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ui.R
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#
# This is the user-interface definition of a Shiny web application. You can
# run the application by clicking 'Run App' above.
#
# Find out more about building applications with Shiny here:
#
# http://shiny.rstudio.com/
#
# Define UI for application that draws a histogram
shinyUI(
tagList(
#tags$script(src = "selectize_override.js"),
tags$head(includeHTML("www/google_analytics.html")),
tags$head(tags$style(HTML("body{ background: #F7F7F7; }"))),
tags$head(
tags$link(rel = "stylesheet", type = "text/css", href = "custom.css")
),
tags$head(tags$style(type="text/css", ".container-fluid { max-width: 1100px; /* or 950px */}")),
fluidPage(
useShinyjs(),
div(
style = 'background-color: #990000;height:50px;',
fluidRow(
column(4, tags$h3("Kidney Cell Explorer", class = "topbar-element", style = "color:white;"),
pivot_help_UI("choose_stats_info",title = NULL, label = NULL, icn="question-circle", type = "link", tooltip = T, style = "padding-left:10px;color:white;padding-top:5px;")),
column(5,
uiOutput("input_gene_ui"),
actionLink("reset_gene", NULL, icon = icon("chevron-circle-left", "fa-1x"), class = "btn_leftAlign topbar-element", style = "padding-top:5px;"),
shinyBS::bsTooltip(
"reset_gene",
title = "Reset gene selection",
options = list(container = "body")
)
),
column(3,
tags$p("* Multiple genes accepted for heatmap. Feature plot use the first gene.", style = "font-size:11px; padding-right:10px; color: white;/*", class = "topbar-element")
)
)
),
tabPanel(
title = NULL,
#style = 'width:1000px;',
div(
style= "padding: 5px 5px 5px 5px;",
fluidRow(
column(5,
wellPanel(
tags$b("tSNE of"),
tags$select(id="tsne_id",
class = "customDrop",
tags$option(value = "global", "adult mouse kidney", selected=T),
tags$option(value = "nephrogenic", "nephrogenic lineage"),
tags$option(value = "ureteric", "ureteric lineage")
),
tags$b("color by"),
conditionalPanel("input.tsne_id == 'global'",
style="display: inline-block;",
tags$select(id="colorBy1",
class = "customDrop",
tags$option(value = "Lineages", "grouping", selected=T),
tags$option(value = "Ontology_ID", "ontology ID"),
tags$option(value = "orig.ident", "zonation"),
tags$option(value = "sex", "gender")
)
),
conditionalPanel("input.tsne_id != 'global'",
style="display: inline-block;",
tags$select(id="colorBy2",
class = "customDrop",
tags$option(value = "Ontology_ID", "ontology ID"),
tags$option(value = "orig.ident", "zonation"),
tags$option(value = "sex", "gender")
)
),
plotOutput("plot2d", height="270px")
)
#uiOutput("plot2d_tooltip")
),
column(4,
wellPanel(
tags$div(
uiOutput("curg_text1", inline=T),
tags$select(id="palette",
class="customDrop btn_rightAlign",
tags$option(value = "RedGrey", "RedGrey", selected=T),
tags$option(value = "RdBu", "RedBlue"),
tags$option(value = "RdYlBu", "RedYellowBlue"),
tags$option(value = "viridis", "viridis"),
tags$option(value = "inferno", "inferno")
)
),
plotOutput("exprPlot", height="270px")
)
),
column(3,
wellPanel(
uiOutput("featurePlot_ui")
)
)
)
),
wellPanel(
fluidRow(
column(5, uiOutput("heat_strip_title")),
column(3,
tags$br(),
uiOutput("bin_stats_ui")
),
column(2,
tags$br(),
tags$b("Palette"),
tags$select(id="bin_pal",
class="customDrop",
tags$option(value = "RdYlBu", "RdYlBu", selected=T),
tags$option(value = "RdBu", "RedBlue"),
tags$option(value = "viridis", "viridis"),
tags$option(value = "inferno", "inferno")
)
),
column(2,
tags$br(),
uiOutput("bin_cut_ui")
)
),
uiOutput("heat_strip_ui"),
tags$p("* numbers in boxes correspond to schematic. 'Rescaled' value is original value rescaled (gene-wise) to 0-1 range.", style = "font-size:12px; margin-bottom:0px;")
),
wellPanel(
fluidRow(
column(5,
img(src ="onto_plot.png", width = "100%")
),
column(7,
DT::dataTableOutput("otg_show", width = "95%"),
tags$br(),
tags$p("For detailed information on the kidney anatomy please visit GUDMAP:", style="font-style: italic; line-height: 0.5;font-size:12px;"),
tags$a("https://www.gudmap.org/tutorials/kidney-dev/", href = "https://www.gudmap.org/tutorials/kidney-dev/", style="font-size:12px;"),
tags$br(),
tags$a("https://www.gudmap.org/tutorials/urogenital-dev/devmus.html#DMK", href = "https://www.gudmap.org/tutorials/urogenital-dev/devmus.html#DMK", style="font-size:12px;")
)
)
),
wellPanel(
fluidRow(
column(12, tags$h4("Number of genes detected in metacell", class = "panel-title"))
),
plotlyOutput("gene_num_plot", height="200px")
)
),
br(),
HTML("<p>Cite Kidney Cell Explorer:"),
tags$em("Ransick, A., Lindström, N.O., Liu, J., Zhu, Q., Guo, J.J., Alvarado, G.F., Kim, A.D., Black, H.G., Kim, J. and McMahon, A.P., 2019. Single-Cell Profiling Reveals Sex, Lineage, and Regional Diversity in the Mouse Kidney. Developmental cell, 51(3), pp.399-413."),
tags$p("If showing views of data from the website in any published form (grant, paper, presentation), one should include a citation and link to the website in the Figure legend: data from KidneyCellExplorer (https://cello.shinyapps.io/kidneycellexplorer/; Ransick et al., 2019). "),
br(),
HTML("<li>Source code for Kidney Cell Explorer has been deposited to <a href=https://github.com/qinzhu/kidneycellexplorer>https://github.com/qinzhu/kidneycellexplorer</li>"),
# Sidebar with a slider input for number of bins
br(),
br(),
br(),
br(),
br(),
br()
)
)
)