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app_ui.R
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app_ui.R
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library(shiny)
library(shinydashboard)
library(shinycssloaders)
# Add www subdirectory for images and stuff
addResourcePath(prefix = 'www', directoryPath = paste0(getwd(), '/www'))
# We'll do a dynamic redirect after authenticating
# https://stackoverflow.com/questions/57755830/how-to-redirect-to-a-dynamic-url-in-shiny
jscode <- "Shiny.addCustomMessageHandler('customredirect', function(message) { window.location = message;});"
drift_js <- '<script>
"use strict";
!function() {
var t = window.driftt = window.drift = window.driftt || [];
if (!t.init) {
if (t.invoked) return void (window.console && console.error && console.error("Drift snippet included twice."));
t.invoked = !0, t.methods = [ "identify", "config", "track", "reset", "debug", "show", "ping", "page", "hide", "off", "on" ],
t.factory = function(e) {
return function() {
var n = Array.prototype.slice.call(arguments);
return n.unshift(e), t.push(n), t;
};
}, t.methods.forEach(function(e) {
t[e] = t.factory(e);
}), t.load = function(t) {
var e = 3e5, n = Math.ceil(new Date() / e) * e, o = document.createElement("script");
o.type = "text/javascript", o.async = !0, o.crossorigin = "anonymous", o.src = "https://js.driftt.com/include/" + n + "/" + t + ".js";
var i = document.getElementsByTagName("script")[0];
i.parentNode.insertBefore(o, i);
};
}
}();
drift.SNIPPET_VERSION = "0.3.1";
drift.load("579ukhxa5466");
</script>'
source('plot_helpers.R')
# ------------------------------- Pre-login UI ------------------------------ #
AnonymousUI <- fluidPage(
tags$head(tags$link(rel="stylesheet", type="text/css", href="bootstrap_rani.css"),
HTML('<link rel="icon" href="www/favicon.ico" type="image/x-icon"/>')),
title = 'Transcriptomics Explorer',
# Wyss logo
div(img(src = paste0('www/wyss-logo-white.png'), width = '200px'),
style='text-align: center; padding-top: 30px;'),
h1('Transcriptomics Explorer'),
# DNA
div(style='position: relative; height: 300px; margin-top: -80px;',
HTML('<div class="dna" style="--strands: 16;">
<div class="strand" style="--s: 0;"></div>
<div class="strand" style="--s: 1;"></div>
<div class="strand" style="--s: 2;"></div>
<div class="strand" style="--s: 3;"></div>
<div class="strand" style="--s: 4;"></div>
<div class="strand" style="--s: 5;"></div>
<div class="strand" style="--s: 6;"></div>
<div class="strand" style="--s: 7;"></div>
<div class="strand" style="--s: 8;"></div>
<div class="strand" style="--s: 9;"></div>
<div class="strand" style="--s: 10;"></div>
<div class="strand" style="--s: 11;"></div>
<div class="strand" style="--s: 12;"></div>
<div class="strand" style="--s: 13;"></div>
<div class="strand" style="--s: 14;"></div>
<div class="strand" style="--s: 15;"></div>
</div>')
),
# Login button
tags$head(tags$script(jscode),
HTML(drift_js)),
div(actionButton("action", "Log in with Synapse"),
style='text-align: center; padding-bottom: 100px;'),
div(p("Don't have a Synapse account yet?", style='text-align: center; font-size: 10pt;'),
p("Follow the ",
a(href = 'https://midas-wyss.github.io/synapse_instructions_predictive_bioanalytics.html',
target = '_blank', 'instructions for registering here', style='font-size: 10pt;'),
'.', style='text-align: center; font-size: 10pt;'))
)
# ------------------------------ Post-login UI ------------------------------ #
AuthenticatedUI <- dashboardPage(
skin = 'blue',
dashboardHeader(title = 'Transcriptomics Explorer',
titleWidth = 250,
tags$li(class = "dropdown",
tags$li(class = "dropdown",
actionLink("user_account_modal", textOutput("logged_user")),
style = "color: #fff;"))
),
dashboardSidebar(
width = 250,
tags$head(tags$style(HTML('.logo {
background-color: #1ea0cf !important;
}
.navbar {
background-color: #27adde !important;
}
.sidebar-toggle {
background-color: #27adde !important;
}
.skin-blue .sidebar-menu > li.active > a,
.skin-blue .sidebar-menu > li:hover > a { border-left-color: #1ea0cf;}
.table.dataTable tbody tr.active td {
background-color: #27adde !important;
color: white;
}
.table.dataTable tbody tr.active td a {
color: white;
}'
))),
selectInput('project_select', 'Project', 'Loading...'),
div(actionLink('info_projects_modal', 'What are Projects?',
style = 'color: #27adde;'),
style = 'font-size: 8pt; margin: 0px 5px 20px 0px;'),
sidebarMenu(
menuItem("Samples overview", tabName = "tab_samples", icon = icon("vial")),
menuItem("Differential expression", tabName = "tab_diff_expr", icon = icon("chart-bar")),
menuItem("Expression profiling", tabName = "tab_expr_profiles", icon = icon("th")),
menuItem("Pathway enrichment", tabName = "tab_pathway_enrichment", icon = icon("align-left")),
menuItem("Biomarkers analysis", tabName = "tab_biomarkers", icon = icon("share-alt")),
menuItem("DRUID", tabName = "tab_druid", icon = icon("star"))
),
br(),
div(style = 'position: fixed; bottom: 20px; margin: 0px 20px 0 20px; width: 180px;',
img(src = 'www/wyss-logo-white-square.png', width = '140px'),
p('This tool was developed by the Predictive BioAnalytics group',
style = 'font-size: 8pt; margin-top: 10px',),
a('View our other apps', href = 'https://midas-wyss.github.io/',
target = '_blank', style = 'font-size: 8pt; color: #27adde;')
)
),
dashboardBody(
tags$head(includeHTML('www/analytics.html'),
HTML(drift_js),
tags$style(".shiny-output-error { color: white; }
.progress-bar { background-color: #00aeed; }
.shiny-notification {
position: fixed;
top: 70%;
left: 40%;
right: 40%;"
),
HTML('<link rel="icon" href="www/favicon.ico" type="image/x-icon"/>')),
tabItems(
tabItem(tabName = "tab_samples",
h2('Samples overview'),
fluidRow(
box(title = tagList("Between-sample variability (UMAP algorithm)",
HTML(' '),
tags$i(
class = "fa fa-info-circle",
style = "color: #27adde; font-size: 8pt;"
),
actionLink('info_umap_modal', label = 'What is this?',
style = 'font-size: 8pt; color: #27adde;')),
width = 7,
height = 500,
div(style = 'padding-left: 20px;',
p(style='color: #D2D6DD;', 'Hover over a point to view the sample name')
),
div(withSpinner(plotlyOutput('umap_plot'),
type = 4, color = '#27adde'),
style = "overflow-y: auto;")),
box(title = "UMAP plot settings",
width = 5,
height = 500,
div(style = 'padding: 0 30px 20px 30px; float: left;',
radioButtons('umap_color_by',
label = 'Color samples by',
choices = 'Loading...',
selected = character(0))),
div(style = 'float: left;',
radioButtons('umap_shape_by',
label = 'Shape samples by',
choices = 'Loading...',
selected = character(0))
),
div(style = 'padding-top: 50px; padding-left: 20px; clear: left;',
downloadButton('download_umap_pdf', 'Download plot (.pdf)',
style = 'color: #ffffff; background-color: #27adde; border-color: #1ea0cf;
border-radius: 5px;')
),
div(style = 'padding-top: 20px; padding-left: 20px; clear: left;',
downloadButton('download_umap_methods', 'Download figure legend (.txt)',
style = 'color: #ffffff; background-color: #27adde; border-color: #1ea0cf;
border-radius: 5px;')
)
)
),
fluidRow(
box(title = tagList("Sample metadata",
HTML(' '),
tags$i(
class = "fa fa-info-circle",
style = "color: #27adde; font-size: 8pt;"
),
actionLink('info_sample_metadata_modal', label = 'What is this?',
style = 'font-size: 8pt; color: #27adde;')),
div(style='padding-left: 20px; padding-bottom: 10px;',
uiOutput('info_samples')),
width = 12,
div(style = 'padding-left: 20px; overflow-y: auto;',
withSpinner(dataTableOutput('table_sample_metadata'),
type = 4, color = '#27adde')),
div(style = 'padding-left: 20px; padding-bottom: 40px;',
downloadButton('download_metadata_table', 'Download full table (.csv)',
style = 'color: #ffffff; background-color: #27adde; border-color: #1ea0cf;
border-radius: 5px;')
)
)
)
),
tabItem(tabName = "tab_expr_profiles",
h2("Expression profiling"),
h5('Check back soon!')
),
tabItem(tabName = "tab_diff_expr",
h2('Differential Expression'),
fluidRow(
box(title = tagList("Set parameters for analysis",
HTML(' '),
tags$i(
class = "fa fa-info-circle",
style = "color: #27adde; font-size: 8pt;"
),
actionLink('info_preproc_modal', label = 'How was my data preprocessed?',
style = 'font-size: 8pt; color: #27adde;')),
div(style = 'padding-left: 20px;',
p(style='color: #D2D6DD;', 'Select the criteria for comparing two sample groups')
),
width = 6,
height = 500,
div(style='padding-left: 20px;',
div(style='width: 180px;',
selectInput('select_volcano_column', 'Split groups by',
'Loading...', selected = character(0))),
div(style='float: left; width: 180px;',
#textInput('text_group1', 'Group A Name', 'Group A'),
selectInput('select_group1_criteria', 'Group A criteria',
'Loading...', selected = character(0))
),
div(style='float: left; width: 240px; padding-left: 50px;',
#textInput('text_group2', 'Group B Name', 'Group B'),
selectInput('select_group2_criteria', 'Group B criteria',
'Loading...', selected = character(0))
),
),
div(style = 'padding-left: 20px; width: 440px;',
verbatimTextOutput('group1_group2_selected', F),
div(style = 'color: #D2D6DD;',
uiOutput('message_diff_expr')
)
),
div(style = 'padding-top: 40px; padding-left: 20px; clear: left;',
actionButton('button_run_volcano', 'Run analysis',
icon = icon("angle-double-right"),
style = 'color: #ffffff; background-color: #27adde; border-color: #1ea0cf; border-radius: 5px;')
),
div(style = 'padding-top: 20px; padding-left: 20px; clear: left;',
div(style = 'float: left; padding-right: 20px;',
downloadButton('download_volcano_pdf', 'Download volcano plot (.pdf)',
style = 'color: #ffffff; background-color: #27adde; border-color: #1ea0cf; border-radius: 5px;')
),
div(style = 'float: left;',
downloadButton('download_volcano_methods', 'Download methods (.txt)',
style = 'color: #ffffff; background-color: #27adde; border-color: #1ea0cf; border-radius: 5px;')
)
)
),
box(title = tagList("Volcano plot of differentially expressed genes",
HTML(' '),
tags$i(
class = "fa fa-info-circle",
style = "color: #27adde; font-size: 8pt;"
),
actionLink('info_volcano_modal', label = 'What is this?',
style = 'font-size: 8pt; color: #27adde;')),
width = 6,
height = 500,
uiOutput('volcano_message'),
div(withSpinner(plotlyOutput('volcano_plot'),
type = 4, color = '#27adde'))
)
),
fluidRow(
uiOutput('row_diff_expr_results')
)
),
tabItem(tabName = "tab_pathway_enrichment",
h2("Pathway enrichment"),
h5('Check back soon!')
),
tabItem(tabName = "tab_biomarkers",
h2("Biomarker Identification"),
h5('Check back soon!')
),
tabItem(tabName = "tab_druid",
h2("DRUID"),
h5('Check back soon!')
)
)
)
)