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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;});"
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 = 'GlycoBase',
# Wyss logo
div(img(src = paste0('www/wyss-logo-white.png'), width = '200px'),
style='text-align: center; padding-top: 30px;'),
h1('GlycoBase'),
# Glycan logo
div(img(src = paste0('www/glycobase_home.png'), width = '100px'),
style='text-align: center; padding-top: 30px; padding-bottom: 60px;'),
# Login button
tags$head(tags$script(jscode)),
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 = 'GlycoBase',
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: #0f9971ff !important;
}
.main-header .logo {
font-family: "GraphikMedium",Helvetica,Arial,sans-serif;
}
.navbar {
background-color: #00B07D !important;
}
.sidebar-toggle {
background-color: #00B07D !important;
}
.skin-blue .sidebar-menu > li.active > a,
.skin-blue .sidebar-menu > li:hover > a { border-left-color: #0f9971ff;}
.alignment_row1, .alignment_row2 {
border: 1px solid #e2e2e2;
}
.no-header-box .box-header {
display: none;
}
.alignment_row1 .alignment_item, .alignment_row2 .alignment_item {
display: inline-block;
width: 10%;
border-right: 1px solid #e2e2e2;
padding: 10px;
text-align: center;
min-width: 80px;
position: relative;
}
.alignment_row1 {
background-color: #f2f2f2;
margin-bottom: -1px;
}
.alignment_row1 .alignment_item {
}
.info-tip:hover {
text-decoration: underline;
}'
))),
sidebarMenu(id='tabs',
p(),
menuItem("GlycoBase overview", tabName = "home", icon = icon("star")),
menuItem("Glycan alignment", tabName = "alignment", icon = icon("stream"),
badgeLabel = 'New!', badgeColor = 'green'),
menuItem("Characteristic environment", tabName = "structuralcontext", icon = icon("chart-bar")),
menuItem("Submit a glycan", tabName = "submit", icon = icon("plus-square")),
#menuItem("SweetTalk", tabName = "tab_sweettalk", icon = icon("comment-dots")),
#menuItem("SweetOrigins", tabName = "tab_sweetorigins", icon = icon("project-diagram")),
#menuItem("Biomining", tabName = "tab_biomining", icon = icon("microscope")),
div(actionLink('citation_modal', 'Citing GlycoBase',
style = 'color: #00B07D; padding-top: 30px;'),
style = 'font-size: 10pt; margin: 0px 5px 20px 0px;')
),
br(),
div(style = 'position: fixed; bottom: 20px; margin: 0px 20px 0 20px; width: 180px;',
img(src = 'www/wyss-logo-white.png', width = '160px'),
p('This app was built at the Wyss Institute for Biologically Inspired Engineering',
style = 'font-size: 8pt; margin-top: 10px',),
a('Visit our website to learn more', href = 'https://wyss.harvard.edu/',
target = '_blank', style = 'font-size: 8pt; color: #00B07D;')
)
),
dashboardBody(
tags$head(includeHTML('www/analytics.html'),
tags$style('.shiny-output-error{color: white;}
.progress-bar { background-color: #00B07D; }
.shiny-notification {
position: fixed;
top: 40%;
left: 40%;
right: 40%;"'),
HTML('<link rel="icon" href="www/favicon.ico" type="image/x-icon"/>')),
tags$style(
type = 'text/css',
'.bg-aqua { background-color: #019DB0 !important; }
.bg-fuchsia { background-color: #903C83 !important; }
.bg-yellow { background-color: #B09001 !important; }
.bg-green { background-color: #01B07D !important; }
.bg-lime { background-color: #16D69E !important; }
.bg-olive { background-color: #3BF1BC !important; }
.hoverbox:hover { opacity: 0.85 !important; }
'
),
# green = darkest green
# lime = medium green
# olive = light green
tabItems(
tabItem(tabName = 'home',
h2('GlycoBase overview'),
fluidRow(
actionLink('modal_glycans', class='hoverbox',
box(title = 'Unique glycans',
height = 120, width = 4,
background = 'green', solidHeader = T,
div(style = 'float: left; padding-left: 20px;',
img(src = 'www/icon_glycan.png', width = '100px')),
div(style = 'float: left; padding-left: 30px; font-size: 28px;',
textOutput('num_glycans'))
)),
actionLink('modal_glycowords', class='hoverbox',
box(title = 'Unique glycowords',
height = 120, width = 4,
background = 'aqua', solidHeader = T,
div(style = 'float: left; padding-left: 20px; padding-top: 10px;',
img(src = 'www/icon_glycoword.png', width = '75px')),
div(style = 'float: left; padding-left: 30px; font-size: 28px;',
textOutput('num_glycowords'))
)),
actionLink('modal_glycoletters', class='hoverbox',
box(title = 'Unique glycoletters',
height = 120, width = 4,
background = 'fuchsia', solidHeader = T,
div(style = 'float: left; padding-left: 20px; padding-top: 3px;',
img(src = 'www/icon_glycoletters.png', width = '70px')),
div(style = 'float: left; padding-left: 30px; font-size: 28px;',
textOutput('num_glycoletters'))
))
),
fluidRow(
class = 'no-header-box',
div(downloadButton('button_download_glycobase', label = 'Download full (csv)', style = 'margin-right: 15px; float: right;', icon = icon('download')),
HTML('<h2>Search GlycoBase <span style="font-size: 10pt;">(v2.0)</span></h2>'),
style = 'padding-left: 15px;'),
box(title = '',
width = 12,
div(withSpinner(dataTableOutput('table_glycobase'), type = 4, color = '#00B07D')))
)
),
tabItem(tabName = 'structuralcontext',
h2('Characteristic environment'),
fluidRow(
box(title = tagList("Query local structural context for a glycoletter",
HTML(' '),
tags$i(
class = "fa fa-info-circle",
style = "color: #00B07D; font-size: 8pt;"
),
actionLink('info_environment_modal',
label = 'What is this?',
class = 'info-tip',
style = 'font-size: 8pt; color: #00B07D;')),
width = 7, height = 320,
div(selectInput('select_context_criteria', label = 'Query type',
choices = c('Observed monosaccharides paired with:',
'Observed monosaccharides making bond:',
'Observed bonds made by:')),
style = 'width: 53%; display: inline-block; max-width: 380px; min-width: 300px; padding-top: 20px; padding-left: 15px;'),
div(selectInput('select_context_glycoletter', label = 'Glycoletter',
choices = 'Loading...'),
style = 'width: 40%; display: inline-block; max-width: 175px;'),
hr(style = 'margin-top: 0'),
div(selectInput('select_context_taxonomy_level', label = 'Taxonomic filter',
choices = c('Kingdom', 'Species')),
style = 'width: 49%; display: inline-block; max-width: 150px; padding-left: 15px;'),
div(selectInput('select_context_taxonomy_value', label = 'Kingdom',
choices = 'Loading...'),
style = 'width: 49%; display: inline-block; max-width: 350px;')
),
box(title='Frequency of glycoletter by position',
width = 5, height = 320,
div(withSpinner(plotlyOutput('context_main_side_barplot', height = '240px'),
type = 4, color = '#00B07D')))
),
fluidRow(
box(title = 'Structural context',
width = 12,
div(withSpinner(plotlyOutput('context_observed_barplot'), type = 4, color = '#00B07D'))
)
)
),
tabItem(tabName = 'alignment',
h2('Glycan alignment'),
fluidRow(
box(title = tagList("Input a glycan sequence to perform pairwise alignment",
HTML(' '),
tags$i(
class = "fa fa-info-circle",
style = "color: #00B07D; font-size: 8pt;"
),
actionLink('info_alignment_modal',
label = 'What is this?',
class = 'info-tip',
style = 'font-size: 8pt; color: #00B07D;')),
width = 12,
div(style='padding-left: 15px; padding-bottom: 15px;',
textInput('glycan_query', label = 'Query sequence',
placeholder = 'Glycan sequence in IUPAC condensed format'),
actionButton('button_run_alignment', label = 'Align sequence',
style = 'color: #ffffff; background-color: #00B07D; border-color: #0f9971ff; border-radius: 5px;'),
actionButton('button_show_alignment_example', label = 'Give me an example', style = 'margin-left: 10px;'),
textOutput('message_run_alignment')
)
)
),
fluidRow(
uiOutput('alignments_ui')
)
),
tabItem(tabName = 'tab_sweettalk',
h2('SweetTalk'),
p('Coming soon')
),
tabItem(tabName = 'tab_sweetorigins',
h2('SweetOrigins'),
p('Coming soon')
),
tabItem(tabName = 'tab_biomining',
h2('Biomining'),
p('Coming soon')
),
tabItem(tabName = 'submit',
h2('Submit a new glycan'),
HTML('<div class="typeform-widget" data-url="https://ranipowers.typeform.com/to/gmNmrW" style="width: 100%; height: 600px;"></div> <script> (function() { var qs,js,q,s,d=document, gi=d.getElementById, ce=d.createElement, gt=d.getElementsByTagName, id="typef_orm", b="https://embed.typeform.com/"; if(!gi.call(d,id)) { js=ce.call(d,"script"); js.id=id; js.src=b+"embed.js"; q=gt.call(d,"script")[0]; q.parentNode.insertBefore(js,q) } })() </script> <div style="font-family: Sans-Serif;font-size: 12px;color: #999;opacity: 0.5; padding-top: 5px;"> powered by <a href="https://admin.typeform.com/signup?utm_campaign=gmNmrW&utm_source=typeform.com-01E4M277GRYSX45RZ0PSMP63SW-free&utm_medium=typeform&utm_content=typeform-embedded-poweredbytypeform&utm_term=EN" style="color: #999" target="_blank">Typeform</a> </div>')
)
) # end tabItems
) # end dashboardBody
) # end dashboardPage