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Commit 0187367c authored by Bagueneau Mathias's avatar Bagueneau Mathias
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- Texte indiquant si les données doivent être recalculées ou non

parent 62861858
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app.R
View file @ 0187367c
......@@ -74,6 +74,7 @@ sidebar <- dashboardSidebar(
uiOutput("group"), br(),
radioButtons("gographtype", label="Choose a graph type :", choices=c("Dotplot"="dplot", "Barplot"="bplot", "Emapplot" = "eplot")), br(),
radioButtons("ontology", label="Choose an ontology :", choices=c("Biological Process"="BP", "Molecular Function"="MF", "Cellular Component" = "CC")), br(),
textOutput("genesstatut"),
actionButton("gogo", icon = icon("far fa-arrow-alt-circle-right"), label="Do Gene Ontology")
)
)
......@@ -107,7 +108,8 @@ sidebar <- dashboardSidebar(
conditionalPanel(condition = "input.choice_compare == 'f_compare'",
checkboxInput(inputId="show_clusters_compare", label="Clusters information", value=FALSE)
),
radioButtons("ontology2", label="Choose an ontology :", choices=c("Biological Process"="BP", "Molecular Function"="MF", "Cellular Component" = "CC"))
radioButtons("ontology2", label="Choose an ontology :", choices=c("Biological Process"="BP", "Molecular Function"="MF", "Cellular Component" = "CC")),
textOutput("comparestatut")
)
)
)
......@@ -122,6 +124,7 @@ sidebar <- dashboardSidebar(
conditionalPanel(condition= "output.fileUploaded",align="center",
uiOutput("fchoice3"), br(),
uiOutput("heat_numb"), br(),
textOutput("heatmapstatut"),
actionButton("goheatmap", icon = icon("far fa-arrow-alt-circle-right"), label="Do Heatmap")
)
)
......@@ -424,9 +427,11 @@ server <- function(input, output, session) {
output$heat_numb <- renderUI ({
sliderInput("top_number", label="Choose the number of top genes :", min=1, max=10, step=1, value=3)
})
observeEvent(input$goheatmap, {
observeEvent({list(input$fsel3,input$top_number)},
{output$heatmapstatut <- renderText({"Needs recalculation"})})
observeEvent(input$goheatmap, {
output$heatmapstatut <- renderText({""})
if (is.null(wrfile()@misc$markers[[input$fsel3]])) {
showModal(modalDialog("The markers may have not been calculated for this factor yet.", title=strong("Warning !"), easyClose=TRUE, footer = NULL ))
tempfile <- wrfile()
......@@ -463,12 +468,15 @@ server <- function(input, output, session) {
})
## Genes Page --------
observeEvent({list(input$fsel4,input$group_genepage,input$gographtype,input$ontology)},
{output$genesstatut <- renderText({"Needs recalculation"})})
observeEvent(input$gogo, {
if (is.null(input$group_genepage)) {
showModal(modalDialog("You must choose at least one group to do the Gene Ontology.", title=strong("Warning !"), easyClose=TRUE, footer = NULL ))
} else {
output$genesstatut <- renderText({""})
if (is.null(wrfile()@misc$markers[[input$fsel4]])) {
showModal(modalDialog("The markers may have not been calculated for this factor yet.", title=strong("Warning !"), easyClose=TRUE, footer = NULL ))
tempfile <- wrfile()
......@@ -838,9 +846,12 @@ server <- function(input, output, session) {
)
})
## Compare Page - Graphs generations, outputs and downloads --------
observeEvent({list(input$library1_compare,input$library2_compare,input$add_group1,input$add_group2,input$fsel2,input$add_factor,input$graph_compare,input$ptsize_compare,input$choice_compare,input$featuresel2,input$nsel2,input$genes2,input$ontology2,input$top1,input$top2)},
{output$comparestatut <- renderText({"Needs recalculation"})})
observeEvent (input$gographs, {
output$comparestatut <- renderText({""})
# Data for Compare Left Graph
if (input$add %% 2 != 0) {
subset1 <- SubsetData(object = wrfile(), cells=rownames(wrfile()@meta.data)[which(eval(parse(text=paste0("wrfile()@meta.data$",input$fsel2))) %in% input$library1_compare)] )
......@@ -850,7 +861,6 @@ server <- function(input, output, session) {
}
# Left Graph Compare page
scalex1 <- scale_x_continuous(limits = c(min(wrfile()@reductions[[input$graph_compare]]@cell.embeddings[,1]), max(wrfile()@reductions[[input$graph_compare]]@cell.embeddings[,1])))
scaley1 <- scale_y_continuous(limits = c(min(wrfile()@reductions[[input$graph_compare]]@cell.embeddings[,2]), max(wrfile()@reductions[[input$graph_compare]]@cell.embeddings[,2])))
......@@ -871,8 +881,7 @@ server <- function(input, output, session) {
}
}
# Data for Compare Right Graph
if (input$add %% 2 != 0) {
subset2 <- SubsetData(object = wrfile(), cells=rownames(wrfile()@meta.data)[which(eval(parse(text=paste0("wrfile()@meta.data$",input$fsel2))) %in% input$library2_compare)] )
......@@ -902,10 +911,6 @@ server <- function(input, output, session) {
}
}
output$plot1_compare <- renderPlotly ({ # Output Graph 1
req(wrfile())
if (input$choice_compare == "features_compare") {
......@@ -924,12 +929,7 @@ server <- function(input, output, session) {
}
})
output$dl_compare1 <- downloadHandler( # Download Graph 1
filename = function() {
if (input$choice_compare == "f_compare") {
......@@ -981,8 +981,6 @@ server <- function(input, output, session) {
return (barcodes2)
})
output$dl_comparebarcodes1 <- downloadHandler( # Download Barcodes 1
filename = function() {
paste0(file_path_sans_ext(filedata$name),"_selectedbarcodes.csv")
......@@ -1001,18 +999,10 @@ server <- function(input, output, session) {
}
)
})
## Compare Page - FindMarkers --------
output$markbutton <- renderUI ({
req(wrfile())
......
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