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ui.R
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ui.R
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# some other code for webpage functions
jscodega <- '
$(document).on("shiny:sessioninitialized",function(){
$("#Find").on("click", function() {
ga("send", "event", "button", "Find", $("#geneID").val());
});
});
'
jscode <- '
$(function() {
var $els = $("[data-proxy-click]");
$.each(
$els,
function(idx, el) {
var $el = $(el);
var $proxy = $("#" + $el.data("proxyClick"));
$el.keydown(function (e) {
if (e.keyCode == 13) {
$proxy.click();
}
});
}
);
});
'
jsResetCode <- "shinyjs.reset = function() {history.go(0)}"
# Define UI for application that draws the UMAP
ui <- fluidPage(
title = "PFA Ependymoma Spatial Transcriptomics Atlas",
theme = shinytheme(set_shinytheme),
tags$style("
.nav-tabs{
font-weight:bold;
font-size:13px;
}
# .btn-default, .btn-options{
# display:inline-block;
# padding:0.3em 1.2em;
# margin:0 0.1em 0.1em 0;
# border:0.16em solid rgba(255,255,255,0);
# border-radius:2em;
# box-sizing: border-box;
# text-decoration:none;
# font-family:'Roboto',sans-serif;
# font-weight:300;
# color:#FFFFFF;
# text-shadow: 0 0.04em 0.04em rgba(0,0,0,0.35);
# text-align:center;
# transition: all 0.2s;
# background-color:#4e9af1;
# }
# .btn-default:hover{
# border-color: rgba(255,255,255,1);
# }
.checkbox {
line-height: 20px;
margin-top: -15px;
margin-bottom: -15px;
}
.header {
position:fixed;
z-index:100;
width: calc(100% - 70px);
}
.BioCircosARCTooltip {
z-index:10
}
.BioCircosHISTOGRAMTooltip {
z-index:10
}
"),
tags$head(tags$style(
HTML(
"
#SIDE {
background-color: #F8F8F8;
}",
".btn-options {
background-color: #F8F8F8;
}",
".btn {
text-transform: unset !important;
}",
".shiny-notification {
position:fixed;
top: 10px;
right: 10px);
}"
)
)),
tags$head(includeHTML(("www/google-analytics.html"))),
useShinyjs(),
introjsUI(),
use_bs_tooltip(),
tags$style("
.introjs-helperLayer {
background: transparent;
}
.introjs-overlay {
opacity: 0 !important;
z-index: 99999999!important;
}
.introjs-helperLayer:before {
opacity: 0;
content: '';
position: absolute;
width: inherit;
height: inherit;
border-radius: 0.5em;
border: .2em solid rgba(255, 217, 68, 0.8);
box-shadow: 0 0 0 1000em rgba(0,0,0, .7);
opacity: 1;
}
.introjs-helperLayer:after {
content: '';
left: 0;
right: 0;
top: 0;
bottom: 0;
position: absolute;
z-index: 1000;
}
"),
tags$style(".mock {position:fixed;width:7%;margin-top: 60px;z-index:10;}"),
tags$style("
.download_this{
margin-right: 1px;
}"),
tags$script(src = "shinyBS_mod.js"),
tags$head(tags$script(HTML(jscode))),
tags$head(tags$script(HTML(jscodega))),
tags$head(tags$script(HTML(jsResetCode))),
tags$head(tags$style(
type = "text/css",
".shiny-output-error { visibility: hidden; }",
".shiny-output-error:before { visibility: hidden; }",
".shiny-output-warning { visibility: hidden; }",
".shiny-output-warning:before { visibility: hidden; }"
)),
titlePanel(div(
class = "header",
a(
img(src = "logo.png", alt = "RNA Bioscience Initiative", style = "width:29px;"),
href = "https://github.com/rnabioco/",
target="_blank"
) %>%
bs_embed_tooltip("The RNA Bioscience Initiative at the University of Colorado Anschutz Medical Campus", placement = "bottom"),
span(a(
strong(apptitle_short),
href = url,
target="_blank"
) %>%
bs_embed_tooltip("part of Pediatric Neuro-oncology Cell Atlas project", placement = "bottom"),
div(
code(apptitle),
style = "font-size:15px;margin-top:2px;display:inline"
)),
style = "font-size:30px;background-color:rgba(255,255,255,0.5);background-clip:inherit;text-align:center;margin:0px;padding:1px 1px;"
)),
fixedPanel(
style = "z-index:100;",
right = 10,
top = 22,
tags$head(
tags$style(HTML("#tutorial{background-color:gold;z-index:100;}"))
),
introBox(
actionButton("tutorial", "", icon = icon("question"),
style = "padding:4px 10px;margin:0px;") %>%
bs_embed_tooltip("Take a tour through the browser!", placement = "bottom"),
data.step = 1,
data.intro = "Welcome to the PFA Spatial Transcriptomics Atlas.<br><br>
Please hover over buttons, tabs, etc for tips/explanations.",
data.position = "left"
)
),
sidebarLayout(
sidebarPanel(
tags$head(tags$script('
var dimension = [0, 0];
$(document).on("shiny:connected", function(e) {
dimension[0] = window.innerWidth;
dimension[1] = window.innerHeight;
Shiny.onInputChange("dimension", dimension);
});
$(window).resize(function(e) {
dimension[0] = window.innerWidth;
dimension[1] = window.innerHeight;
Shiny.onInputChange("dimension", dimension);
});
')),
id = "SIDE",
style = "position:fixed;width:16%;margin-top:60px;z-index:50;border:solid 2.3px;
border-top-color: #4e9af1;
border-left-color: #4e9af1;
border-right-color: #9BE7FF;
border-bottom-color: #9BE7FF;",
width = 2,
div(
id = "sideall",
div(
id = "sidediv",
tabsetPanel(
id = "side1",
tabPanel(
span(icon("link", class = NULL, lib = "font-awesome"), "Gene",
title = "plot expression a specific query gene"
),
br(.noWS = "outside"),
introBox(
div(
div(
style = "display:inline-block;vertical-align:top;width:100%;",
tagAppendAttributes(selectizeInput("geneID",
label = NULL,
selected = "",
choices = ""
),
`data-proxy-click` = "Find"
)
),
div(
style = "display: inline-block;vertical-align:top; width: 10px;",
actionButton("Find", "Find", icon = icon("search"),
style = "padding:3px 9px;float:left;margin:3px;") %>%
bs_embed_tooltip("gene symbols accepted", placement = "right")
)
),
data.step = 2,
data.intro = "Query individual gene by symbol.",
data.position = "bottom"
)
),
tabPanel(
span(icon("cogs", class = NULL, lib = "font-awesome"), "Options", title = "additional global options"),
br(.noWS = "outside"),
div(
id = "doLockdiv",
checkboxInput("doLock", "lock panel order", value = FALSE, width = NULL) %>%
bs_embed_tooltip("if unlocked, tabs, sections, and table columns can be dragged and reordered",
placement = "right"
)
),
tags$table(
tags$head(
tags$style(HTML("#pval{margin-top: 0px; margin-bottom: -10px; font-size:12px;}"))
),
tags$head(
tags$style(HTML("#ncol{margin-top: 0px; margin-bottom: -10px; font-size:12px;}"))
),
tags$head(
tags$style(HTML("#plotw{margin-top: 0px; margin-bottom: -10px; font-size:12px;}"))
),
tags$head(
tags$style(HTML("#ploth{margin-top: 0px; margin-bottom: -10px; font-size:12px;}"))
),
tags$tr(
width = "100%",
tags$td(width = "50%", tags$div(style = "font-size:12px;", "plot height")),
tags$td(width = "50%", textInput("ploth", NULL, value = plot_height, width = "100px") %>%
bs_embed_tooltip("plot height for app (px) and saved pdf (in)", placement = "right"))
),
tags$tr(
width = "100%",
tags$td(width = "50%", tags$div(style = "font-size:12px;", "plot width")),
tags$td(width = "50%", textInput("plotw", NULL, value = plot_width, width = "100px") %>%
bs_embed_tooltip("plot width for app (px) and saved pdf (in)", placement = "right"))
)
)
)
)
)
)
),
mainPanel(
id = "MAIN",
width = 10,
style = "z-index:1;margin-top: 60px;",
tabsetPanel(
id = "tabMain",
tabPanel(
introBox(
span(icon("pencil-ruler", class = NULL, lib = "font-awesome"),
"Feature Plot",
title = "Plot expression or category data in 2D UMAP or space"
),
data.step = 3,
data.intro = "For a query gene, this tab displays the SCT normalized count expression.",
data.position = "top"
),
value = "Gene_query",
div(
id = "sorted",
div(
introBox(
div(
selectInput("sel1", NULL, choices = slides, selected = "821_H&E"),
style = "border-radius:0px;vertical-align:top;margin:0px;padding-top:10px;padding-bottom:-200px;width:100px;"
),
data.step = 4,
data.intro = "Choose between umap/H&Eonly/slides.",
data.position = "right"
),
div(
uiOutput("dimPlotUI1"),#%>% withLoader(proxy.height = proxy_height),
),
style = "display: inline-block;"
),
div(
div(
selectInput("sel2", NULL, choices = slides, selected = "821"),
style = "border-radius:0;pxvertical-align:top;margin:0px;padding-top:10px;padding-bottom:-900px;width:100px;"
),
div(
uiOutput("dimPlotUI2"), #%>% withLoader(proxy.height = proxy_height),
),
style = "display: inline-block;"
),
tags$style(HTML(".panel-group {margin-bottom:5px;margin-top:2px;}"))
)
),
tabPanel(
introBox(
span(icon("align-center", class = NULL, lib = "font-awesome"),
"Violin Plot",
title = "Plot expression or category data by category"
),
data.step = 5,
data.intro = "For a query gene, this tab displays the SCT normalized count expression violin plot.",
data.position = "top"
),
value = "Gene_violin",
uiOutput("violinPlotUI1")
),
tabPanel(
introBox(
span(icon("info", class = NULL, lib = "font-awesome"),
"About",
title = "View version and author info",
),
value = "about",
data.step = 6,
data.intro = "Additional information on the study and authors.",
data.position = "top"
),
value = "about",
h5("About the dataset"),
uiOutput("GitHub"),
# tags$a(
# href = manuscriptL,
# target="_blank",
# div(
# img(src = 'Placeholder.png', height = "100",
# alt = manuscriptT),
# style = "text-align: left;display: inline;"
# )
# ),
uiOutput("intro"),
uiOutput("intro2"),
uiOutput("rawdata"),
uiOutput("version"),
# hr(),
# div(
# style = "display: inline-block;vertical-align:bottom;",
# h5("Included Data Files")
# ),
# p("click to preview"),
# fluidRow(
# column(width = 1),
# column(width = 9, DT::dataTableOutput("explain3"))
# )
)
)
)
)
)