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iPSCeq-server.R
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#---------------------------------------------------------------------
# Title: NCATS SEQUIN - Server Script
# Author: Marissa Hirst
# Author2: Ben Ernest
# Last Modified: 2022-02-08
# --
# Created: 2018-01-26 11:29:39 CDT
#---------------------------------------------------------------------
#---------------------------------------------------------------------
# CONTENTS
#---------------------------------------------------------------------
#
# NCATS server function organization
#
# 01 SHINY OPTIONS
# 02 LAYOUT OF APP... ui elements for bulk/sc layout
# 03 DATA & QC....... data loading & quality control for preliminary analysis
# 04 DISCOVERY....... correlation by cells/samples, distances, pca/tsne/umap
# 05 DGE............. differential gene expression analysis: bulk or scRNA-seq
# 06 iPSC PROFILER... module score profiler for scRNA-seq
# 07 MORE............ tutorial, faq, about us, session info
#
#---------------------------------------------------------------------
#
# NCATS SEQUIN application layout
#
# SEQUIN
# |- Shiny options & bulk/scRNA-seq dataset list load from SQL
# |- Layout of app for bulk/scRNA-Seq side
# |- d: Store reactive values in the app here
# |- Defaults: Image type (png), annotation type (HS) and cell markers
# |- Toggle tab panel elements on bulk/scRNA-Seq
# |- ui element layout for bulk/scRNA-Seq
# |- Submit and quality control
# |- Select dataset: bulk, scRNA-Seq
# |- File summary
# |- Count summary
# |- Discovery-driven analysis
# |- Correlation & scatterplot
# |- Distance matrix (bulk RNA-Seq only)
# |- Clustering: PCA (bulk only), tSNE, uMAP
# |- DGE analysis:
# |- Bulk RNA-seq:
# |- Overview: BULK-DGE-OVER
# |- Volcano plots: BULK-DGE-VOL
# |- Gene set enrichment & heatmap: BULK-DGE-GSE
# |- Clustering: BULK-DGE-CLUS
# |- scRNA-seq:
# |- Overview: SC-DGE-OVER
# |- Gene expression: SC-DGE-GE
# |- DGE analysis: SC-DGE-DGE
# |- Custom DGE analysis: SC-DGE-CUST
# |- Volcano plots: SC-DGE-VOL
# |- Gene set enrichment & heatmap: SC-DGE-GSE
# |- Manually select cells for DGE: SC-DGE-MSC
# |- Clustering: SC-DGE-CLUS
# |- Combine clusters or cells: SC-DGE-CCC
# | iPSC profiler for scRNA-Seq
# |- More
# |- Tutorial
# |- FAQ
# |- About us
# |- Session info
# Change file upload size to 200 MB and sanitize errors
error_log <- "error_log.txt"
options(
shiny.maxRequestSize = 2000 * 1024^2,
shiny.sanitize.errors = TRUE,
getClass.msg = F,
spinner.color = "black",
spinner.color.background = "white"
)
# Server function
iPSCeqServer <- function(input, output, session) {
# Hide tabs initially
hideTab(inputId = "tab_structure", target = "val4")
hideTab(inputId = "tab_structure", target = "val3")
hideTab(inputId = "tab_structure", target = "val2")
hideTab(inputId = "tab_structure", target = "summary")
# Initial popup
showModal(modalDialog(
size = "m",
title = fluidPage(
div(
style = "height: 80px",
img(
src = "ncats-logo.png", height = 60,
style = "display: inline-block; vertical-align: top; margin-top: 12px; padding-left: 10px;"
),
div(
style = paste0(
"display: inline-block; height: 60px; color: #672e6c; font-size: 60px;",
" font-weight: 350; float: right; padding-right: 10px; margin-top: -5px;"
),
"SEQUIN"
)
),
div(
style = "font-size: 16px; margin-top: 5px; padding-left: 10px; color: #636569;",
"Stem Cell Translation Laboratory"
)
),
footer = div(style = "float: right;", actionButton(inputId = "closeSplash", label = "Enter")),
includeMarkdown(path = "markdown/splash.md")
))
observeEvent(input$closeSplash, {
removeModal()
updateTabsetPanel(inputId = "main_tabsetPanel", selected = "mainApp")
})
output$placeholderDesc <- renderUI({
if(!is.null(d$cts_out)) return()
div(
style = "width: 800px; margin-left: 50px; font-size: 14px; font-weight: 300;",
HTML(paste0(
"Load data to get started. For help, see the tutorial under ",
strong("More"), " or click the ", strong("Help"), " link to ",
"the right."
))
)
})
# Store all reactive values used in app
d <- reactiveValues(
MD = NULL,
SCV = NULL,
inD = NULL,
res = NULL,
a = NULL,
b = NULL,
compNames = NULL,
cts_out = NULL,
dgeContrast = NULL,
newExpSetup = T,
newGSE = T,
newHeat = T,
newCluster = T,
dge_warning_msg = "",
x = NULL, # for lasso selection tool for inter-cluster DE boxplots
y = NULL, # for lasso selection tool for inter-cluster DE boxplots
genes_debug = NULL,
n_genes = 100,
n_genes_heatmap = 100,
n_genes_sc = 100,
n_genes_heatmap_sc = 100,
n_genes_manuallyselectcells_sc = 100,
fea_all_genes = F, # whether to use all genes in GSE
fea_all_genes_heatmap = F,
sc_mytabTemp = NULL,
filts = NULL,
gse_warning_msg = "",
heatmap_warning_msg = "",
calcTextVal = "",
dge_info = NULL,
dge_info_heatmap = NULL,
dge_info_sc = NULL,
dge_info_heatmap_sc = NULL,
dge_info_manuallyselectcells_sc = NULL,
clust_time = 0,
bulkExpFactorInfo = NULL,
drt = 0.1,
pcaVarianceFraction = 1,
fdr = 0.05,
goqc_or_relaunch = 0,
sc_meta = NULL,
clustList = NULL,
numClust = NULL,
seurat_only = NULL,
seurat_sc = NULL,
test = "none",
selectedDatasetsTable = NULL,
selectSamplesTable = NULL,
selectSamplesTableList = NULL,
selectSamplesTableVarsList = NULL,
selectSamplesTableSelectedVar = NULL,
selectedData = NULL,
upload_warn = NULL,
inD_orig = NULL,
setNames = NULL,
cellSets = list(),
addCellsClicks = list(),
observeCount = 0,
addCellsOverlap = list(),
data_info = NULL,
corplotClick = NULL,
heatmap1Click = NULL,
heatmap1Hover = NULL,
legendList_sc = NULL,
moduleScoreSeurat = NULL,
inD_withModuleScore = NULL,
moduleNamesRefVec = NULL,
selected_modules = NULL,
inD_goi = NULL,
goqc_warning = NULL,
wgcna_warning = NULL,
wgcna_minModuleSizeTried = NULL,
wgcna_warning_sc = NULL,
wgcna_minModuleSizeTried_sc = NULL,
inputFactors = NULL,
timeStamps = list(),
newCorplot = T,
newDistplot = T,
sc_dge_byfactor = list(),
sc_dge_byfactor_msg = NULL,
sc_dge_byfactor_novars_msg = NULL,
allowPrecomputedClusters = F,
datasetsRowsSelected = NULL,
datasetNames = NULL,
data_type = NULL,
resType = NULL,
showDataSummaryLinks = T,
showQCLinks = F,
showCorrelationLinks = T,
correlation_showLabels = F,
distance_showLabels = F,
showClusteringLinks = F,
enrichRLib = NULL,
enrichRLib_sc = NULL,
enrichRLib_manuallyselectcells = NULL,
sc_showOverviewLinks = T,
sc_showClusteringLinks = F,
sc_showGeneExpressionLinks = F,
sc_showDGELinks = F,
showTabs = T,
totalFigureHeight = NULL,
totalFigureHeight_sc = NULL,
resValues = NULL,
sc_dge_factor_lfcThreshold = 0.25,
sc_dge_factor_test = "wilcox",
sc_dge_factor_minPct = 0.1,
sc_dge_factor_minDiffPct = -1
)
# Dataset names in row at top of app
output$datasetNames <- renderUI({
req(SubmitData$data_type, d$datasetNames, input$tab_structure)
txt <- paste(d$datasetNames, collapse = ", ")
dataType <- "Bulk RNA-seq experiment"
if(length(d$datasetNames) > 1) dataType <- "Bulk RNA-seq experiments"
if(SubmitData$data_type == "Single-cell") {
dataType <- "Single-cell RNA-seq experiment"
if(length(d$datasetNames) > 1) dataType <- "Single-cell RNA-seq experiments"
}
if(SubmitData$data_type == "RASL") {
dataType <- "RASL-seq experiment"
if(length(d$datasetNames) > 1) dataType <- "RASL-seq experiments"
}
h4(strong(paste0(dataType, ":")), txt)
})
# Show selected resolution for single-cell in top bar
output$sc_res <- renderUI({
req(SubmitData$data_type, d$resType, d$res)
if(SubmitData$data_type != "Single-cell") return()
myRes <- "pre-computed"
if(d$resType == "seurat_res") {
myRes <- gsub("RNA_snn_res\\.", replacement = "", x = d$res)
}
h4(strong("Resolution: "), myRes)
})
# Button to download Seurat and scClustViz data
output$download_sc <- renderUI({
req(SubmitData$data_type)
if(SubmitData$data_type != "Single-cell" || is.null(d$inD) || is.null(d$seurat_sc)) return()
actionButton("download_sc", label = "Download", icon = icon("download"))
})
output$downloadSeurat_msg <- renderUI({
req(d$resType)
txt <- "Download data in Seurat format as an RDS file which can be loaded into R."
if(d$resType == "seurat_res") {
txt <- paste0(
"Download a ",
strong("Seurat"),
" object containing data at the current resolution or a ",
strong("List"),
" of Seurat objects from all resolutions. Data will be saved as an",
" RDS file which can be directly loaded in R."
)
}
HTML(txt)
})
output$downloadSCV_msg <- renderUI({
req(d$resType)
txt <- paste0(
"Download data in sCVdata format (scClustViz package) as an RDS file",
" which can be loaded into R."
)
if(d$resType == "seurat_res") {
txt <- paste0(
"Download an ",
strong("sCVdata"),
" object (scClustViz package) containing data at the current resolution or a ",
strong("List"),
" of sCVdata objects from all resolutions. Data will be saved as an",
" RDS file which can be directly loaded in R."
)
}
HTML(txt)
})
output$downloadSeurat_format <- renderUI({
req(d$resType)
if(d$resType != "seurat_res") return()
awesomeRadio(
inputId = "downloadSeurat_format",
label = NULL,
choices = c(
"Seurat (current resolution)" = "single",
"List (all resolutions)" = "multi"
),
selected = "single",
status = "success",
width = "240px"
)
})
output$downloadSCV_format <- renderUI({
req(d$resType)
if(d$resType != "seurat_res") return()
awesomeRadio(
inputId = "downloadSCV_format",
label = NULL,
choices = c(
"sCVdata (current resolution)" = "single",
"List (all resolutions)" = "multi"
),
selected = "single",
status = "success",
width = "240px"
)
})
observeEvent(input$download_sc, {
showModal(modalDialog(
title = "Download single-cell data",
size = "l",
easyClose = T,
fluidPage(
fluidRow(h4(strong("Seurat"))),
fluidRow(uiOutput("downloadSeurat_msg")),
br(),
fluidRow(
div(
style = "display: inline-block;",
uiOutput("downloadSeurat_format"),
),
div(
style = "display: inline-block;",
downloadButton(
outputId = "downloadSeurat",
label = "Download Seurat",
style = "vertical-align: bottom;"
)
)
),
br(), br(),
fluidRow(h4(strong("scClustViz"))),
fluidRow(uiOutput("downloadSCV_msg")),
br(),
fluidRow(
div(
style = "display: inline-block;",
uiOutput("downloadSCV_format"),
),
div(
style = "display: inline-block;",
downloadButton(
outputId = "downloadSCV",
label = "Download scClustViz",
style = "vertical-align: bottom;"
)
)
)
)
))
})
output$downloadSeurat <- downloadHandler(
filename = function() {
if(!is.null(input$downloadSeurat_format) &&
input$downloadSeurat_format == "multi" && d$resType == "seurat_res") {
return("SeuratList.rds")
}
return("Seurat.rds")
},
content = function(file) {
if(!is.null(input$downloadSeurat_format) &&
input$downloadSeurat_format == "multi" && d$resType == "seurat_res") {
saveRDS(seurat_only(), file = file)
} else {
saveRDS(d$inD, file = file)
}
}
)
output$downloadSCV <- downloadHandler(
filename = function() {
if(!is.null(input$downloadSCV_format) &&
input$downloadSCV_format == "multi" && d$resType == "seurat_res") {
return("sCVdataList.rds")
}
return("sCVdata.rds")
},
content = function(file) {
if(!is.null(input$downloadSCV_format) &&
input$downloadSCV_format == "multi" && d$resType == "seurat_res") {
saveRDS(d$SCV, file = file)
} else {
saveRDS(d$SCV[[d$res]], file = file)
}
}
)
# Reset app after user clicks "Reset" and confirms
observeEvent(input$reset, {
showModal(modalDialog(
easyClose = T,
footer = NULL,
fluidPage(
p("Do you really want to reset the app? All loaded data and analyses will be erased."),
p("Click anywhere outside this box to cancel or click ", strong("OK"), "to reset."),
actionButton("reset_ok", label = "OK")
)
))
})
observeEvent(input$reset_ok, {
removeModal()
shinyjs::refresh()
})
# Go back to Load Data page when user clicks "Update"
observeEvent(input$update, {
updateNavbarPage(inputId = "tab_structure", selected = "val1")
})
# Update button
output$update <- renderUI({
req(input$tab_structure)
if(input$tab_structure == "val1") return()
actionButton("update", label = "Update", icon = icon("edit"))
})
# Reset button
output$reset <- renderUI({
actionButton("reset", label = "Reset", icon = icon("redo"))
})
# Top bar with dataset names and reset button
output$topBar <- renderUI({
req(input$tab_structure, SubmitData)
if(input$tab_structure == "val1" & is.null(SubmitData$selectedData)) return()
div(
style = "background-color: #eee; vertical-align: middle; margin-bottom: 20px;",
fluidPage(
# br(),
div(
style = "margin-top: 10px; margin-bottom: 10px;",
fluidRow(
column(
width = 6,
div(
# style = "font-size: 20px; vertical-align: center;",
uiOutput("datasetNames")
)
),
column(
width = 3,
uiOutput("sc_res")
),
column(
width = 3,
align = "right",
fluidRow(
div(style = "display: inline-block;", uiOutput("download_sc")),
div(style = "display: inline-block;", uiOutput("update")),
div(style = "display: inline-block; margin-right: 15px;", uiOutput("reset"))
)
)
)
)
# br()
)
)
})
# Bulk toggle for sidebar elements to only appear in certain tabs
observe({
# Reactive values for # genes to use in GSE/heatmap
if(is.null(input$n_genes)) {
d$n_genes <- 100
} else {
d$n_genes <- input$n_genes
}
if(!IsInteger(input$n_genes_heatmap) || input$n_genes_heatmap < 1) {
if(!is.null(dgeout3()) && nrow(dgeout3()) > 1) {
maxGenes <- nrow(dgeout3())
d$n_genes_heatmap <- min(nrow(dgeout3()), 100)
} else {
d$n_genes_heatmap <- 100
}
} else {
d$n_genes_heatmap <- input$n_genes_heatmap
}
})
# scRNA-Seq toggle for sidebar elements to only appear in certain tabs
observe({
# Reactive values for # genes to use in GSE/heatmap
if(is.null(input$n_genes_sc)) {
d$n_genes_sc <- 100
} else {
d$n_genes_sc <- input$n_genes_sc
}
if(!IsInteger(input$n_genes_heatmap_sc) || input$n_genes_heatmap_sc < 1) {
if(!is.null(sc_mytab_heatmap()) && nrow(sc_mytab_heatmap()) > 1) {
maxGenes <- nrow(sc_mytab_heatmap())
d$n_genes_heatmap_sc <- min(nrow(sc_mytab_heatmap()), 100)
} else {
d$n_genes_heatmap_sc <- 100
}
} else {
d$n_genes_heatmap_sc <- input$n_genes_heatmap_sc
}
if(is.null(input$n_genes_manuallyselectcells_sc)) {
d$n_genes_manuallyselectcells_sc <- 100
} else {
d$n_genes_manuallyselectcells_sc <- input$n_genes_manuallyselectcells_sc
}
})
############################################################
############################################################
### UI OUTPUT FOR DGE ANALYSIS: BULK & scRNA-SEQ
############################################################
############################################################
# bulk rna-seq uiOutput for DGE Analysis tab
output$showRunDGE <- renderUI({
req(input$dge, SubmitData$data_type)
if(SubmitData$data_type != "Bulk") return()
myLab <- "Run DGE"
if(input$dge == "runDGE") myLab <- strong(myLab)
actionLink(
inputId = "showRunDGE",
style = "font-size: 16px; color: black;",
label = myLab
)
})
output$showOverview <- renderUI({
req(SubmitData$data_type, dgeover(), input$dge)
if(SubmitData$data_type == "Single-cell") return()
if(is.null(dgeover())) return()
if(d$dge_warning_msg != "") return()
myLab <- "Overview"
if(input$dge == "overview") myLab <- strong(myLab)
actionLink(
inputId = "showOverview",
label = myLab,
style = "font-size: 16px; color: black;"
)
})
output$showVolcano <- renderUI({
req(SubmitData$data_type, dgeout1(), input$dge)
if(SubmitData$data_type == "Single-cell") return()
if(is.null(dgeout1())) return()
if(d$dge_warning_msg != "") return()
myLab <- "Volcano plot"
if(input$dge == "volcano") myLab <- strong(myLab)
actionLink(
inputId = "showVolcano",
label = myLab,
style = "font-size: 16px; color: black;"
)
})
output$showGSE <- renderUI({
req(SubmitData$data_type, input$dge)
if(SubmitData$data_type == "Single-cell") return()
myLab <- "Gene set enrichment"
if(input$dge == "gse") myLab <- strong(myLab)
actionLink(
inputId = "showGSE",
label = myLab,
style = "font-size: 16px; color: black;"
)
})
output$showHeatmap <- renderUI({
req(SubmitData$data_type, input$dge)
if(SubmitData$data_type == "Single-cell") return()
myLab <- "Heatmap"
if(input$dge == "heatmap") myLab <- strong(myLab)
actionLink(
inputId = "showHeatmap",
label = myLab,
style = "font-size: 16px; color: black;"
)
})
output$showDGEClustering <- renderUI({
req(input$dge)
myLab <- "Clustering"
if(input$dge == "clustering") myLab <- strong(myLab)
actionLink(
inputId = "showDGEClustering",
style = "font-size: 16px; color: black;",
label = myLab
)
})
output$clusteringLinks <- renderUI({
req(input$clustalg, clustout(), d$showClusteringLinks, input$clustering_tabsetPanel)
if(length(clustout()) != 2 & length(clustout()) != 8) return()
if(length(clustout()) == 8) {
lab2 <- "WGCNA - dendrogram"
lab3 <- "WGCNA - TOM"
if(input$clustering_tabsetPanel == "clustPlotW02") lab2 <- strong(lab2)
if(input$clustering_tabsetPanel == "clustPlotW03") lab3 <- strong(lab3)
fluidPage(
fluidRow(
style = "margin-left: 6px;",
actionLink(
inputId = "showClustPlotW02",
label = lab2,
style = "color: black;"
)
),
fluidRow(
style = "margin-left: 6px;",
actionLink(
inputId = "showClustPlotW03",
label = lab3,
style = "color: black;"
)
)
)
} else {
fluidPage(
fluidRow(
style = "margin-left: 6px;",
actionLink(
inputId = "showClustPlotW01",
label = strong("K-medoids"),
style = "color: black;"
)
)
)
}
})
observeEvent(input$showRunDGE, {
d$showClusteringLinks <- F
updateTabsetPanel(inputId = "dge", selected = "runDGE")
})
observeEvent(input$showOverview, {
d$showClusteringLinks <- F
updateTabsetPanel(inputId = "dge", selected = "overview")
})
observeEvent(input$showVolcano, {
d$showClusteringLinks <- F
updateTabsetPanel(inputId = "dge", selected = "volcano")
})
observeEvent(input$showGSE, {
d$showClusteringLinks <- F
updateTabsetPanel(inputId = "dge", selected = "gse")
})
observeEvent(input$showHeatmap, {
d$showClusteringLinks <- F
updateTabsetPanel(inputId = "dge", selected = "heatmap")
})
observeEvent(input$showDGEClustering, {
d$showClusteringLinks <- ifelse(
test = (input$dge == "clustering"),
yes = ifelse(
test = d$showClusteringLinks,
yes = F,
no = T
),
no = T
)
updateTabsetPanel(inputId = "dge", selected = "clustering")
})
observeEvent(input$showClustPlotW01, {
updateTabsetPanel(inputId = "clustering_tabsetPanel", selected = "clustPlotW01")
})
observeEvent(input$showClustPlotW02, {
updateTabsetPanel(inputId = "clustering_tabsetPanel", selected = "clustPlotW02")
})
observeEvent(input$showClustPlotW03, {
updateTabsetPanel(inputId = "clustering_tabsetPanel", selected = "clustPlotW03")
})
output$dge_bulk <- renderUI({
# if(is.null(SubmitData$goqc) || SubmitData$goqc == 0) return()
req(SubmitData$goqc, SubmitData$data_type)
sidebarLayout(
sidebarPanel(
width = 2,
style = "width: 190px;",
fluidRow(div(style = "margin-left: 10px;", uiOutput("showRunDGE"))),
fluidRow(div(style = "margin-left: 10px;", uiOutput("showOverview"))),
fluidRow(div(style = "margin-left: 10px;", uiOutput("showVolcano"))),
fluidRow(div(style = "margin-left: 10px;", uiOutput("showHeatmap"))),
fluidRow(div(style = "margin-left: 10px;", uiOutput("showGSE"))),
fluidRow(div(style = "margin-left: 10px;", uiOutput("showDGEClustering"))),
fluidRow(div(style = "margin-left: 4px;", uiOutput("clusteringLinks")))
),
mainPanel(
width = 10,
tabsetPanel(
id = "dge",
type = "hidden",
selected = ifelse(
test = (SubmitData$data_type == "Bulk"),
yes = "runDGE",
no = "heatmap"
),
tabPanelBody(
value = "runDGE",
fluidPage(
fluidRow(
div(style = "display: inline-block;", h3("DGE options", style = "margin-top: 0px;")),
div(
style = "display: inline-block; margin-top: 0px; float: right;",
actionLink("overview_help_button", label = "Help")
)
),
fluidRow(
column(
width = 4,
style = "background-color: #eee; width: 380px; height: 160px;",
fluidPage(
fluidRow(uiOutput("dgeexpsetup")),
fluidRow(
div(style = "display: inline-block; width: 160px;", uiOutput("dgemethod")),
div(style = "display: inline-block; width: 160px; margin-left: 10px;", uiOutput("dgeexpedgernorm"))
)
)
),
column(
width = 2,
style = "background-color: #eee; width: 160px; height: 160px; margin-left: 20px;",
fluidPage(
fluidRow(div(style = "width: 120px;", uiOutput("dgepadjcutoff"))),
fluidRow(div(style = "width: 120px;", uiOutput("dgefcmin")))
)
),
column(
width = 3,
style = "background-color: #eee; width: 280px; height: 160px; margin-left: 20px;",
fluidPage(
fluidRow(div(style = "width: 160px;", uiOutput("batchFactor"))),
fluidRow(uiOutput("housekeepingSelect"))
)
)
),
br(),
conditionalPanel(
condition = "input.dgeexpsetup == 'exp1'",
fluidRow(
style = "background-color: #eee; width: 860px;",
div(style = "display: inline-block; width: 200px; margin-left: 10px;", uiOutput("dgeexp1a")),
div(style = "display: inline-block; width: 200px; margin-left: 10px;", uiOutput("dgeexp1b")),
div(style = "display: inline-block; width: 200px; margin-left: 10px;", uiOutput("dgeexp1c"))
)
),
conditionalPanel(
condition = "input.dgeexpsetup == 'exp2'",
fluidRow(
style = "background-color: #eee; width: 860px;",
div(style = "display: inline-block; width: 200px; margin-left: 10px;", uiOutput("dgeexp2a")),
div(style = "display: inline-block; width: 200px; margin-left: 10px;", uiOutput("dgeexp2c")),
div(style = "display: inline-block; width: 200px; margin-left: 10px;", uiOutput("dgeexp2c5"))
),
fluidRow(
style = "background-color: #eee; width: 860px;",
div(style = "display: inline-block; width: 200px; margin-left: 10px;", uiOutput("dgeexp2b")),
div(style = "display: inline-block; width: 200px; margin-left: 10px;", uiOutput("dgeexp2d")),
div(style = "display: inline-block; width: 200px; margin-left: 10px;", uiOutput("dgeexp2d5"))
)
),
conditionalPanel(
condition = "input.dgeexpsetup == 'exp3'",
fluidRow(
style = "background-color: #eee; width: 860px;",
div(style = "display: inline-block; width: 200px; margin-left: 10px;", uiOutput("dgeexp3a")),
div(style = "display: inline-block; width: 200px; margin-left: 10px;", uiOutput("dgeexp3c")),
div(style = "display: inline-block; width: 200px; margin-left: 10px;", uiOutput("dgeexp3b")),
div(style = "display: inline-block; width: 200px; margin-left: 10px;", uiOutput("dgeexp3d"))
)
),
conditionalPanel(
condition = "input.dgeexpsetup == 'exp4'",
fluidRow(
style = "background-color: #eee; width: 860px;",
div(style = "display: inline-block; width: 200px; margin-left: 10px;", uiOutput("dgeexp4a")),
div(style = "display: inline-block; width: 200px; margin-left: 10px;", uiOutput("dgeexp4c")),
div(style = "display: inline-block; width: 200px; margin-left: 10px;", uiOutput("dgeexp4b")),
div(style = "display: inline-block; width: 200px; margin-left: 10px;", uiOutput("dgeexp4d"))
)
),
conditionalPanel(
condition = "input.dgeexpsetup == 'exp5'",
fluidRow(
style = "background-color: #eee; width: 860px;",
div(style = "display: inline-block; width: 200px; margin-left: 10px;", uiOutput("dgeexp5a")),
div(style = "display: inline-block; width: 200px; margin-left: 10px;", uiOutput("dgeexp5b")),
div(style = "display: inline-block; width: 200px; margin-left: 10px;", uiOutput("dgeexp5c")),
div(style = "display: inline-block; width: 200px; margin-left: 10px;", uiOutput("dgeexp5d"))
)
),
conditionalPanel(
condition = "input.dgeexpsetup == 'exp6'",
fluidRow(
style = "background-color: #eee; width: 860px;",
div(style = "display: inline-block; width: 200px; margin-left: 10px;", uiOutput("dgeexp6c")),
div(style = "display: inline-block; width: 200px; margin-left: 10px;", uiOutput("dgeexp6d")),
div(style = "display: inline-block; width: 200px; margin-left: 10px;", uiOutput("dgeexp6e")),
div(style = "display: inline-block; width: 200px; margin-left: 10px;", uiOutput("dgeexp6f"))
),
fluidRow(
style = "background-color: #eee; width: 860px;",
div(style = "display: inline-block; width: 200px; margin-left: 10px;", uiOutput("dgeexp6a")),
div(style = "display: inline-block; width: 200px; margin-left: 10px;", uiOutput("dgeexp6b"))
)
),
br(),
fluidRow(
style = "background-color: #eee; width: 860px;",
div(style = "display: inline-block; margin-left: 10px; margin-top: 5px; margin-bottom: 10px;", uiOutput("dgeexpformhead")),
div(
style = "display: inline-block; margin-left: 20px; margin-top: 5px; margin-bottom: 10px; vertical-align: top;",
conditionalPanel(condition = "input.dgeexpsetup == 'exp1'", uiOutput("dgeexpform1")),
conditionalPanel(condition = "input.dgeexpsetup == 'exp2'", uiOutput("dgeexpform2")),
conditionalPanel(condition = "input.dgeexpsetup == 'exp3'", uiOutput("dgeexpform3")),
conditionalPanel(condition = "input.dgeexpsetup == 'exp4'", uiOutput("dgeexpform4")),
conditionalPanel(condition = "input.dgeexpsetup == 'exp5'", uiOutput("dgeexpform5")),
conditionalPanel(
condition = "input.dgeexpsetup == 'exp6'",
uiOutput("dgeexpform6a"),
uiOutput("dgeexpform6b"),
uiOutput("dgeexpform6c"),
uiOutput("dgeexpform6d")
)
),
div(style = "display: inline-block; margin-left: 40px; margin-top: 5px; margin-bottom: 10px; vertical-align: top;", uiOutput("godge"))
),
br(),
fluidRow(uiOutput("dge_expdesign_warning_ui")),
fluidRow(uiOutput("dge_warning_msg_ui")),
br()
)
),
tabPanelBody(
value = "overview",
fluidPage(
fluidRow(uiOutput("dgeoverviewHeader")),
fluidRow(div(style = "width: 600px;", uiOutput("dgeoverview"))),
br(),
fluidRow(uiOutput("dgeplot2Header")),
fluidRow(plotlyOutput("dgeplot2", width = "600px", height = "400px")),
fluidRow(
div(style = "display:inline-block", uiOutput("dldgeoverpdf")),
div(style = "display:inline-block", uiOutput("dldgeoverpng"))
),
br()
)
),
tabPanelBody(
value = "volcano",
fluidPage(
fluidRow(
div(style = "display: inline-block; width: 280px;", uiOutput("dgemaincontrasts")),
div(style = "display: inline-block; margin-left: 20px; vertical-align: top;", uiOutput("vistype")),
actionLink(
inputId = "volcanoplots_help_button",
label = "Help",
style = "display: inline-block; float: right;"
)
),
fluidRow(plotlyOutput("volplots")),
br(),
fluidRow(
div(style = "display:inline-block;", uiOutput("dldgemavolpdf")),
div(style = "display:inline-block; margin-left: 10px;", uiOutput("dldgemavolpng")),
),
br(),
fluidRow(uiOutput("mytableHeader")),
fluidRow(DT::dataTableOutput("mytable")),
br(),
fluidRow(uiOutput("downloadall")),
br()
)
),
tabPanelBody(
value = "gse",
fluidPage(
shinyjs::useShinyjs(),
div(
style = "border: 1px solid #eee; padding: 20px;",
fluidRow(
div(
style = "display: inline-block; margin-top: 0px; margin-left: 10px;",
h3("Gene set enrichment options", style = "margin-top: 0px;")
),
div(
style = "display: inline-block; float: right; margin-right: 10px;",
actionLink("gse_help_button", label = "Help"),
)
),
fluidRow(
div(
style = "display: inline-block; margin-left: 10px; vertical-align: top;",
uiOutput("dge_list")
),
div(
style = "display: inline-block; vertical-align: top;",
uiOutput("dgemaincontrasts_gse")
),
div(style = "display: inline-block;", uiOutput("geneOptions_ui")),
div(
style = "display: inline-block; vertical-align: top;",
uiOutput("gene_list_filtering")
),
div(style = "display: inline-block;", uiOutput("gene_list"))
),
fluidRow(div(style = "margin-left: 10px;", uiOutput("enrichRLib"))),
),
br(),
div(uiOutput("dgeInfoSubmitWarning_ui")),
hr(),
uiOutput("tbl_func_enrHeader"),
DT::dataTableOutput("func_enr_tbl"),
br(),
br(),
textOutput("no_list"),
br()
)
),
tabPanelBody(
value = "heatmap",
fluidPage(
div(
style = "border: 1px solid #eee; padding: 20px;",
fluidRow(
div(
style = "display: inline-block; margin-left: 10px;",
h3("Heatmap options", style = "margin-top: 0px;")
),
div(
style = "display: inline-block; float: right; margin-right: 10px;",
actionLink("heatmap_help_button", label = "Help"),
)
),
fluidRow(
div(
style = "display: inline-block; vertical-align: top;",
uiOutput("dge_list_heatmap")
),
div(
style = "display: inline-block; vertical-align: top;",
uiOutput("dgemaincontrasts_heatmap")
),
div(style = "display: inline-block;", uiOutput("geneOptions_heatmap_ui")),
div(
style = "display: inline-block; vertical-align: top;",
uiOutput("gene_list_filtering_heatmap")
),
div(style = "display: inline-block;", uiOutput("gene_list_heatmap")),
div(style = "display: inline-block;", uiOutput("filterFactor_heatmap")),
div(style = "display: inline-block;", uiOutput("filterFactorSelection_heatmap"))
),