require(shinydashboard)
require(shinyjs)
require(shinyBS)
require(shinycssloaders)
require(DT)
require(shiny)
require(Seurat)
require(dplyr)
require(Matrix)
require(V8)
require(sodium)
ui <- tagList(
dashboardPage(
dashboardHeader(title = "Seurat Wizard"),
dashboardSidebar(
sidebarMenu(
id = "tabs",
menuItem("User Guide", tabName = "introTab", icon = icon("info-circle")),
menuItem("Input Data", tabName = "datainput", icon = icon("upload")),
menuItem("QC & Filter", tabName = "qcFilterTab", icon = icon("th")),
menuItem("Vln Plot", tabName = "vlnplot", icon = icon("bar-chart")),
menuItem(
"Filter & Normalize",
tabName = "filterNormSelectTab",
icon = icon("th")
),
menuItem(
"Dispersion Plot",
tabName = "dispersionPlot",
icon = icon("bar-chart")
),
menuItem("Scale and Run PCA", tabName = "runPcaTab", icon = icon("th")),
menuItem(
"Viz PCA Plot",
tabName = "vizPcaPlot",
icon = icon("bar-chart")
),
menuItem("PCA Plot", tabName = "pcaPlot", icon = icon("bar-chart")),
menuItem(
"PC Heatmap",
tabName = "heatmapPlot",
icon = icon("bar-chart")
),
menuItem("JackStraw", tabName = "jackStrawPlot", icon = icon("th")),
menuItem("Cluster Cells", tabName = "clusterCells", icon = icon("th")),
menuItem(
"TSNE (Non-linear)",
tabName = "tsneTab",
icon = icon("th")
),
menuItem(
"Download Seurat Obj",
tabName = "finishTab",
icon = icon("download")
),
menuItem("Cluster Markers", tabName = "findMarkersTab", icon = icon("th")),
menuItem(
"Viz Markers",
tabName = "vizMarkersTab",
icon = icon("bar-chart")
)
)
),
dashboardBody(
shinyjs::useShinyjs(),
extendShinyjs(script = "www/custom.js"),
tags$head(
tags$style(HTML(
" .shiny-output-error-validation {color: darkred; } "
)),
tags$link(rel = "stylesheet", type = "text/css", href = "custom.css"),
tags$link(rel = "stylesheet", type = "text/css", href = "buttons.css")
),
tabItems(
source("ui-tab-intro.R", local = TRUE)$value,
source("ui-tab-inputdata.R", local = TRUE)$value,
source("ui-tab-qcfilter.R", local = TRUE)$value,
source("ui-tab-vln.R", local = TRUE)$value,
source("ui-tab-filterNormSelect.R", local = TRUE)$value,
source("ui-tab-dispersionPlot.R", local = TRUE)$value,
source("ui-tab-runPca.R", local = TRUE)$value,
source("ui-tab-vizPcaPlot.R", local = TRUE)$value,
source("ui-tab-pcaPlot.R", local = TRUE)$value,
source("ui-tab-pcHeatmapPlot.R", local = TRUE)$value,
source("ui-tab-jackStrawPlot.R", local = TRUE)$value,
source("ui-tab-clusterCells.R", local = TRUE)$value,
source("ui-tab-tsne.R", local = TRUE)$value,
source("ui-tab-finish.R", local = TRUE)$value,
source("ui-tab-findMarkers.R", local = TRUE)$value,
source("ui-tab-vizMarkers.R", local = TRUE)$value
)
)
),
tags$footer(
wellPanel(
HTML(
'
<p align="center" width="4">Developed and maintained by: Core Bioinformatics, Center for Genomics and Systems Biology, NYU Abu Dhabi</p>
<p align="center" width="4">Copyright (C) 2016, code licensed under GPLv3</p>
<p align="center" width="4">Using Seurat version 2.3.0</p>
<p align="center" width="4"><strong>Acknowledgements: </strong></p>
<p align="center" width="4">1) Rahul Satija, Andrew Butler and Paul Hoffman (2017). Seurat: Tools for Single Cell Genomics. R package
version 2.2.1. <a href="https://CRAN.R-project.org/package=Seurat" target="_blank">https://CRAN.R-project.org/package=Seurat</a></p>
<p align="center" width="4">2) <a href="http://satijalab.org/seurat/" target="_blank">Satija Lab</a></p>'
)
),
tags$script(src = "imgModal.js")
)
)
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