMMA", tabName = "limma")
))
),
tags$footer(HTML(paste0("<footer>",
"<div class='footer-copyright text-center py-3'>© 2021 - ISGlobal-BRGE. v",
tryCatch({as.character(read.dcf("DESCRIPTION", fields = "Version"))}, # Docker
error = function(w){as.character(read.dcf("../../DESCRIPTION", fields = "Version"))}), # Local
"</div></footer>")),
style = "background-color:transparent;
position:absolute;
bottom:0;")
)
body <- dashboardBody(
tags$head(includeCSS("www/theme.css")),
# use_theme(custom_theme),
useShinyalert(),
useShinyjs(),
extendShinyjs(text = jscode_tab, functions = c("enableTab", "disableTab")),
inlineCSS(css_tab),
# inlineCSS(n_bar_css),
# inlineCSS(tabbox_css),
tabItems(
tabItem(tabName = "server_connect",
tabPanel('server_connect',
fluidRow(
# actionButton("stop", "stop"),
tabBox(
title = p(circleButton("add", size = "sm", icon = icon("plus"), status = "primary"),
circleButton("remove", size = "sm", icon = icon("minus"), status = "primary")
),
id = "tabset1", width = 12,
tabPanel("Server1",
fluidRow(
column(6,
h3("URL"),
textInput("url1", "Opal server", value = "https://opal-demo.obiba.org/")
),
column(6,
h3("Credentials"),
conditionalPanel(
condition = "input.pat_switch1 == true",
passwordInput("pat1", "Personal Access Token"),
),
conditionalPanel(
condition = "input.pat_switch1 == false",
textInput("user1", "User", value = "dsuser"),
tags$head(tags$script(HTML(jscode))),
passwordInput("password1", "Password", value = "P@ssw0rd")
),
materialSwitch(inputId = "pat_switch1", label = "Use Personal Access Token", status = "primary")
)
),
hr(),
fluidRow(
column(6,
hidden(tags$div(id = "tb_1",
materialSwitch(inputId = "tbl_res1", label = "Resources", inline = TRUE, value = T),
tags$span("Tables")
))
),
column(6,
uiOutput("profile_selector1")
)
),
fluidRow(
column(6,
uiOutput("project_selector1"),
),
column(6,
uiOutput("resource_selector1"),
)
),
fluidRow(
column(6,actionButton("connect_server1", "Connect"))
),
hidden(actionButton("add_server1", "Add selected item(s)")),
hidden(actionButton("info_opal_1", "Further information of selection"))
)
)
),
fluidRow(
column(6,
hidden(actionButton("remove_item", "Remove selected item(s)")),
hidden(actionButton("connect_selected", "Connect"))
)
),
dataTableOutput("server_resources_table"),
)
),
tabItem(tabName = "table_columns_a",
fluidRow(
tabBox(width = 12, id = "table_columns_selection",
tabPanel("Available tables", value = "a_tables",
uiOutput("available_tables_cols"),
actionButton("select_tables_cols", "Select tables")
),
tabPanel("Column types", value = "col_tables",
# actionButton("stop","stop"),
DTOutput("column_types_table")
)
)
)
),
tabItem(tabName = "d_statistics",
fluidRow(
tabBox(width = 12, id = "d_statistics_t",
tabPanel("Available tables", value = "a_tables",
uiOutput("available_tables"),
actionButton("select_tables_descr_stats", "Select tables")
),
tabPanel("Summary", value = "summary",
uiOutput("d_statistics_variable_selector_approach"),
uiOutput("d_statistics_variable_selector"),
dataTableOutput("descriptive_summary"),
downloadButton("descriptive_summary_download", "Download")
),
tabPanel("Scatter plot", value = "s_plot",
uiOutput("d_statistics_variable_selector_scatter_approach"),
uiOutput("d_statistics_variable_selector_scatter"),
uiOutput("d_statistics_variable_selector_scatter2"),
withSpinner(plotOutput("d_statistics_scatter_plot")),
downloadButton("d_statistics_scatter_plot_download", "Download plot")
),
tabPanel("Histogram", value = "h_plot",
uiOutput("d_statistics_variable_selector_histogram_approach"),
uiOutput("d_statistics_variable_selector_histogram"),
withSpinner(plotOutput("d_statistics_histogram_plot")),
downloadButton("d_statistics_histogram_plot_download", "Download plot")
),
tabPanel("Heatmap", value = "hm_plot",
uiOutput("d_statistics_variable_selector_heatmap_approach"),
uiOutput("d_statistics_variable_selector_heatmap"),
uiOutput("d_statistics_variable_selector_heatmap2"),
withSpinner(plotOutput("d_statistics_heatmap_plot")),
downloadButton("d_statistics_heatmap_plot_download", "Download plot")
),
tabPanel("Box plot", value = "box_plot",
fluidRow(
column(6,
uiOutput("d_statistics_variable_selector_boxplot_approach"),
uiOutput("d_statistics_variable_selector_boxplot"),
# actionButton("stop", "stop")
),
column(6,
uiOutput("d_statistics_variable_selector_boxplot2"),
uiOutput("d_statistics_variable_selector_boxplot3")
)
),
withSpinner(plotOutput("d_statistics_boxplot_plot")),
ggeditLiteUI("d_statistics_boxplot_plot_edit"),
# downloadButton("d_statistics_boxplot_plot_download", "Download plot")
)
)
)
),
tabItem(tabName = "statistic_models",
fluidRow(
tabBox(width = 12, id = "statistic_models_t",
tabPanel("Available tables", value = "a_tables_sm",
uiOutput("available_tables_sm"),
actionButton("select_tables_sm", "Select tables")
),
tabPanel("Generalized linear model", value = "glm",
fluidRow(
column(6,
textInput("glm_formula", "Input GLM formula:"),
hidden(selectInput("glm_approach", "Select the approach:",
c("Pooled", "Study Level Meta Analysis"))),
actionButton("trigger_formula_help_glm", "Formula input help"),
actionButton("perform_glm", "Perform GLM")
),
column(6,
selectInput("gml_output_family", "Output family:", c("gaussian", "poisson", "binomial")),
actionButton("gml_toggle_variables_table","Toggle variables table"),
)
),
hidden(dataTableOutput("available_variables_type")),
dataTableOutput("glm_results_table"),
hidden(downloadButton("glm_results_table_download", "Download GLM results")),
hidden(selectInput("glm_slma_method", "Meta analysis to visualize", c("Maximum Likelihood",
"REstricted Maximum Likelihood",
"Fixed-Effects meta-analysis"))),
hidden(plotOutput("glm_slma_plot")),
hidden(downloadButton("glm_slma_down", "Download Forestplot"))
),
tabPanel("Mixed effects model", value = "mixed_model",
fluidRow(
column(6,
textInput("glmer_formula", "Input GLMer formula:"),
actionButton("trigger_formula_help_glmer", "Formula input help"),
actionButton("perform_glmer", "Perform GLMer")
),
column(6,
selectInput("gmler_output_family", "Output family:", c("poisson", "binomial")),
actionButton("gmler_toggle_variables_table","Toggle variables table")
)
),
hidden(dataTableOutput("available_variables_type2")),
# uiOutput("glmer_server_select"),
uiOutput("glmer_results_select"),
dataTableOutput("glmer_results_table"),
hidden(downloadButton("glmer_results_table_download", "Download GLMer results")),
hidden(selectInput("glmer_slma_method", "Meta analysis to visualize", c("Maximum Likelihood",
"REstricted Maximum Likelihood",
"Fixed-Effects meta-analysis"))),
hidden(plotOutput("glmer_slma_plot")),
hidden(downloadButton("glmer_slma_down", "Download Forestplot"))
),
tabPanel("Survival analysis", value = "survival_analysis",
fluidRow(column(12,
tabBox(width = 12, id = "survival_tabs",
tabPanel("Create survival object", value = "survival_tab_object",
fluidRow(
column(6,
uiOutput("survival_time_start_ui"),
uiOutput("survival_time_end_ui"),
actionButton("create_survival_object", "Create survival object")
),
column(6,
uiOutput("survival_event_ui"),
selectInput("survival_type", "Type of censoring:", c("right", "left",
"counting", "interval",
"interval2", "mstate"))
)
)
),
tabPanel("Fit survival model", value = "survival_tab_formula",
fluidRow(
column(12,
hidden(textInput("survival_formula", "Formula:", width = "100%")),
)
),
fluidRow(
column(4,
hidden(actionButton("survival_run_model", "Run Cox survival model"))
),
column(4,
actionButton("survival_toggle_variables_table","Toggle variables table"),
),
column(4,
actionButton("trigger_formula_help_survival", "Formula input help"),
)
),
fluidRow(
column(12,
hidden(dataTableOutput("available_variables_type3")),
)
),
fluidRow(
column(12,
hidden(uiOutput("survival_study_ui")),
hidden(dataTableOutput("survival_results_table")),
hidden(downloadButton("survival_results_table_download", "Download survival results"))
)
)
),
tabPanel("Meta analysis", value = "survival_tab_meta_analysis",
fluidRow(
column(6,
hidden(actionButton("survival_meta_analysis", "Perform meta-analysis"))
),
column(6,
hidden(selectInput("survival_meta_analysis_method", "Meta-analysis method",
c("REML", "DL", "HE", "SJ", "ML", "EB", "HS", "GENQ"))),
hidden(uiOutput("survival_meta_analysis_variable_ui"))
)
),
fluidRow(
column(12, hidden(plotOutput("survival_meta_analysis_plot")))
)
),
tabPanel("Visualization of model", value = "survival_tab_visualization",
fluidRow(
column(12,
withSpinner(plotOutput("survival_plot")),
downloadButton("survival_plot_download", "Download plot")
)
)
)
)
))
)
)
)
),
tabItem(tabName = "plink",
fluidRow(
tabBox(width = 12, id = "plink_t",
tabPanel("Available SSH resources",
uiOutput("available_tables_ssh"),
actionButton("select_tables_ssh", "Select SSH")
),
tabPanel("PLINK", value = "plink",
textInput("command", "PLINK Shell command", width = "100%"),
h5("NOTE: we avoid –out to indicate the output file"),
h5("NOTE: No need to input plink as in a shell command"),
code("plink < >"),
h5("can be inputed as"),
code("< >"),
h5(""),
actionButton("run_shell", "Run Shell command"),
hidden(actionButton("plink_show_plain", "Show PLINK terminal output")),
dataTableOutput("plink_results_table"),
hidden(downloadButton("plink_results_table_download", "Download PLINK results")),
bsModal("plink_results_terminal", "PLINK Terminal output", "plink_show_plain",
verbatimTextOutput("plink_results_terminal_render")
)
),
tabPanel("Manhattan Plot", value = "plink_plot",
withSpinner(plotOutput("manhattan2")),
downloadButton("genomics_manhattan_plink_plot_download", "Download plot")
)
)
)
),
tabItem(tabName = "vcf_files",
fluidRow(
tabBox(width = 12, id = "vcf_files_t",
tabPanel("Available resources",
uiOutput("available_tables_vcf"),
actionButton("select_tables_vcf", "Select VCF resource and covariates table")
),
tabPanel("GWAS", value = "gwas",
uiOutput("vcf_selector_var"),
uiOutput("vcf_selector_cov"),
actionButton("gwas_trigger", "Perform GWAS"),
dataTableOutput("vcf_results"),
hidden(downloadButton("vcf_results_table_download", "Download GWAS results"))
),
tabPanel("Manhattan Plot", value = "gwas_plot",
withSpinner(plotOutput("manhattan")),
# ggeditLiteUI("manhattan_edit"),
downloadButton("genomics_manhattan_vcf_plot_download", "Download plot", "genomics_manhattan_vcf_plot")
)
)
)
),
tabItem(tabName = "limma",
fluidRow(
tabBox(width = 12, id = "limma_t",
tabPanel("Available resources", value = "limma_a",
uiOutput("available_tables_lim"),
actionButton("select_tables_lim", "Select resource")
),
tabPanel("Limma", value = "limma",
fluidRow(
column(6,
uiOutput("limma_variables_selector_condition"),
uiOutput("limma_variables_selector_covars"),
uiOutput("limma_sva_selector"),
uiOutput("limma_run")
),
column(6,
uiOutput("limma_labels_selector"),
selectInput("limma_data_type", "Data type:", c("RNAseq", "microarray"))
)
),
fluidRow(
column(12,
dataTableOutput("limma_results_table"),
hidden(downloadButton("limma_results_table_download", "Download LIMMA results"))
)
)
)
)
)
)
)
)
# Put them together into a dashboardPage
dashboardPage(
dashboardHeader(title = "DataSHIELD",
tags$li(a(href = 'https://isglobal-brge.github.io/ShinyDataSHIELD_bookdown/',
icon("book"),
title = "User guide",
target = "_blank"),
class = "dropdown")),
sidebar,
body
)
isglobal-brge/ShinyDataSHIELD documentation built on Dec. 13, 2021, 1:35 p.m.
R Package Documentation
Browse R Packages
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
library(DSI)
library(DSOpal)
library(dsBaseClient)
library(dsOmicsClient)
library(dsSurvivalClient)
library(shinydashboard)
library(shiny)
library(shinyalert)
library(DT)
library(data.table)
library(shinyjs)
library(shinyBS)
library(ggplot2)
library(shinycssloaders)
library(shinyWidgets)
library(stringr)
#library(thematic)
library(fresh)
library(ggthemr)
source("ggeditLiteModule.R", local = TRUE)
# thematic::thematic_shiny()
jscode <- '
$(document).keyup(function(event) {
if ($("#password1").is(":focus") && (event.keyCode == 13)) {
$("#connect_server1").click();
};
if ($("#pat1").is(":focus") && (event.keyCode == 13)) {
$("#connect_server1").click();
}
});
'
jscode_tab <- "
shinyjs.disableTab = function(name) {
var tab = $('.nav li a[data-value=' + name + ']');
tab.bind('click.tab', function(e) {
e.preventDefault();
return false;
});
tab.addClass('disabled');
}
shinyjs.enableTab = function(name) {
var tab = $('.nav li a[data-value=' + name + ']');
tab.unbind('click.tab');
tab.removeClass('disabled');
}
"
css_tab <- "
.nav li a.disabled {
background-color: #aaa !important;
color: #333 !important;
cursor: not-allowed !important;
border-color: #aaa !important;
}"
# Insert Favicon
tags$head(tags$link(rel="shortcut icon", type = "image/x-icon", href="www/favicon.ico"))
options(sass.cache = FALSE)
sass::sass(
sass::sass_file("www/theme.scss"),
output = "www/theme.css"
)
p_color <- fread("www/theme.scss", skip = "$top_bar_colour: ", nrows = 1)
p_color <- substr(colnames(p_color), 18,24)[1]
# Set p_color for withSpinner CSS
options(spinner.color = p_color)
## ui.R ##
sidebar <- dashboardSidebar(
sidebarMenu(
id = "tabs",
uiOutput("userpanel"),
menuItem("Connect to server", tabName = "server_connect"),
hidden(menuItem("Table columns types", tabName = "table_columns_a")),
hidden(menuItem("Descriptive statistics", tabName = "d_statistics")),
hidden(menuItem("Statistic models", tabName = "statistic_models")),
# hidden(menuItem("Mixed statistic models", tabName = "statistic_models_mixed")),
hidden(menuItem("Genomics", tabName = "genomics",
menuSubItem("Analysis with BioConductor", tabName = "vcf_files"),
menuSubItem("Analysis with PLINK", tabName = "plink")
)),
hidden(menuItem("Omics", tabName = "omics",
menuSubItem("LIMMA", tabName = "limma")
))
),
tags$footer(HTML(paste0("<footer>",
"<div class='footer-copyright text-center py-3'>© 2021 - ISGlobal-BRGE. v",
tryCatch({as.character(read.dcf("DESCRIPTION", fields = "Version"))}, # Docker
error = function(w){as.character(read.dcf("../../DESCRIPTION", fields = "Version"))}), # Local
"</div></footer>")),
style = "background-color:transparent;
position:absolute;
bottom:0;")
)
body <- dashboardBody(
tags$head(includeCSS("www/theme.css")),
# use_theme(custom_theme),
useShinyalert(),
useShinyjs(),
extendShinyjs(text = jscode_tab, functions = c("enableTab", "disableTab")),
inlineCSS(css_tab),
# inlineCSS(n_bar_css),
# inlineCSS(tabbox_css),
tabItems(
tabItem(tabName = "server_connect",
tabPanel('server_connect',
fluidRow(
# actionButton("stop", "stop"),
tabBox(
title = p(circleButton("add", size = "sm", icon = icon("plus"), status = "primary"),
circleButton("remove", size = "sm", icon = icon("minus"), status = "primary")
),
id = "tabset1", width = 12,
tabPanel("Server1",
fluidRow(
column(6,
h3("URL"),
textInput("url1", "Opal server", value = "https://opal-demo.obiba.org/")
),
column(6,
h3("Credentials"),
conditionalPanel(
condition = "input.pat_switch1 == true",
passwordInput("pat1", "Personal Access Token"),
),
conditionalPanel(
condition = "input.pat_switch1 == false",
textInput("user1", "User", value = "dsuser"),
tags$head(tags$script(HTML(jscode))),
passwordInput("password1", "Password", value = "P@ssw0rd")
),
materialSwitch(inputId = "pat_switch1", label = "Use Personal Access Token", status = "primary")
)
),
hr(),
fluidRow(
column(6,
hidden(tags$div(id = "tb_1",
materialSwitch(inputId = "tbl_res1", label = "Resources", inline = TRUE, value = T),
tags$span("Tables")
))
),
column(6,
uiOutput("profile_selector1")
)
),
fluidRow(
column(6,
uiOutput("project_selector1"),
),
column(6,
uiOutput("resource_selector1"),
)
),
fluidRow(
column(6,actionButton("connect_server1", "Connect"))
),
hidden(actionButton("add_server1", "Add selected item(s)")),
hidden(actionButton("info_opal_1", "Further information of selection"))
)
)
),
fluidRow(
column(6,
hidden(actionButton("remove_item", "Remove selected item(s)")),
hidden(actionButton("connect_selected", "Connect"))
)
),
dataTableOutput("server_resources_table"),
)
),
tabItem(tabName = "table_columns_a",
fluidRow(
tabBox(width = 12, id = "table_columns_selection",
tabPanel("Available tables", value = "a_tables",
uiOutput("available_tables_cols"),
actionButton("select_tables_cols", "Select tables")
),
tabPanel("Column types", value = "col_tables",
# actionButton("stop","stop"),
DTOutput("column_types_table")
)
)
)
),
tabItem(tabName = "d_statistics",
fluidRow(
tabBox(width = 12, id = "d_statistics_t",
tabPanel("Available tables", value = "a_tables",
uiOutput("available_tables"),
actionButton("select_tables_descr_stats", "Select tables")
),
tabPanel("Summary", value = "summary",
uiOutput("d_statistics_variable_selector_approach"),
uiOutput("d_statistics_variable_selector"),
dataTableOutput("descriptive_summary"),
downloadButton("descriptive_summary_download", "Download")
),
tabPanel("Scatter plot", value = "s_plot",
uiOutput("d_statistics_variable_selector_scatter_approach"),
uiOutput("d_statistics_variable_selector_scatter"),
uiOutput("d_statistics_variable_selector_scatter2"),
withSpinner(plotOutput("d_statistics_scatter_plot")),
downloadButton("d_statistics_scatter_plot_download", "Download plot")
),
tabPanel("Histogram", value = "h_plot",
uiOutput("d_statistics_variable_selector_histogram_approach"),
uiOutput("d_statistics_variable_selector_histogram"),
withSpinner(plotOutput("d_statistics_histogram_plot")),
downloadButton("d_statistics_histogram_plot_download", "Download plot")
),
tabPanel("Heatmap", value = "hm_plot",
uiOutput("d_statistics_variable_selector_heatmap_approach"),
uiOutput("d_statistics_variable_selector_heatmap"),
uiOutput("d_statistics_variable_selector_heatmap2"),
withSpinner(plotOutput("d_statistics_heatmap_plot")),
downloadButton("d_statistics_heatmap_plot_download", "Download plot")
),
tabPanel("Box plot", value = "box_plot",
fluidRow(
column(6,
uiOutput("d_statistics_variable_selector_boxplot_approach"),
uiOutput("d_statistics_variable_selector_boxplot"),
# actionButton("stop", "stop")
),
column(6,
uiOutput("d_statistics_variable_selector_boxplot2"),
uiOutput("d_statistics_variable_selector_boxplot3")
)
),
withSpinner(plotOutput("d_statistics_boxplot_plot")),
ggeditLiteUI("d_statistics_boxplot_plot_edit"),
# downloadButton("d_statistics_boxplot_plot_download", "Download plot")
)
)
)
),
tabItem(tabName = "statistic_models",
fluidRow(
tabBox(width = 12, id = "statistic_models_t",
tabPanel("Available tables", value = "a_tables_sm",
uiOutput("available_tables_sm"),
actionButton("select_tables_sm", "Select tables")
),
tabPanel("Generalized linear model", value = "glm",
fluidRow(
column(6,
textInput("glm_formula", "Input GLM formula:"),
hidden(selectInput("glm_approach", "Select the approach:",
c("Pooled", "Study Level Meta Analysis"))),
actionButton("trigger_formula_help_glm", "Formula input help"),
actionButton("perform_glm", "Perform GLM")
),
column(6,
selectInput("gml_output_family", "Output family:", c("gaussian", "poisson", "binomial")),
actionButton("gml_toggle_variables_table","Toggle variables table"),
)
),
hidden(dataTableOutput("available_variables_type")),
dataTableOutput("glm_results_table"),
hidden(downloadButton("glm_results_table_download", "Download GLM results")),
hidden(selectInput("glm_slma_method", "Meta analysis to visualize", c("Maximum Likelihood",
"REstricted Maximum Likelihood",
"Fixed-Effects meta-analysis"))),
hidden(plotOutput("glm_slma_plot")),
hidden(downloadButton("glm_slma_down", "Download Forestplot"))
),
tabPanel("Mixed effects model", value = "mixed_model",
fluidRow(
column(6,
textInput("glmer_formula", "Input GLMer formula:"),
actionButton("trigger_formula_help_glmer", "Formula input help"),
actionButton("perform_glmer", "Perform GLMer")
),
column(6,
selectInput("gmler_output_family", "Output family:", c("poisson", "binomial")),
actionButton("gmler_toggle_variables_table","Toggle variables table")
)
),
hidden(dataTableOutput("available_variables_type2")),
# uiOutput("glmer_server_select"),
uiOutput("glmer_results_select"),
dataTableOutput("glmer_results_table"),
hidden(downloadButton("glmer_results_table_download", "Download GLMer results")),
hidden(selectInput("glmer_slma_method", "Meta analysis to visualize", c("Maximum Likelihood",
"REstricted Maximum Likelihood",
"Fixed-Effects meta-analysis"))),
hidden(plotOutput("glmer_slma_plot")),
hidden(downloadButton("glmer_slma_down", "Download Forestplot"))
),
tabPanel("Survival analysis", value = "survival_analysis",
fluidRow(column(12,
tabBox(width = 12, id = "survival_tabs",
tabPanel("Create survival object", value = "survival_tab_object",
fluidRow(
column(6,
uiOutput("survival_time_start_ui"),
uiOutput("survival_time_end_ui"),
actionButton("create_survival_object", "Create survival object")
),
column(6,
uiOutput("survival_event_ui"),
selectInput("survival_type", "Type of censoring:", c("right", "left",
"counting", "interval",
"interval2", "mstate"))
)
)
),
tabPanel("Fit survival model", value = "survival_tab_formula",
fluidRow(
column(12,
hidden(textInput("survival_formula", "Formula:", width = "100%")),
)
),
fluidRow(
column(4,
hidden(actionButton("survival_run_model", "Run Cox survival model"))
),
column(4,
actionButton("survival_toggle_variables_table","Toggle variables table"),
),
column(4,
actionButton("trigger_formula_help_survival", "Formula input help"),
)
),
fluidRow(
column(12,
hidden(dataTableOutput("available_variables_type3")),
)
),
fluidRow(
column(12,
hidden(uiOutput("survival_study_ui")),
hidden(dataTableOutput("survival_results_table")),
hidden(downloadButton("survival_results_table_download", "Download survival results"))
)
)
),
tabPanel("Meta analysis", value = "survival_tab_meta_analysis",
fluidRow(
column(6,
hidden(actionButton("survival_meta_analysis", "Perform meta-analysis"))
),
column(6,
hidden(selectInput("survival_meta_analysis_method", "Meta-analysis method",
c("REML", "DL", "HE", "SJ", "ML", "EB", "HS", "GENQ"))),
hidden(uiOutput("survival_meta_analysis_variable_ui"))
)
),
fluidRow(
column(12, hidden(plotOutput("survival_meta_analysis_plot")))
)
),
tabPanel("Visualization of model", value = "survival_tab_visualization",
fluidRow(
column(12,
withSpinner(plotOutput("survival_plot")),
downloadButton("survival_plot_download", "Download plot")
)
)
)
)
))
)
)
)
),
tabItem(tabName = "plink",
fluidRow(
tabBox(width = 12, id = "plink_t",
tabPanel("Available SSH resources",
uiOutput("available_tables_ssh"),
actionButton("select_tables_ssh", "Select SSH")
),
tabPanel("PLINK", value = "plink",
textInput("command", "PLINK Shell command", width = "100%"),
h5("NOTE: we avoid –out to indicate the output file"),
h5("NOTE: No need to input plink as in a shell command"),
code("plink < >"),
h5("can be inputed as"),
code("< >"),
h5(""),
actionButton("run_shell", "Run Shell command"),
hidden(actionButton("plink_show_plain", "Show PLINK terminal output")),
dataTableOutput("plink_results_table"),
hidden(downloadButton("plink_results_table_download", "Download PLINK results")),
bsModal("plink_results_terminal", "PLINK Terminal output", "plink_show_plain",
verbatimTextOutput("plink_results_terminal_render")
)
),
tabPanel("Manhattan Plot", value = "plink_plot",
withSpinner(plotOutput("manhattan2")),
downloadButton("genomics_manhattan_plink_plot_download", "Download plot")
)
)
)
),
tabItem(tabName = "vcf_files",
fluidRow(
tabBox(width = 12, id = "vcf_files_t",
tabPanel("Available resources",
uiOutput("available_tables_vcf"),
actionButton("select_tables_vcf", "Select VCF resource and covariates table")
),
tabPanel("GWAS", value = "gwas",
uiOutput("vcf_selector_var"),
uiOutput("vcf_selector_cov"),
actionButton("gwas_trigger", "Perform GWAS"),
dataTableOutput("vcf_results"),
hidden(downloadButton("vcf_results_table_download", "Download GWAS results"))
),
tabPanel("Manhattan Plot", value = "gwas_plot",
withSpinner(plotOutput("manhattan")),
# ggeditLiteUI("manhattan_edit"),
downloadButton("genomics_manhattan_vcf_plot_download", "Download plot", "genomics_manhattan_vcf_plot")
)
)
)
),
tabItem(tabName = "limma",
fluidRow(
tabBox(width = 12, id = "limma_t",
tabPanel("Available resources", value = "limma_a",
uiOutput("available_tables_lim"),
actionButton("select_tables_lim", "Select resource")
),
tabPanel("Limma", value = "limma",
fluidRow(
column(6,
uiOutput("limma_variables_selector_condition"),
uiOutput("limma_variables_selector_covars"),
uiOutput("limma_sva_selector"),
uiOutput("limma_run")
),
column(6,
uiOutput("limma_labels_selector"),
selectInput("limma_data_type", "Data type:", c("RNAseq", "microarray"))
)
),
fluidRow(
column(12,
dataTableOutput("limma_results_table"),
hidden(downloadButton("limma_results_table_download", "Download LIMMA results"))
)
)
)
)
)
)
)
)
# Put them together into a dashboardPage
dashboardPage(
dashboardHeader(title = "DataSHIELD",
tags$li(a(href = 'https://isglobal-brge.github.io/ShinyDataSHIELD_bookdown/',
icon("book"),
title = "User guide",
target = "_blank"),
class = "dropdown")),
sidebar,
body
)
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