Commit 13a669a8 authored by Bagueneau Mathias's avatar Bagueneau Mathias
Browse files

- Corrections de bug

parent 013a1966
......@@ -69,7 +69,7 @@ sidebar <- dashboardSidebar(
column(1),
column(10, h4(align="center", "Control Panel"),
div(actionLink("help2", "", icon = icon("far fa-question-circle")), align="center"),
verbatimTextOutput(outputId = "no_file2"),
htmlOutput(outputId = "no_file2"),
conditionalPanel(condition= "output.fileUploaded",align="center",
uiOutput("fchoice4"), br(),
uiOutput("group"), br(),
......@@ -95,7 +95,7 @@ sidebar <- dashboardSidebar(
column(1),
column(10, h4(align="center", "Control Panel"),
div(actionLink("help3", "", icon = icon("far fa-question-circle")), align="center"),
verbatimTextOutput(outputId = "no_file3"),
htmlOutput(outputId = "no_file3"),
conditionalPanel(condition= "output.fileUploaded",align="center",
radioButtons(inputId="choice_compare", label= "Compare :", c("Class" = "f_compare", "Features" = "features_compare"), selected = "f_compare"),
conditionalPanel(condition = "input.choice_compare == 'features_compare'",
......@@ -120,7 +120,7 @@ sidebar <- dashboardSidebar(
column(1),
column(10, h4(align="center", "Control Panel"),
div(actionLink("help4", "", icon = icon("far fa-question-circle")), align="center"),
verbatimTextOutput(outputId = "no_file4"),
htmlOutput(outputId = "no_file4"),
conditionalPanel(condition= "output.fileUploaded",align="center",
uiOutput("fchoice3"), br(),
uiOutput("heat_numb"), br(),
......@@ -154,7 +154,7 @@ sidebar <- dashboardSidebar(
column(1),
column(10, h4(align="center", "Control Panel"),
div(actionLink("help5", "", icon = icon("far fa-question-circle")), align="center"),
verbatimTextOutput(outputId = "no_file5"),
htmlOutput(outputId = "no_file5"),
conditionalPanel(condition= "output.fileUploaded",align="center",
radioButtons(inputId="graph_grid", label= "Choose the graph mode :", c("t-SNE" = "tsne", "UMAP" = "umap"), selected = "umap"),
sliderInput(inputId="ptsize_grid", label="Point size :", min=0.1, max=2, step=0.1, value = 0.6, ticks = FALSE),
......@@ -186,7 +186,7 @@ body <- dashboardBody(
br(),
fluidRow(column(align="center", width = 6, plotlyOutput("plot_factors", width='500px', height='500px'), uiOutput("fchoice"),downloadButton("dlleftplot", label="Export Plot")),
column(align="center", width = 6, plotlyOutput("plot_numerics", width='500px', height='500px'),uiOutput("featurechoice"), uiOutput("nchoice"),
conditionalPanel(condition ="input.featuresel == 'g'", selectizeInput(inputId="genes", label="Choose a gene :", choices ="")),downloadButton("dlrightplot", label="Export Plot"))# br(), verbatimTextOutput(outputId="genes_analyse"))
conditionalPanel(condition ="input.featuresel == 'g'", selectizeInput(inputId="genes", label="Choose a gene :", choices ="")),downloadButton("dlrightplot", label="Export Plot"))
),
hr(),
br(),
......@@ -306,10 +306,10 @@ server <- function(input, output, session) {
filedata$data <- withProgress(readRDS(paste0("./data/",input$file)), message = "Uploading File...", value=1)
filedata$name <- input$file
}
genesList <- filedata$data@assays$SCT@data@Dimnames[1]
updateSelectizeInput(session, "genes", choices = genesList[[1]], selected = "IGKC")
updateSelectizeInput(session, "genes2", choices = genesList[[1]], selected = "IGKC")
updateSelectizeInput(session, "listminigenes", choices = genesList[[1]], selected = "")
genesList <- rownames(filedata$data)
updateSelectizeInput(session, "genes", choices = genesList, selected = "IGKC")
updateSelectizeInput(session, "genes2", choices = genesList, selected = "IGKC")
updateSelectizeInput(session, "listminigenes", choices = genesList, selected = "")
return(filedata$data)
return(filedata$name)
})
......@@ -337,7 +337,7 @@ server <- function(input, output, session) {
})
# Assign.colors function
assign.colors <- function(obj, ident, palette="Dark2"){
assign.colors <- function(obj, ident, palette){
ident <- as.factor(ident)
nr.groups <- length(levels(ident))
colors <- colorRampPalette(brewer.pal(8, palette))(nr.groups)
......@@ -596,7 +596,7 @@ server <- function(input, output, session) {
req(!is.null(input$group_genepage)) # Genes Table
filegene <- wrfile()
Idents(filegene) <- as.factor(paste0(eval(parse(text=paste0("filegene@meta.data$",input$fsel4)))))
dtgoData <- data.table(filegene@misc$markers[[input$fsel4]]$gene[which(eval(parse(text=paste0("filegene@misc$markers$",input$fsel4,"$cluster"))) %in% input$group_genepage)])
dtgoData <- data.table(genes[1])
setDT(dtgoData)[]
names(dtgoData)[1] <- "Gene"
......
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