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server.R
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server.R
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#
# This is the server logic 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/
#
server <- function(input, output, session) {
# Define variables for each user session
source("setglobs.R")
#source("sessionCommon.R", local=TRUE)
do.call(file.remove, list(list.files("/tmpfiles", full.names = TRUE)))
createAlert(session, "alertCITE", "success", title = "How to cite:",
content = "Mitulkumar V Patel (2018). iS-CellR: a user-friendly tool for analyzing and visualizing single-cell RNA sequencing data, Bioinformatics, 1-2. doi: 10.1093/bioinformatics/bty517. https://doi.org/10.1093/bioinformatics/bty517", style="success", dismiss = FALSE, append = FALSE)
dataModal <- function(failed = FALSE) {
tags$div(id="loginBOX",
modalDialog(
title="Information",
textInput("username", "User*"),
textInput("projectid", "Project id"),
textInput("projectname", "Project name"),
textInput("sampleinfo", "Sample info"),
#passwordInput("password", "Password:"),
size = "s",
fade = TRUE,
footer = tagList(
# modalButton("Cancel"),
div(style="display:inline-block", actionButton("ok", "OK", icon("user-circle"),
style="color: #fff; background-color: #009933; border-color: #2e6da4"))
)
),
tags$head(tags$style("#loginBOX .modal-body {padding: 10px}
#loginBOX .modal-content {-webkit-border-radius: 8px !important;-moz-border-radius: 8px !important;}
#loginBOX .modal-dialog { display: inline-block; text-align: left; vertical-align: top;}
#loginBOX .modal-header {background-color: #337ab7; color: white; font-weight: bold !important;border-top-left-radius: 8px;border-top-right-radius: 8px;}
#loginBOX .modal { text-align: center; padding-left:10px; font-weight: bold !important; padding-right:10px; padding-top: 24px;}"
))
)
}
# Show modal when button is clicked.
# This `observe` is suspended only whith right user credential
obs1 <- observe({
showModal(dataModal())
})
# When OK button is pressed, attempt to authenticate. If successful,
# remove the modal.
obs2 <- observeEvent(input$ok,{
isolate({
Username <- input$username
values$ProjectID <- input$projectid
values$ProjectName <- input$projectname
values$SampleInfo <- input$sampleinfo
#Password <- input$password
})
if (input$username != "") {
Logged <<- TRUE
values$authentication <- Username
obs1$suspend()
removeModal()
} #else {
#Logged <<- TRUE
#values$authentication <- Username
#obs1$suspend()
#removeModal()
#}
})
output[["userName"]] <- renderUI({
sidebarUserPanel(values$authentication, subtitle = a(href = "#", icon("user", class = "text-success"), "Current user"))
})
isRequiredSTEP <- reactive({ # reactive part = thos code is repeated when user input changes
validate( # define error messages if user doesn't choose anything
need(input$seuratSteps != "",
"Please select at least one step to run the pipeline"),
need(input$file1 != "", "Please upload a count file")
)
})
output$showbusy <-
renderText({
c(
'<img align="middle",
src="',
"ajax-loader-bar.gif",
'">'
)
})
# observeEvent(input$ok,{
# #req(input$ok)
# if(is.null(FItSNEpath$val)){
# useShinyalert()
# shinyalert('Please provide path of FItSNE', type='input', callbackR = mycallback)
# }
# })
# mycallback <- function(value) {
# FItSNEpath$val <- as.character(value)
# }
#observeEvent(c(input$file1,input$sep,input$quote,input$header),{
observe({
if (!is.null(input$file1)) {
createAlert(session, "alert", "info", title = "Reading file contents .....",
content = "Please wait...", style="warning", dismiss = FALSE, append = FALSE)
}
})
output[["DTshow"]] <- renderUI({
#box(solidHeader = TRUE, width=7,
fluidRow(
column(4,
noUiSliderInput(inputId = "DTgenes", label = "Number of rows", step = 1, min = 1,
max = 100, value = 50, color = "#ff9933", tooltips = TRUE, behaviour = "tap")),
column(4,
noUiSliderInput(inputId = "DTcells", label = "Number of columns", step = 1, min = 1,
max = 50, value = 10, color = "#ff9933", tooltips = TRUE, behaviour = "tap")),
tags$br())#,
#fluidRow(tags$br())
})
shinyFileChoose(input, 'sfile', session = session, roots = c(root='.'), filetypes=c('', 'txt','csv','tsv','rds','mtx','h5'))
shinyFileChoose(input, 'sfile_interHet', session = session, roots = c(root='.'), filetypes=c('', 'txt','csv','tsv'))
count_data <- reactive({
if(input$SwitchUpload == "TRUE"){
inFile <- input$file1
} else {
inFile <- parseFilePaths(roots=c(root='.'), input$sfile)
}
if (is.null(inFile)){
#return(NULL)
createAlert(session, "alert", "warning", title = "File Not Loaded Yet!",
content = "Please upload file...", style="danger", dismiss = FALSE, append = FALSE)
} else {
if(input$load10x){
filesdir = dirname(inFile[1,4])
file.rename(inFile$datapath[1],paste0(filesdir,'/',inFile$name[1]))
file.rename(inFile$datapath[2],paste0(filesdir,'/',inFile$name[2]))
file.rename(inFile$datapath[3],paste0(filesdir,'/',inFile$name[3]))
count10X <- Read10X(data.dir = filesdir)
countMatrix <- as.data.frame(as.matrix(count10X))
} else if(file_ext(inFile$name) == "h5"){
count10X <- Read10X_h5(inFile$datapath)
countMatrix <- as.data.frame(as.matrix(count10X))
} else if(file_ext(inFile$name) == "rds"){
countRds$val <- readRDS(file = inFile$datapath)
countMatrix <- as.data.frame(GetAssayData(object = countRds$val))
} else {
countMatrix <- fread(inFile$datapath, header = input$header,
sep = input$sep, quote = input$quote, stringsAsFactors=FALSE)
countMatrix <- as.matrix(countMatrix, rownames=1)
}
rownames(countMatrix) = make.unique(rownames(countMatrix), sep = "_")
countFile$val <- countMatrix
geneID <- rownames(countMatrix)
GeneNames$val <- geneID
#rownames(countMatrix) <- sapply(rownames(countMatrix), function(geneID)
# toString(tags$a(href=paste0(link2Ens(geneID)), geneID, target="_blank")))
if (!is.null(countMatrix)){
updateNoUiSliderInput(session, "DTgenes", range = c(1,nrow(data.matrix(countMatrix))))
updateNoUiSliderInput(session, "DTcells", range = c(1,ncol(data.matrix(countMatrix))))
createAlert(session, "alert", "success", title = "File Loading Complete",
content = "You can now proceed...", style="success", dismiss = FALSE, append = FALSE)
if(!is.null(input$DTgenes) && !is.null(input$DTcells) && input$DTgenes <= nrow(countMatrix) && input$DTcells <= ncol(countMatrix)){
countMatrix[(1:input$DTgenes),c(1:input$DTcells), drop=FALSE]
}
}
}
})
# read in the data
count_datalocal <- reactive({
#validate(need(input$file1 != "", "Please upload a count file"))
#if(input$SwitchUpload == "TRUE"){
# inFile <- input$file1
#} else {
inFile <- parseFilePaths(roots=c(wd='.'), input$sfile)
#}
if (is.null(inFile)){
#return(NULL)
createAlert(session, "alert", "warning", title = "File Not Loaded Yet!",
content = "Please upload file...", style="danger", dismiss = FALSE, append = FALSE)
} else {
if(input$load10x){
filesdir = dirname(inFile[1,4])
file.rename(inFile$datapath[1],paste0(filesdir,'/',inFile$name[1]))
file.rename(inFile$datapath[2],paste0(filesdir,'/',inFile$name[2]))
file.rename(inFile$datapath[3],paste0(filesdir,'/',inFile$name[3]))
count10X <- Read10X(data.dir = filesdir)
countMatrix <- as.data.frame(as.matrix(count10X))
} else if(file_ext(input$file1$name) == "rds"){
countRds$val <- readRDS(file = inFile$datapath)
countMatrix <- as.data.frame(GetAssayData(object = countRds$val))
} else {
countMatrix <- fread(inFile$datapath, header = input$header,
sep = input$sep, quote = input$quote, stringsAsFactors=FALSE)
countMatrix <- as.matrix(countMatrix, rownames=1)
#countMatrix <- read.delim(inFile$datapath, header = input$header,
# sep = input$sep, quote = input$quote, stringsAsFactors=FALSE, row.names = 1)
#after <- Sys.time()
#cat(after-before)
}
countFile$val <- countMatrix
geneID <- rownames(countMatrix)
GeneNames$val <- geneID
#rownames(countMatrix) <- sapply(rownames(countMatrix), function(geneID)
# toString(tags$a(href=paste0(link2Ens(geneID)), geneID, target="_blank")))
if (!is.null(countMatrix)){
updateNoUiSliderInput(session, "DTgenes", range = c(1,nrow(data.matrix(countMatrix))))
updateNoUiSliderInput(session, "DTcells", range = c(1,ncol(data.matrix(countMatrix))))
#Sys.sleep(1)
createAlert(session, "alert", "success", title = "File Loading Complete",
content = "You can now proceed...", style="success", dismiss = FALSE, append = FALSE)
if(!is.null(input$DTgenes) && !is.null(input$DTcells) && input$DTgenes <= nrow(countMatrix) && input$DTcells <= ncol(countMatrix)){
countMatrix[(1:input$DTgenes),c(1:input$DTcells), drop=FALSE]
}
}
}
})
# observeEvent(input$sfile,{
# observe({
# if(!is.null(countFile$val)){
output$dt <- DT::renderDataTable({
#DT::datatable(count_data(), escape=FALSE, selection = 'none', options = list(scrollX = TRUE)) %>% formatStyle(0, cursor = 'pointer')
DT::datatable(count_data(), escape=FALSE, selection = 'none', options = list(searchHighlight = TRUE, scrollX = TRUE))
})
#})
# observe({
# if(!is.null(countFile$val)){
# updateSliderInput(session, "DTgenes", max = nrow(data.matrix(countFile$val)))
# updateSliderInput(session, "DTcells", max = ncol(data.matrix(countFile$val)))
# }
# })
observeEvent(c(input$sfile,input$file1,input$load10x,input$sep,input$quote,input$header),{
output$DataSummary <- renderFormattable({
if(!is.null(countFile$val)) {
countFile <- data.matrix(countFile$val)
#genes50 <- rowSums(countFile>0) # genes found in > 50 cells
expr0 <- sum(colSums(countFile == 0))
expr <- sum(colSums(countFile > 0))
percentZero <- expr0*100/(expr0 + expr)
ZeroExpr <- countFile[apply(countFile[, -1], MARGIN = 1, function(x) all(x == 0)), ] # Select all genes that has 0expr in all cells
SummaryInfo$val$nCells <- ncol(countFile)
SummaryInfo$val$nGenes <- nrow(countFile)
SummaryInfo$val$nZero <- nrow(ZeroExpr)
summaryProjectID <- data.table("Project ID :", values$ProjectID)
summaryProjectName <- data.table("Project name :", values$ProjectName)
summarySampleInfo <- data.table("Sample info :", values$SampleInfo)
summaryCells <- data.table("Total cells :", ncol(countFile))
summaryGenes <- data.table("Total genes :", nrow(countFile))
#summarygenes50 <- data.table("Genes found in >50 cells", genes50)
summaryZero <- data.table("Genes 0Expr :", nrow(ZeroExpr))
summaryTab1 <- rbind(summaryProjectID, summaryProjectName, summarySampleInfo)
summaryTab2 <- rbind(summaryCells, summaryGenes, summaryZero)
summary <- cbind(summaryTab1, summaryTab2)
colnames(summary) <- c("col1", "col2", "col3", "col4")
align_column=c("l","l","l","r")
formattable(summary, align=align_column,
list(col1 = formatter("span",
style = x ~ ifelse(x == c("Project ID :", "Project name :", "Sample info :"), style(color = "Gray", font.size = "14px", font.weight = "bold"), NA)),
col2 = formatter(.tag = "span", style = function(x) style(font.size = "14px")),
col3 = formatter("span",
style = x ~ ifelse(x == c("Total cells :", "Total genes :", "Genes 0Expr :"), style(color = "Gray", font.size = "14px", font.weight = "bold"), NA)),
#col4 = color_bar("orange")
col4 = formatter("span", style = function(x) style(display = "bar", direction = "rtl", font.size = "15px", `border-radius` = "5px", `padding-left` = "4px", `padding-right` = "4px", width = paste(proportion(x),"px",sep=""), `background-color` = csscolor("#ffa31a")))
))
#colnames(summary) <- c("", "", "", "")
#summary
}
})
})
observeEvent(input$seuratSteps,{
output$chsteps <- renderText({
#isRequiredSTEP()
runsteps <- paste(input$seuratSteps, collapse = ", ")
runsteps
#Selected$steps <<- runsteps
})
})
####### Enable/Disable UI elements #########
observeEvent(input$SwitchUpload,{
if(input$SwitchUpload == "TRUE"){
shinyjs::show("file1")
shinyjs::hide("sfile")
}
else{
shinyjs::hide("file1")
shinyjs::show("sfile")
}
})
observe({
if(!is.null(input$seuratSteps) && (!is.null(input$file1) || !is.null(input$sfile))){
shinyjs::enable("seuratRUN")
}
else{
shinyjs::disable("seuratRUN")
}
})
observe({
if(!is.null(countFile$val)){
shinyjs::show("DTshow")
}
else{
shinyjs::hide("DTshow")
}
})
# observe({
# if("_" %in% colnames(countFile$val)){
# updateRadioButtons(session, 'clustLabels', 'Lables for clusters:', choices=c("Labels from header"='useheader',
# "Custom labels"='customLabels',
# "Auto"='defLabels'),
# selected='defLabels',inline=F)
# }
# else{
# updateRadioButtons(session, 'clustLabels', 'Lables for clusters:', choices=c("Custom labels"='customLabels',
# "Auto"='defLabels'),
# selected='defLabels',inline=F)
# }
# })
observe({
if((!is.null(input$seuratSteps) || !is.null(input$file1) || !is.null(input$sfile)) && (!is.null(DownloadPlot$val$PCAplot2D) || !is.null(DownloadPlot$val$tSNEplot2D) || !is.null(DownloadPlot$val$Joyplot) || !is.null(DownloadPlot$val$Vlnplot) || !is.null(DownloadPlot$val$Featureplot) || !is.null(DownloadPlot$val$Dotplot) || !is.null(DownloadPlot$val$Heatmap) || !is.null(DownloadPlot$val$CoExprplot) || !is.null(DownloadPlot$val$InterHet) || !is.null(DownloadPlot$val$IntraHetplotly))){
shinyjs::enable("clustLabels")
}
else{
shinyjs::disable("clustLabels")
}
})
observe({
if(!is.null(DownloadPlot$val$Summaryplot)){
shinyjs::enable("summaryplotfull")
shinyjs::enable("downsummaryplot")
shinyjs::enable("ApplyFilter")
}
else{
shinyjs::disable("summaryplotfull")
shinyjs::disable("downsummaryplot")
shinyjs::disable("ApplyFilter")
}
})
observeEvent(input$ApplyFilter,{
shinyjs::enable("RemoveFilter")
})
observe({
if(!is.null(DownloadPlot$val$Summaryplot) || !is.null(DownloadPlot$val$PCAplot2D) || !is.null(DownloadPlot$val$Vizplot) || !is.null(DownloadPlot$val$tSNEplot2D) || !is.null(DownloadPlot$val$Joyplot) || !is.null(DownloadPlot$val$Vlnplot) || !is.null(DownloadPlot$val$Featureplot) || !is.null(DownloadPlot$val$Dotplot) || !is.null(DownloadPlot$val$Heatmap) || !is.null(DownloadPlot$val$CoExprplot) || !is.null(DownloadPlot$val$InterHet) || !is.null(DownloadPlot$val$IntraHetplot)){
shinyjs::enable("iSCellRreport")
}
else{
shinyjs::disable("iSCellRreport")
}
})
observe({
if(!is.null(DownloadPlot$val$PCAplot)){
shinyjs::enable("PCA2Dfull")
shinyjs::enable("downPCA2D")
shinyjs::show("SwitchLabelPCA")
}
else{
shinyjs::disable("PCA2Dfull")
shinyjs::disable("downPCA2D")
shinyjs::hide("SwitchLabelPCA")
}
})
observe({
if(!is.null(DownloadPlot$val$Vizplot)){
shinyjs::enable("Vizplotfull")
shinyjs::enable("downVizplot")
}
else{
shinyjs::disable("Vizplotfull")
shinyjs::disable("downVizplot")
}
})
observe({
if(!is.null(DownloadPlot$val$PCAHeatmap)){
shinyjs::enable("PCAHeatmapfull")
shinyjs::enable("downPCAHeatmap")
}
else{
shinyjs::disable("PCAHeatmapfull")
shinyjs::disable("downPCAHeatmap")
}
})
observe({
if(!is.null(DownloadPlot$val$tSNEplot)){
shinyjs::enable("tSNE2Dfull")
shinyjs::enable("downtSNE2D")
shinyjs::show("SwitchLabeltSNE")
shinyjs::show("choose_Dimreduction1")
}
else{
shinyjs::disable("tSNE2Dfull")
shinyjs::disable("downtSNE2D")
shinyjs::hide("SwitchLabeltSNE")
shinyjs::hide("choose_Dimreduction1")
}
})
observe({
if(length(input$brush1_rows_all) > 0){
shinyjs::enable("tSNEbrushdata")
}
else{
shinyjs::disable("tSNEbrushdata")
}
})
observe({
if(length(input$JoyplotGenes) == 0){
shinyjs::disable("updateJoyplot")
}
else{
shinyjs::enable("updateJoyplot")
}
})
observe({
if(!is.null(DownloadPlot$val$Joyplot)){
shinyjs::enable("Joyplotfull")
shinyjs::enable("downJoyplot")
}
else{
shinyjs::disable("Joyplotfull")
shinyjs::disable("downJoyplot")
}
})
observe({
if(length(input$VlnplotGenes) == 0){
shinyjs::disable("updateVlnplot")
}
else{
shinyjs::enable("updateVlnplot")
}
})
observe({
if(!is.null(DownloadPlot$val$Vlnplot)){
shinyjs::enable("Vlnplotfull")
shinyjs::enable("downVlnplot")
}
else{
shinyjs::disable("Vlnplotfull")
shinyjs::disable("downVlnplot")
}
})
observe({
if(length(input$DotplotGenes) == 0){
shinyjs::disable("updateDotplot")
}
else{
shinyjs::enable("updateDotplot")
}
})
observe({
if(!is.null(DownloadPlot$val$Dotplot)){
shinyjs::enable("Dotplotfull")
shinyjs::enable("downDotplot")
}
else{
shinyjs::disable("Dotplotfull")
shinyjs::disable("downDotplot")
}
})
observe({
if(length(input$FeatureGenes) == 0){
shinyjs::disable("updateFeatplot")
}
else{
shinyjs::enable("updateFeatplot")
}
})
observe({
if(!is.null(DownloadPlot$val$Featureplot)){
shinyjs::enable("Featureplotfull")
shinyjs::enable("downFeatureplot")
shinyjs::show("SwitchLabelFeatPlot")
shinyjs::show("choose_Dimreduction2")
shinyjs::show("ExprCutoffFeat")
}
else{
shinyjs::disable("Featureplotfull")
shinyjs::disable("downFeatureplot")
shinyjs::hide("SwitchLabelFeatPlot")
shinyjs::hide("choose_Dimreduction2")
shinyjs::hide("ExprCutoffFeat")
}
})
observe({
if(length(input$HeatmapGenes) == 0){
shinyjs::disable("updateHeatmap")
}
else{
shinyjs::enable("updateHeatmap")
}
})
observeEvent(input$SwitchHeatmap,{
if(input$SwitchHeatmap == "TRUE"){
shinyjs::disable("choose_HeatmapGenes")
shinyjs::show("TopDiffHeatmap")
if(!is.null(DownloadPlot$val$Heatmap)){
shinyjs::enable("TopDiffHeatmap")
} else {
shinyjs::disable("TopDiffHeatmap")
}
}
else{
shinyjs::enable("choose_HeatmapGenes")
shinyjs::hide("TopDiffHeatmap")
}
})
observe({
if(!is.null(DownloadPlot$val$Heatmap)){
shinyjs::enable("Heatmapfull")
shinyjs::enable("downHeatmap")
shinyjs::enable("TopDiffHeatmap")
} else {
shinyjs::disable("Heatmapfull")
shinyjs::disable("downHeatmap")
shinyjs::disable("TopDiffHeatmap")
}
})
#observeEvent(input$changeLabels,{
# req(input$changeLabels)
# if(input$ClusterSel %in% scObject$val@ident){
# shinyjs::disable("UpCluster")
# }
# else{
# shinyjs::enable("UpCluster")
# }
# })
observe({
if(length(input$CoExprGenes) <= 1){
shinyjs::disable("updateCoExprplot")
}
else{
shinyjs::enable("updateCoExprplot")
}
})
observe({
if(!is.null(DownloadPlot$val$CoExprplot)){
shinyjs::enable("CoExprplotfull")
shinyjs::enable("downCoExprplot")
shinyjs::show("SwitchLabelCoExpr")
shinyjs::show("GeneNotFound_CoExpr")
shinyjs::show("choose_Dimreduction3")
}
else{
shinyjs::disable("CoExprplotfull")
shinyjs::disable("downCoExprplot")
shinyjs::hide("SwitchLabelCoExpr")
shinyjs::show("GeneNotFound_CoExpr")
shinyjs::hide("choose_Dimreduction3")
}
})
observe({
if(!is.null(input$MarkersCluster1) && length(input$MarkersCluster2) >= 1){
shinyjs::enable("ShowMarkers")
}
else{
shinyjs::disable("ShowMarkers")
}
})
observeEvent(input$SwitchUpload2,{
if(input$SwitchUpload2 == "TRUE"){
shinyjs::show("geneList")
shinyjs::hide("sfile_interHet")
}
else{
shinyjs::hide("geneList")
shinyjs::show("sfile_interHet")
}
})
observe({
if(!is.null(input$geneList) || !is.null(input$sfile_interHet)){
shinyjs::enable("updateInterHetplot")
}
else{
shinyjs::disable("updateInterHetplot")
}
})
observe({
if(!is.null(DownloadPlot$val$InterHet)){
shinyjs::enable("downInterHet")
}
else{
shinyjs::disable("downInterHet")
}
})
observe({
if(length(input$IntraHetGenes) == 0){
shinyjs::disable("updateIntraHetplot")
}
else{
shinyjs::enable("updateIntraHetplot")
}
})
observe({
if(!is.null(DownloadPlot$val$IntraHetplot)){
shinyjs::enable("IntraHetplotfull")
shinyjs::enable("downIntraHetplot")
}
else{
shinyjs::disable("IntraHetplotfull")
shinyjs::disable("downIntraHetplot")
}
})
observe({
if(input$selectall == 0) return(NULL)
else if(input$selectall %% 2 == 0)
{
updatePrettyCheckboxGroup(session = session, inputId = "seuratSteps", label = "Select iS-CellR step to perform:", choices = selectSteps, prettyOptions = list(thick = TRUE, animation = "pulse", status = "success"))
}
else #if(input$selectall > 0)
{
updatePrettyCheckboxGroup(session = session, inputId = "seuratSteps", label = "Select iS-CellR step to perform:", choices = selectSteps, selected = unlist(selectSteps), prettyOptions = list(thick = TRUE, animation = "pulse", status = "success"))
}
})
observeEvent(input$clustLabels,{
if(input$clustLabels == "customLabels") {
toggleModal(session, modalId = "ClusterLabels", toggle = "open")
}
})
observeEvent(input$changeLabels,{
toggleModal(session, modalId = "ClusterLabels", toggle = "close")
})
output$defCluster <- DT::renderDataTable({
#DT::datatable(count_data(), escape=FALSE, selection = 'none', options = list(scrollX = TRUE)) %>% formatStyle(0, cursor = 'pointer')
DT::datatable(ClusterLabInfo$val, escape=FALSE, selection = 'none',
editable = TRUE, extensions = 'KeyTable', options = list(searchHighlight = TRUE, scrollX = TRUE, keys = TRUE))
})
proxy2 = dataTableProxy('defCluster')
#observeEvent(input$reset_barcodeDT, {
# withBusyIndicatorServer("reset_barcodeDT", {
# proxy2 %>% selectRows(NULL)
# })
#})
observeEvent(input$defCluster_cell_edit, {
info = input$defCluster_cell_edit
str(info)
i = info$row
j = info$col
v = info$value
df <- ClusterLabInfo$val
df[i, 2] <- DT::coerceValue(v, df[i, 2])
replaceData(proxy2, df, resetPaging = FALSE) # important
ClusterLabInfo$val <<- df
})
observeEvent(input$defCluster_cell_edit,{
df <- data.frame(ClusterLabInfo$val)
is.na(df$new.cluster.ids) <- df$new.cluster.ids == ''
if(any(is.na(df$new.cluster.ids))){
shinyjs::disable("changeLabels")
} else {
shinyjs::enable("changeLabels")
}
})
observe({
if(input$clustLabels == "customLabels") {
output[["defineLable"]] <- renderUI({
fluidRow(
box(title = "Current clusters", status = "primary", solidHeader = FALSE,
collapsed = FALSE, collapsible = FALSE, width=12,
DT::dataTableOutput('defCluster')
)
)
})
}
})
#####################################################################################################
###### info boxes
output$pipeline <- renderInfoBox({
box1<-infoBox(
"Pipeline",
HTML(paste("<b>Pipeline steps</b>",
"Find out more...",
sep = "<br/>")),
icon = icon("gears"),
href = "#",
color = "aqua", fill = TRUE)
box1$children[[1]]$attribs$class<-"action-button"
box1$children[[1]]$attribs$id<-"button_box_01"
return(box1)
})
observeEvent(input$button_box_01, {
toggleModal(session,"workflow","open")
})
output$tools <- renderInfoBox({
box2<-infoBox(
"Tools",
HTML(paste("Tools in pipeline",
"Find out more...",
sep = "<br/>")),
icon = icon("cubes"),
href = "#",
color = "green", fill = TRUE)
box2$children[[1]]$attribs$class<-"action-button"
box2$children[[1]]$attribs$id<-"button_box_02"
return(box2)
})
observeEvent(input$button_box_02, {
toggleModal(session,"wktools","open")
})
output$example <- renderInfoBox({
box3<-infoBox(
"Run demo",
HTML(paste("Run demo",
"Find out more...",
sep = "<br/>")),
icon = icon("edit"),
href = "#",
color = "yellow", fill = TRUE)
box3$children[[1]]$attribs$class<-"action-button"
box3$children[[1]]$attribs$id<-"button_box_03"
return(box3)
})
observeEvent(input$button_box_03, {
toggleModal(session,"wkDemo","open")
})
output$ToolList <- renderFormattable({
pkgLIST <- data.matrix(sort(pkgs, decreasing=FALSE))
p1 <- data.frame()
p2 <- data.frame()
for (i in seq(1,length(pkgLIST), 3)) {
p1 <- cbind(pkgLIST[i], pkgLIST[i+1], pkgLIST[i+2])
p2 <- rbind(p2, p1)
}
align_column=c("l","l","l")
colnames(p2) <- c("col1","col2","col3")
formattable(p2, align=align_column,
list(
col1 = formatter("span", style = function(x) style(font.size = "14px")),
col2 = formatter("span", style = function(x) style(font.size = "14px")),
col3 = formatter("span", style = function(x) style(font.size = "14px"))
))
})
output$DemoInfo <- renderText({
paste("<b> Run demo with the data from Tirosh et al., 2016.</b><br/><br/>How to Get Started and Load Data<br/>
It is important that the input file should follow the same format as descibed below.<br/><br/>
To get started, please load in a CSV/TSV separated values file. The file should contain the count data where:<br/>
1. Columns are Cells<br/>
2. Rows are Genes<br/>
3. Cell names or Cell type in Column header followed by Cell id. eg. Tcell_TC1_fcount_1.<br/><br/>
<strong>NOTE:</strong> An example CSV file can be accessed <a href='data/Maligant50.csv', target='blank', download = 'Maligant50.csv'><strong>HERE</strong>.</a> (right click save as).<br/><br/>
Notes on Plots and Processed Data<br/>
All plots can be downloaded at a high resolution in PDF. This functionality works best in <strong>Chrome</strong> and <strong>Firefox</strong>. Within the Shiny app, user can control the labelling of clusters. User can also provide list of genes to compare their expression levels.<br/>
")
})
############################## RUN Seurat and render plots ################################
observeEvent(input$seuratRUN,{
source("scripts/SeuratRUN.R", local=TRUE)
})
observeEvent(c(input$seuratRUN,input$ApplyFilter,input$RemoveFilter),{
output$seuratresTab1 <- renderPlot({
req(c(input$seuratRUN,input$ApplyFilter,input$RemoveFilter))
isolate({
source("scripts/variablegenes.R", local = TRUE)$value
})
})
})
observeEvent(c(input$seuratRUN,input$ApplyFilter,input$RemoveFilter),{
output$summaryplot <- renderPlot({
req(c(input$seuratRUN,input$ApplyFilter,input$RemoveFilter))
isolate({
source("scripts/SummaryPlot.R", local = TRUE)$value
})
})
})
observeEvent(input$ApplyFilter, {
# When the button is clicked, wrap the code in a call to `withBusyIndicatorServer()`
withBusyIndicatorServer("ApplyFilter", {
Sys.sleep(1)
source("scripts/QCrun.R", local = TRUE)
source("scripts/SummaryPlot.R", local = TRUE)$value
})
})
observeEvent(input$RemoveFilter,{
# When the button is clicked, wrap the code in a call to `withBusyIndicatorServer()`
withBusyIndicatorServer("RemoveFilter", {
Sys.sleep(1)
# if (input$select == "error") {
#isolate({
shinyjs::reset("QCoptions")
source("scripts/SeuratRUN.R", local=TRUE)
source("scripts/SummaryPlot.R", local = TRUE)$value
})
})
output$summaryplotZoom <- renderPlot({
req(input$summaryplotfull)
isolate({
print(DownloadPlot$val$Summaryplot)
})
})
output$seuratVizPCA <- renderPlot({
req(input$updateVizplot)
isolate({
source("scripts/PCAViZplot.R", local = TRUE)$value
})
})
output$seuratVizPCAZoom <- renderPlot({
req(input$Vizplotfull)
isolate({
print(DownloadPlot$val$Vizplot)
})
})
output$seuratPCAHeatmap <- renderPlot({
req(input$updatePCAHeatmap)
#isolate({
source("scripts/PCAHeatmap.R", local = TRUE)$value
#})
})
output$seuratPCAHeatmapZoom <- renderPlot({
req(input$PCAHeatmapfull)
#isolate({
print(DownloadPlot$val$PCAHeatmap)
#})
})
observeEvent(input$changeLabels,{
output$seuratPCAplot <- renderPlotly({
req(c(input$changeLabels,input$SwitchLabelPCA))
isolate({
source("scripts/PCAplot.R", local = TRUE)$value
})
})
})
toListen <- eventReactive(input$clustLabels, {
# toListen <- reactive({
if(input$clustLabels == "defLabels" || input$clustLabels == "useheader"){
list(input$seuratRUN,input$clustLabels,input$ApplyFilter,input$RemoveFilter)
}
})
observeEvent(toListen(),{
output$seuratPCAplot <- renderPlotly({
obsList <- list()
obsList[[length(toListen())+1]] <- input$SwitchLabelPCA
req(obsList)
isolate({
source("scripts/PCAplot.R", local = TRUE)$value
})
})
})
output$PCA2DplotZoom <- renderPlotly({
req(input$PCA2Dfull)
#isolate({
print(DownloadPlot$val$PCAplot)
#})
})
observeEvent(toListen(),{
output$seuratPCAplot3D <- renderPlotly({
obsList <- list()
obsList[[length(toListen())+1]] <- input$changeLabels
req(obsList)
isolate({
source("scripts/PCAplot3D.R", local = TRUE)$value
})
})
})
output$seuratPCAplot3DZoom <- renderPlotly({
req(input$PCAfull)
isolate({
print(DownloadPlot$val$PCA3D)
})
})
observeEvent(input$changeLabels,{
output$seurattSNEplot <- renderPlotly({
req(c(input$changeLabels,input$SwitchLabeltSNE,input$DimA))
isolate({
source("scripts/tSNEplot.R", local = TRUE)$value
})
})
})
observeEvent(toListen(),{
output$seurattSNEplot <- renderPlotly({
obsList <- list()
obsList[[length(toListen())+1]] <- input$SwitchLabeltSNE
obsList[[length(toListen())+1]] <- input$DimA
req(obsList)
isolate({
source("scripts/tSNEplot.R", local = TRUE)$value
})
})
})
output$tSNE2DplotZoom <- renderPlotly({
req(input$tSNE2Dfull)
#isolate({
print(DownloadPlot$val$tSNEplot)
#})
})
observeEvent(input$changeLabels,{
output$seurattSNEplot2 <- renderPlot({
req(input$changeLabels)
requireTSNE()
#isolate({
source("scripts/tSNEplot2.R", local = TRUE)$value
})
#})
})
observeEvent(toListen(),{
output$seurattSNEplot2 <- renderPlot({
req(toListen())
requireTSNE()
#isolate({
source("scripts/tSNEplot2.R", local = TRUE)$value
})
#})
})