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server.R
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#This is the file used to define the Shiny Server Functions.
#This includes all of the functions and code necessary to generate plots.
shinyServer(function(session, input, output) {
observeEvent(input$tab, {
if(input$tab == 5){
shinyjs::hide(id = "Sidebar")
}
else{
shinyjs::show(id = "Sidebar")
}
})
plotOptions <- reactive({
list(colorChoice = input$metaVariable, cloneChoice = list(D0 = input$clonesD0variable, D3 = input$clonesD3variable, D13 = input$clonesD13variable), contour = input$contour, plotType = input$tab, geneExpr = input$geneChoice, groupVar = input$groupVariable, stackVar = input$stackedVariable)
}) %>% debounce(millis = 1500)
observeEvent(input$tab, {
if(input$tab == 1 | input$tab == 6){
geneChoice <- rownames(seuratExpr)
geneChoice <- c(Choose = "", geneChoice)
updateSelectInput(session, inputId = "geneChoice", label = "Color by Gene Expression:", choices = geneChoice )
} else if(input$tab == 3){
geneChoice <- rownames(monocleExpr)
geneChoice <- c(Choose = "", geneChoice)
updateSelectInput(session, inputId = "geneChoice", label = "Color by Gene Expression:", choices = geneChoice)
}
})
observe({
rep <- input$rep
if(rep == "HF1"){
all_tags <<- hf1.all_tags
all_tags1 <<- hf1.all_tags1
all_tags2.1 <<- hf1.all_tags2.1
all_tags2.2 <<- hf1.all_tags2.2
linkList <<- hf1.linkList
Nodes <<- hf1.Nodes
tag_info <<- hf1.tag_info
updateSelectInput(
session,
"tag",
label = "HF1 Clones:",
choices = hf1.all_tags,
selected = "CellTag.D0_709"
)
updateSelectInput(
session,
"c",
label = "HF1 Colors",
choices = netColorChoice,
selected = "Cluster.Seurat"
)
} else if (rep == "HF2") {
all_tags <<- hf2.all_tags
all_tags1 <<- hf2.all_tags1
all_tags2.1 <<- hf2.all_tags2.1
all_tags2.2 <<- hf2.all_tags2.2
linkList <<- hf2.linkList
Nodes <<- hf2.Nodes
tag_info <<- hf2.tag_info
updateSelectInput(
session,
"tag",
label = "HF2 Clones:",
choices = hf2.all_tags,
selected = "CellTag.D0_2352"
)
updateSelectInput(
session,
"c",
label = "HF2 Colors",
choices = netColorChoice,
selected = "Cluster.Seurat"
)
}
})
output$tSNEplot <- renderPlot({
generatePlot(
data = celltagData,
colorChoice = plotOptions()[["colorChoice"]],
cloneChoice = plotOptions()[["cloneChoice"]],
tagCols = celltagCols,
contour = plotOptions()[["contour"]],
plotType = plotOptions()[["plotType"]],
geneExpr = plotOptions()[["geneExpr"]]
)
})
output$pseudotime <- renderPlot({
generatePlot(
data = celltagData,
colorChoice = plotOptions()[["colorChoice"]],
cloneChoice = plotOptions()[["cloneChoice"]],
tagCols = celltagCols,
contour = plotOptions()[["contour"]],
plotType = plotOptions()[["plotType"]],
geneExpr = plotOptions()[["geneExpr"]]
)
})
output$StackedBarChart <- renderPlot(
generatePlot(
data = celltagData,
cloneChoice = plotOptions()[["cloneChoice"]],
colorChoice = plotOptions()[["stackVar"]],
groupVar = plotOptions()[["groupVar"]],
plotType = plotOptions()[["plotType"]]
)
)
output$cloneNetwork <- renderForceNetwork({
drawSubnet(input$tag, input$c)
})
output$cloneTable <- DT::renderDataTable({
DT::datatable(celltagData[,c(10:12, 18:20)])
})
output$downloadPlot <- downloadHandler(
filename = function() {
paste0("plot-", Sys.Date(), ".pdf")
},
content = function(file) {
ggsave(
file = file,
plot = generatePlot(
data = celltagData,
colorChoice = plotOptions()[["colorChoice"]],
cloneChoice = plotOptions()[["cloneChoice"]],
tagCols = celltagCols,
contour = plotOptions()[["contour"]],
plotType = plotOptions()[["plotType"]],
geneExpr = plotOptions()[["geneExpr"]]
),
device = "pdf",
width = 11,
height = 8.5,
units = "in"
)
}
)
output$downloadStackedPlot <- downloadHandler(
filename = function() {
paste0("stackedBarPlot", Sys.Date(), ".pdf")
},
content = function(file) {
ggsave(
file = file,
plot = generatePlot(
data = celltagData,
colorChoice = plotOptions()[["colorChoice"]],
groupVar = plotOptions()[["groupVar"]],
plotType = plotOptions()[["plotType"]]
),
device = "pdf",
width = 11,
height = 8.5,
units = "in"
)
}
)
output$downloadCellTagData <- downloadHandler(
filename = "morrislab.celltag.dataset.csv",
content = function(file) {
write.csv(x = celltagData, file = file, row.names = TRUE)
},
contentType = "text/csv"
)
})