Entering edit mode
3.9 years ago
Dataminer
★
2.8k
Dear community,
I am trying to make a shiny app by reading in seurat object. Unfortunately, it doesn't work. I have deployed the following code:
library(shiny)
library(shinythemes)
library(Seurat)
library(ggplot2)
library(gridExtra)
library(egg)
library(RColorBrewer)
library(shinyWidgets)
# Getting the file names
rdsfiles <- list.files("/temp2/data", pattern = "\\.rds$")
# Define UI for dataset viewer application
ui <- shinyUI(fluidPage(theme = shinytheme("cerulean"), pageWithSidebar(
# Application title
headerPanel("Shiny App with multiple datasets"),
# Sidebar with controls to select a dataset and specify the number
# of observations to view
sidebarPanel(
selectInput("dataset", "Choose a dataset:",
choices = rdsfiles),
),
# Show a summary of the dataset and an HTML table with the requested
# number of observations
mainPanel(
tabsetPanel(
tabPanel('UMAP', plotOutput("umap")),
tabPanel('Gene', plotOutput("gene"))
))
)))
# Define server logic required to summarize and view the selected dataset
server <- shinyServer(function(input, output) {
# Return the requested dataset
datasetInput <- reactive({
df <- readRDS(paste0("/temp2/data/", input$dataset))
return(df)
})
# Generate a UMAP of the dataset
output$umap <- renderPlot({
dataset <- datasetInput()
plot(input$dataset, reduction = "umap")
})
# Generate a Feature of the dataset
output$gene <- renderPlot({
dataset <- datasetInput()
FeaturePlot(dataset, reduction = "umap")
})
})
shinyApp(ui, server)
The output is an error "Cannot find "umap" in seurat object" for both the buttons.
I am not sure what I doing wrong. However, I am sure that some of you must have tackled this problem in past. Your input is highly appreciated.
Thank you
Hi, My seurat works fine and I get all the images and analysis done. It is when I try to put the seurat object into R shiny, it throws up this error.